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26 results on '"Science Foundation Ireland (SFI)"'

1. Defective activation and regulation of type I interferon immunity is associated with increasing COVID-19 severity

Author: Nikaïa Smith, Céline Possémé, Vincent Bondet, Jamie Sugrue, Liam Townsend, Bruno Charbit, Vincent Rouilly, Violaine Saint-André, Tom Dott, Andre Rodriguez Pozo, Nader Yatim, Olivier Schwartz, Minerva Cervantes-Gonzalez, Jade Ghosn, Paul Bastard, Jean Laurent Casanova, Tali-Anne Szwebel, Benjamin Terrier, Niall Conlon, Cliona O’Farrelly, Clíona Ní Cheallaigh, Nollaig M. Bourke, Darragh Duffy, Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Trinity College Dublin, Saint James Hospital (SJH), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Datactix, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, CHU Necker - Enfants Malades [AP-HP], Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Rockefeller University [New York], Howard Hughes Medical Institute (HHMI), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This study was supported by the 'URGENCE COVID-19' fundraising campaign of the Institut Pasteur (CoVarImm and Steroid Response), from the Agence Nationale de la Recherche (ANR-flash COVID-19), by the Laboratoire d’Excellence ‘Milieu Intérieur’ (grant no. ANR-10-LABX-69-01) (D.D.), the Fonds IMMUNOV for Innovation in Immunopathology (B.T.), and Science Foundation Ireland (C.O.F., C.N.C., and N.B.). We thank the STTAR-Bioresource of TCD-SJH-TUH COVID-19 bioresource which supported the collection of patient samples. N.S. is a recipient of the Pasteur–Roux–Cantarini Fellowship. C.O.F., N.C., and C.N.C. are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. L.T. is supported by the Irish Clinical Academic Training (ICAT) Program, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland. N.B. is funded under the Science Foundation Ireland Phase 2 COVID-19 Rapid Response Call (20/COV/8487) and the Health Research Board COVID-19 Rapid Response Call (COV19e2020e053). The Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI088364 and R01AI163029), the National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1 TR001866), a Fast Grant from Emergent Ventures, Mercatus Center at George Mason University, the Fisher Center for Alzheimer’s Research Foundation, the Meyer Foundation, the JPB Foundation, the French National Research Agency (ANR) under the 'Investments for the Future' program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (EQU201903007798), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), ANR AABIFNCOV (ANR-20-CO11-0001) and ANR GenMISC (ANR-21-COVR-0039) projects, the European Union’s Horizon 2020 research and innovation program under grant agreement No. 824110 (EASI-genomics), the Square Foundation, Grandir—Fonds de solidarité pour l’enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, The French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), Institut National de la Santé et de la Recherche Médicale (INSERM), REACTing-INSERM and the University of Paris (J.L.C.). P.B. was supported by the MD–Ph.D. program of the Imagine Institute (with the support of the Fondation Bettencourt-Schueller)., We thank the UTechS CB of the Center for Translational Research, Institut Pasteur for supporting Luminex and Nanostring analysis. We thank Quanterix for the provision of IFNα multi-subtype prototype assays. We acknowledge all healthcare workers involved in the diagnosis and treatment of patients in Hopital Cochin, Hopital Bichat, and St James’s Hospital Dublin., ANR-20-COVI-0053,CoVarImm,Variation de la réponse immune systémique et muqueuse pendant l'infection par le SRAS-CoV-2 et la convalescence(2020), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-20-CE93-0003,GENVIR,Analyse multi-omique de l'immunité anti-virale: de l'identification des circuits biologiques pertinents à la découverte de défauts monogéniques héréditaires de l'immunité chez les patients avec infections virales sévères(2020), ANR-20-CO11-0001,AABIFNCOV,Bases génétiques et immunologiques des auto-anticorps contre les interférons de type I prédisposant aux formes sévères de COVID-19.(2020), ANR-21-COVR-0039,GenMIS-C,Recherche des Déficits immunitaires innées monogéniques prédisposant au syndrome inflammatoire multisystémique chez l'enfant.(2021), and European Project: 824110,H2020-INFRAIA-2018-1,EASI-Genomics(2019)
Subjects: Proteomics, Multidisciplinary, SARS-CoV-2, [SDV]Life Sciences [q-bio], Interferon Type I, General Physics and Astronomy, Humans, COVID-19, Interferon-alpha, General Chemistry, Antiviral Agents, General Biochemistry, Genetics and Molecular Biology, Autoantibodies
Abstract: Host immunity to infection with SARS-CoV-2 is highly variable, dictating diverse clinical outcomes ranging from asymptomatic to severe disease and death. We previously reported reduced type I interferon in severe COVID-19 patients preceded clinical worsening. Further studies identified genetic mutations in loci of the TLR3- or TLR7-dependent interferon-I pathways, or neutralizing interferon-I autoantibodies as risk factors for development of COVID-19 pneumonia. Here we show in patient cohorts with different severities of COVID-19, that baseline plasma interferon α measures differ according to the immunoassay used, timing of sampling, the interferon α subtype measured, and the presence of autoantibodies. We also show a consistently reduced induction of interferon-I proteins in hospitalized COVID-19 patients upon immune stimulation, that is not associated with detectable neutralizing autoantibodies against interferon α or interferon ω. Intracellular proteomic analysis shows increased monocyte numbers in hospitalized COVID-19 patients but impaired interferon-I response after stimulation. We confirm this by ex vivo whole blood stimulation with interferon-I which induces transcriptomic responses associated with inflammation in hospitalized COVID-19 patients, that is not seen in controls or non-hospitalized moderate cases. These results may explain the dichotomy of the poor clinical response to interferon-I based treatments in late stage COVID-19, despite the importance of interferon-I in early acute infection and may guide alternative therapeutic strategies.
Published: 2022
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2. Defective type I interferon immunity is associated with increasing COVID-19 severity

Author: Darragh Duffy, Nikaïa SMITH, Céline Possémé, Vincent Bondet, Jamie Sugrue, Liam Townsend, Bruno Charbit, Vincent Rouilly, Violaine Saint-André, Tom Dott, Andre Rodriguez Pozo, Nader Yatim, Olivier Schwartz, Minerva Cervantes-Gonzales, Jade Ghosn, Paul Bastard, Jean-Laurent Casanova, Tali-Anne Szwebel, Benjamin Terrier, Niall Conlon, Cliona O'Farrelly, Cliona Ni Cheallaigh, Nollaig Bourke, Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP), Trinity College Dublin, Datactix, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Hôpital Cochin [AP-HP], St James' Hospital, This study was supported by the 'URGENCE COVID-19' fundraising campaign the Institut Pasteur (CoVarImm and Steroid Response), from the Agence Nationale de la Recherche (ANR-flash COVID-19), by the Laboratoire d’Excellence ‘Milieu Intérieur’ (grant no. ANR-10-LABX-69-01), the Fonds IMMUNOV for Innovation in Immunopathology, and Science Foundation Ireland. We thank the STTAR-Bioresource of TCD-SJH-TUH COVID-19 bioresource which supported collection of patient samples. NS is a recipient of the Pasteur-Roux-Cantarini Fellowship. COF, NC and CNC are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. LT is supported by the Irish Clinical Academic Training (ICAT) Programme, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland. N.B. is funded under the Science Foundation Ireland Phase 2 COVID-19 Rapid Response Call (20/COV/8487) and the Health Research Board COVID-19 Rapid Response Call (COV19e2020e053). The Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI088364 and R01AI163029), the National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1 TR001866), a Fast Grant from Emergent Ventures, Mercatus Center at George Mason University, the Fisher Center for Alzheimer’s Research Foundation, the Meyer Foundation, the JPB Foundation, the French National Research Agency (ANR) under the 'Investments for the Future' program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (EQU201903007798), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), ANR AABIFNCOV (ANR-20-CO11-0001) and ANR GenMISC (ANR-21-COVR-0039) projects, the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824110 (EASI-genomics), the Square Foundation, Grandir - Fonds de solidarité pour l’enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, The French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), Institut National de la Santé et de la Recherche Médicale (INSERM), REACTing-INSERM and the University of Paris. PB was supported by the MD-PhD program of the Imagine Institute (with the support of the Fondation Bettencourt-Schueller)., We thank the UTechS CB of the Center for Translational Research, Institut Pasteur for supporting Luminex and Nanostring analysis. We acknowledge all health-care workers involved in the diagnosis and treatment of patients in Hopital Cochin, Hopital Bichat, and St James’s Hospital Dublin., ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-20-CE93-0003,GENVIR,Analyse multi-omique de l'immunité anti-virale: de l'identification des circuits biologiques pertinents à la découverte de défauts monogéniques héréditaires de l'immunité chez les patients avec infections virales sévères(2020), ANR-20-CO11-0001,AABIFNCOV,Bases génétiques et immunologiques des auto-anticorps contre les interférons de type I prédisposant aux formes sévères de COVID-19.(2020), ANR-21-COVR-0039,GenMIS-C,Recherche des Déficits immunitaires innées monogéniques prédisposant au syndrome inflammatoire multisystémique chez l'enfant.(2021), European Project: 824110,H2020-INFRAIA-2018-1,EASI-Genomics(2019), Institut Pasteur [Paris]-Université Paris Cité (UPC), Institut Pasteur [Paris], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Host immunity to infection with SARS-CoV-2 is highly variable, dictating diverse clinical outcomes ranging from asymptomatic to severe disease and death. We previously reported that reduced blood type I interferon (IFN-I) in severe COVID-19 patients preceded clinical worsening. These results were supported by studies which identified genetic mutations in loci of the TLR3- or TLR7-dependent IFN-I pathways, or autoantibodies neutralizing IFNα or IFNω, as major risk factors for development of severe and critical COVID-19 pneumonia. Here, we analyzed a range of IFN-I associated responses in patient cohorts with different severities of COVID-19, showing that baseline plasma IFNα measures differed significantly according to the immunoassay used, as well as timing of sampling, the IFNα subtype measured, and the presence of autoantibodies. We then compared immune responses induced by ex vivo stimulation between non-hospitalized moderate cases (n=27) and hospitalized (n=17) adult patients that required oxygen supplementation. This showed a consistently reduced induction of IFN-I proteins in hospitalized COVID-19 patients upon stimulation, that was not associated with detectable neutralizing autoantibodies against IFNα or IFNω. We confirmed the poor induction of IFN-I in an independent patient cohort (n=33), and showed it was more pronounced with severe disease. Intracellular proteomic analysis showed that while monocyte numbers were increased in hospitalized COVID-19 patients, they did not secrete IFN-I in response to stimulation. This was further confirmed by ex vivo whole blood stimulation with IFN-I which induced a transcriptomic response associated with inflammation in hospitalized COVID-19 patients, that was not seen in controls or non-hospitalized moderate cases. These results may explain the dichotomy of the poor clinical response to IFN-I based treatments in late stage COVID-19, despite the critical importance of IFN-I in early acute infection. An improved understanding of such variable responses to treatment may help to identify potential alternative therapeutic strategies.
Published: 2022

3. Regulated IRE1 alpha-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer

Author: Aitor Almanza, Katarzyna Mnich, Arnaud Blomme, Claire M. Robinson, Giovanny Rodriguez-Blanco, Sylwia Kierszniowska, Eoghan P. McGrath, Matthieu Le Gallo, Eleftherios Pilalis, Johannes V. Swinnen, Aristotelis Chatziioannou, Eric Chevet, Adrienne M. Gorman, Afshin Samali, National University of Ireland [Galway] (NUI Galway), Cancer Research UK Cambridge Institute [Cambridge, Royaume-Uni] (CRUK), University of Cambridge [UK] (CAM), Oncogenesis, Stress, Signaling (OSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Eugène Marquis (CRLCC), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Biomedical Research Foundation of the Academy of Athens (BRFAA), NUI Galway, Science Foundation Ireland, Irish Government's Program for Research in Third Level Institutions, Cycle 5, European Regional Development Fund, Precision Oncology Ireland - Science Foundation Ireland (SFI) Strategic Partnership Program [18/SPP/3522], EU H2020 MSCA [RISE-734749, ITN-675448], SFI Industry Fellowship [18/IF/6247], Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: EXPRESSION, X-Box Binding Protein 1, GENES, General Physics and Astronomy, [SDV.CAN]Life Sciences [q-bio]/Cancer, IRE1, Protein Serine-Threonine Kinases, General Biochemistry, Genetics and Molecular Biology, ENDOPLASMIC-RETICULUM STRESS, Neoplasms, Endoribonucleases, Humans, RNA, Messenger, Science & Technology, MESSENGER-RNA DECAY, Multidisciplinary, UNFOLDED PROTEIN RESPONSE, General Chemistry, ER STRESS, Endoplasmic Reticulum Stress, Lipid Metabolism, NEGATIVE BREAST-CANCER, XBP1, Multidisciplinary Sciences, Science & Technology - Other Topics, CELL FATE, Transcription Factors
Abstract: International audience; IRE1 alpha cleaves several mRNAs upon accumulation of misfolded proteins. Here the authors show that active IRE1 alpha cleaves DGAT2 mRNA encoding the rate-limiting enzyme in the synthesis of triacylglycerols, suggesting a role of IRE1 alpha in reprogramming lipid metabolism in cancer cells. IRE1 alpha is constitutively active in several cancers and can contribute to cancer progression. Activated IRE1 alpha cleaves XBP1 mRNA, a key step in production of the transcription factor XBP1s. In addition, IRE1 alpha cleaves select mRNAs through regulated IRE1 alpha-dependent decay (RIDD). Accumulating evidence implicates IRE1 alpha in the regulation of lipid metabolism. However, the roles of XBP1s and RIDD in this process remain ill-defined. In this study, transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1 alpha reveals changes in lipid metabolism genes associated with accumulation of triacylglycerols (TAGs). We identify DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Inhibition of IRE1 alpha, leads to DGAT2-dependent accumulation of TAGs in lipid droplets and sensitizes cells to nutritional stress, which is rescued by treatment with the DGAT2 inhibitor PF-06424439. Our results highlight the importance of IRE1 alpha RIDD activity in reprograming cellular lipid metabolism.
Published: 2022
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4. Kinetics of the Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response and Serological Estimation of Time Since Infection

Author: Pelleau, Stéphane, Woudenberg, Tom, Rosado, Jason, Donnadieu, Françoise, Garcia, Laura, Obadia, Thomas, Gardais, Soazic, Elgharbawy, Yasmine, Velay, Aurelie, Gonzalez, Maria, Nizou, Jacques Yves, Khelil, Nizar, Zannis, Konstantinos, Cockram, Charlotte, Merkling, Sarah Hélène, Meola, Annalisa, Kerneis, Solen, Terrier, Benjamin, de Seze, Jerome, Planas, Delphine, Schwartz, Olivier, Dejardin, François, Petres, Stéphane, von Platen, Cassandre, Pellerin, Sandrine Fernandes, Arowas, Laurence, de Facci, Louise Perrin, Duffy, Darragh, Cheallaigh, Clíona Ní, Dunne, Jean, Conlon, Niall, Townsend, Liam, Duong, Veasna, Auerswald, Heidi, Pinaud, Laurie, Tondeur, Laura, Backovic, Marija, Hoen, Bruno, Fontanet, Arnaud, Mueller, Ivo, Fafi-Kremer, Samira, Bruel, Timothée, White, Michael, Epidémiologie et Analyse des Maladies Infectieuses - Infectious Disease Epidemiology and Analytics, Institut Pasteur [Paris] (IP), Malaria : parasites et hôtes - Malaria : parasites and hosts, Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Sorbonne Université (SU), Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Strasbourg, Institut Mutualiste de Montsouris (IMM), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Virologie Structurale - Structural Virology, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), CIC Strasbourg (Centre d’Investigation Clinique Plurithématique (CIC - P) ), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Nouvel Hôpital Civil de Strasbourg-Hôpital de Hautepierre [Strasbourg], Virus et Immunité - Virus and immunity (CNRS-UMR3569), Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Immunologie Translationnelle - Translational Immunology lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Trinity College Dublin, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Direction de la recherche médicale de l'Institut Pasteur, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, Vaccine Research Institute [Créteil, France] (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by the European Research Council (MultiSeroSurv ERC Starting Grant 852373, MW), l’Agence Nationale de la Recherche and Fondation pour la Recherche Médicale (CorPopImm, MW), and the Institut Pasteur International Network (CoronaSeroSurv, MW). JR was supported by the Pasteur Paris University (PPU) International PhD Program. CC was supported by the European Research Council 771813. MB, AL and HA were supported by the « URGENCE COVID-19 » fundraising campaign of Institut Pasteur. HA is supported by Centre for International Migration and Development. NC and CNC are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. LT has been awarded the Irish ClinicalAcademic Training (ICAT) Programme, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland (https://icatprogramme.org/). MB and AM were supported by Institut Pasteur TaskForce funding (TooLab project). IM is supported by a NHMRC Principal Research Fellowship. SFK lab is funded by Strasbourg University Hospitals (SeroCoV-HUS, PRI 7782), the Agence Nationale de la Recherche (ANR-18-CE17-0028), Laboratoire d'Excellence TRANSPLANTEX (ANR-11-LABX-0070_TRANSPLANTEX), and Institut National de la Santé et de la Recherche Médicale (UMR_S1109)., ANR-20-COVI-0052,CorPopImm,Évaluer l'immunité contre SARS-CoV-2 à l'échelle de la population grâce aux tests sérologiques(2020), ANR-18-CE17-0028,HuMABK,Les anticorps monoclonaux humains : une Nouvelle approche thérapeutique contre l'infection par le virus BK et les maladies associées(2018), ANR-11-LABX-0070,TRANSPLANTEX,Nouveaux loci d'histocompatibilité/biomarqueurs en transplantation humaine: de la découverte à l'app(2011), European Project: 852373,ERC-2019-STG,MultiSeroSurv(2020), European Project: 771813,ERC-2017-COG,SynarchiC(2018), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM), HESAM Université (HESAM), Vaccine Research Institute (VRI), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: Male, Aucun, Antibodies, Viral, time since infection, MESH: Aged, 80 and over, Antibody Specificity, Seroepidemiologic Studies, MESH: COVID-19, Aged, 80 and over, MESH: Immunoglobulin G, MESH: Aged, MESH: Middle Aged, seroprevalence, MESH: Kinetics, Middle Aged, MESH: Antibody Formation, AcademicSubjects/MED00290, MESH: Young Adult, surveillance, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, France, Adult, antibody kinetics, Adolescent, SARS-SoV-2, Sensitivity and Specificity, Young Adult, Major Article, Humans, Serologic Tests, MESH: SARS-CoV-2, MESH: Antibody Specificity, Aged, MESH: Adolescent, MESH: Humans, MESH: Seroepidemiologic Studies, SARS-CoV-2, MESH: Serologic Tests, COVID-19, MESH: Adult, MESH: Male, MESH: Sensitivity and Specificity, MESH: France, Kinetics, sero-prevalence, Immunoglobulin G, Antibody Formation, MESH: Female, MESH: Antibodies, Viral
Abstract: Background Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Methods We developed a multiplex serological test for measuring antibodies to 5 SARS-CoV-2 antigens and the spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to 11 months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. Results One year after symptoms, we estimate that 36% (95% range, 11%–94%) of anti-Spike immunoglobulin G (IgG) remains, 31% (95% range, 9%–89%) anti-RBD IgG remains, and 7% (1%–31%) of anti-nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0–3 months, 3–6 months, and 6–12 months. This method was validated using data from a seroprevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. Conclusions In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection, which can be used to reconstruct past epidemics., Longitudinal follow-up of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveals differences in the duration of antibodies to multiple antigens. Mathematical models of antibody waning and statistical algorithms can estimate an individual’s time since SARS-CoV-2 infection, and previous transmission waves in a population.
Published: 2021
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5. Karst modelling challenge 1: Results of hydrological modelling

Author: Dominique Thiéry, Naomi Mazzilli, Guillaume Artigue, Yong Chang, Yan Liu, Philip Schuler, Tanja Liesch, Pierre-Yves Jeannin, Eulogio Pardo-Igúzquiza, Hervé Jourde, Martin P. Lüthi, Laurence Gill, Jean-Baptiste Charlier, Thomas Wöhling, Andreas Wunsch, Arnauld Malard, Lea Duran, Anne Johannet, Thomas Reimann, Andreas Hartmann, Christoph Butscher, Alireza Kavousi, Swiss Institute for Speleology and Karst Studies (SISKA), Centre for Hydrogeology and Geothermics [Switzerland], Université de Neuchâtel (UNINE), IMT Mines Alès - ERT (ERT), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), HYTAKE : Hydrogéologie et Transferts dans les Aquifères Karstiques (HYTAKE), Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Technishe Universität Bergakademie Freiberg (TU Bergakademie Freiberg), Nanjing University (NJU), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Trinity College Dublin, University of Freiburg [Freiburg], Service National d'Observation sur le KARST (SNO Karst), Institut national des sciences de l'Univers (INSU - CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Karlsruhe Institute of Technology (KIT), Universität Zürich [Zürich] = University of Zurich (UZH), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Geológico y Minero de España (IGME), Lincoln Agritech Ltd, Swiss National Research Foundation (SNF) for Swisskarst and Thermokarst projects (Grant Numbers 406140-125962 and 200021_188636), the Deutsche Forschungsgemeinschaft, DFG for the iKarst project (Grant Numbers: LI 727/31-1 and RE 4001/2-1). The work of E. Pardo-Igúzquiza was supported by research project PID2019-106435 GB-I00 of the Ministerio de Ciencia e Innovación of Spain. This TCD-Dublin was conducted within the Irish Centre for Research in Applied Geosciences (ICRAG), supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number 13/RC/2092. The authors would like to thank the French Karst National Observatory Service (SNO KARST) initiative at the INSU/CNRS for their diffusion of KarstMod platform., University of Zurich, Jeannin, Pierre-Yves, Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010504 meteorology & atmospheric sciences, Groundwater flow, Calibration (statistics), Geography & travel, Hydrological modelling, 0207 environmental engineering, Karst, Hydrograph, 02 engineering and technology, Comparison, 01 natural sciences, Modelling, 2312 Water Science and Technology, Statistics, 910 Geography & travel, 020701 environmental engineering, 0105 earth and related environmental sciences, ddc:910, Water Science and Technology, Baseflow, Computational model, Recharge, Data set, 10122 Institute of Geography, 13. Climate action, [SDE]Environmental Sciences, Environmental science, Efficiency criteria, Groundwater model
Abstract: International audience; The complexity of karst groundwater flow modelling is reflected by the amount of simulation approaches. The goal of the Karst Modelling Challenge (KMC) is comparing different approaches on one single system using the same data set. Thirteen teams with different computational models for simulating discharge variations at karst springs have applied their respective models on one single data set coming from the Milandre Karst Hydrogeological System (MKHS). The approaches include neural networks, reservoir models, semi-distributed models and fully distributed groundwater models. Four and a half years of hourly or daily meteorological input and hourly discharge data were provided for model calibration. The validation comprised forecasting one year of discharge, without the observed discharge data. The model performance was evaluated using the volume conservation, Nash-Sutcliffe efficiency (NSE) and the Kling-Gupta efficiency (KGE) applied on the total discharge and individual flow components. As a result, the comparison of model performances is a challenging task due to the differences in the model architecture but also required time steps: some of the models require aggregated daily steps while others could be run using hourly data, which provided some interesting differences depending on how the data was transformed. The use of instantaneous data (e.g. value at noon) produces less bias that averaging hourly data over one day. The transformation of hourly into daily data produces a decrease of Nash and KGE of 0.05 to 0.08 (i.e. from 1 to ~0.93). The resulting simulations (forecasted values for year 2016) produced KGEs ranging between 0.83 and 0.37 (0.83 to −0.24 for NSE). Although the simulations matched the monitored flows reasonably well, most models struggled to simulate baseflow conditions accurately. In general, the models that performed the best for this exercise were the global ones (Gardenia and Varkarst), with a limited number of parameters, which can be calibrated using automatic calibration procedures. The neural network models also showed a fair potential, with one providing reasonable results despite the relatively short dataset available for warming-up (4.5 years). Semi-and fully distributed models also suggested that with some more effort they could perform well. The accuracy of model predictions does not seem to increase by using models with more than 9–12 calibration parameters. An evaluation of the relative errors between the forecasted and the observed values revealed that for most models, 50% of the forecasted values contained more than 50% of difference against the observed discharge rate, with 25% having a difference larger than 100%. A significant part of the poorly forecasted values corresponded to base-flow which was surprising given that as base-flow is generally much easier to predict than peak flow. Hence, this shows that modelling approaches and criteria for the calibration are too oriented towards peak-flow sections of the hydrographs, and that improvements could be gained by more focus on the base-flow.
Published: 2021
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6. Kinetics of the SARS-CoV-2 antibody response and serological estimation of time since infection

Author: Pelleau, Stéphane, Woudenberg, Tom, Rosado, Jason, Donnadieu, Françoise, Garcia, Laura, Obadia, Thomas, Gardais, Soazic, Elgharbawy, Yasmine, Velay, Aurelie, Gonzalez, Maria, Nizou, Jacques Yves, Khelil, Nizar, Zannis, Konstantinos, Cockram, Charlotte, Merkling, Sarah Hélène, Meola, Annalisa, Kerneis, Solen, Terrier, Benjamin, de Seze, Jerome, Planas, Delphine, schwartz, olivier, Dejardin, François, Petres, Stéphane, von Platen, Cassandre, Pellerin, Sandrine Fernandes, Arowas, Laurence, de Facci, Louise Perrin, Duffy, Darragh, Cheallaigh, Clíona Ní, Dunne, Jean, Conlon, Niall, Townsend, Liam, Duong, Veasna, Auerswald, Heidi, Pinaud, Laurie, Tondeur, Laura, Backovic, Marija, Hoen, Bruno, Fontanet, Arnaud, Mueller, Ivo, Fafi-Kremer, Samira, Bruel, Timothée, White, Michael, Epidémiologie et Analyse des Maladies Infectieuses - Infectious Disease Epidemiology and Analytics, Institut Pasteur [Paris], Malaria : parasites et hôtes - Malaria : parasites and hosts, Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Sorbonne Université (SU), Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Strasbourg, Institut Mutualiste de Montsouris (IMM), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Virologie Structurale - Structural Virology, Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), CIC Strasbourg (Centre d’Investigation Clinique Plurithématique (CIC - P) ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)-Hôpital de Hautepierre [Strasbourg]-Nouvel Hôpital Civil de Strasbourg, Virus et Immunité - Virus and immunity, Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Immunologie Translationnelle - Translational Immunology lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Trinity College Dublin, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Direction de la recherche médicale de l'Institut Pasteur, Conservatoire National des Arts et Métiers [CNAM] (CNAM), The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, Vaccine Research Institute (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by the European Research Council (MultiSeroSurv ERC Starting Grant 852373, MW), l’Agence Nationale de la Recherche and Fondation pour la Recherche Médicale (CorPopImm, MW), and the Institut Pasteur International Network (CoronaSeroSurv, MW). JR was supported by the Pasteur Paris University (PPU) International PhD Program. CC was supported by the European Research Council 771813. MB, AL and HA were supported by the « URGENCE COVID-19 » fundraising campaign of Institut Pasteur. HA is supported by Centre for International Migration and Development. NC and CNC are part-funded by a Science Foundation Ireland (SFI) grant, Grant Code 20/SPP/3685. LT has been awarded the Irish ClinicalAcademic Training (ICAT) Programme, supported by the Wellcome Trust and the Health Research Board (Grant Number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning and the Health and Social Care, Research and Development Division, Northern Ireland (https://icatprogramme.org/). MB and AM were supported by Institut Pasteur TaskForce funding (TooLab project). IM is supported by a NHMRC Principal Research Fellowship. SFK lab is funded by Strasbourg University Hospitals (SeroCoV-HUS, PRI 7782), the Agence Nationale de la Recherche (ANR-18-CE17-0028), Laboratoire d'Excellence TRANSPLANTEX (ANR-11-LABX-0070_TRANSPLANTEX), and Institut National de la Santé et de la Recherche Médicale (UMR_S1109)., ANR-20-COVI-0052,CorPopImm,Évaluer l'immunité contre SARS-CoV-2 à l'échelle de la population grâce aux tests sérologiques(2020), ANR-18-CE17-0028,HuMABK,Les anticorps monoclonaux humains : une Nouvelle approche thérapeutique contre l'infection par le virus BK et les maladies associées(2018), ANR-11-LABX-0070,TRANSPLANTEX,Nouveaux loci d'histocompatibilité/biomarqueurs en transplantation humaine: de la découverte à l'app(2011), European Project: 852373,ERC-2019-STG,MultiSeroSurv(2020), European Project: 771813,SynarchiC, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris], and HESAM Université (HESAM)
Subjects: antibody kinetics, time since infection, sero-prevalence, surveillance, [SDV.IMM]Life Sciences [q-bio]/Immunology, SARS-SoV-2
Abstract: All data and code used for reproducing the results is freely available on GitHub: https://github.com/MWhite-InstitutPasteur/SARSCoV2_AB_kinetics.; International audience; Background Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. Methods We developed a multiplex serological test for measuring antibodies to five SARS-CoV-2 antigens and the Spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to eleven months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. Results One year after symptoms, we estimate that 36% (95% range: 11%, 94%) of anti-Spike IgG remains, 31% (9%, 89%) anti-RBD IgG remains, and 7% (1%, 31%) anti-Nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0–3 months, 3–6 months, and 6–12 months. This method was validated using data from a sero-prevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. Conclusions In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection which can be used to reconstruct past epidemics.
Published: 2021
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7. Health-ID: a blockchain-based decentralized identity management for remote healthcare

Author: Badr Bellaj, Kashif Naseer Qureshi, Tiziana Margaria, Noel Crespi, Fares F Alharbi, Ibrahim Tariq Javed, Science Foundation Ireland (SFI Lero), Shaqra University, Institut Polytechnique de Paris (IP Paris), Département Réseaux et Services Multimédia Mobiles (RS2M), Institut Mines-Télécom [Paris] (IMT)-Télécom SudParis (TSP), Réseaux, Systèmes, Services, Sécurité (R3S-SAMOVAR), Services répartis, Architectures, MOdélisation, Validation, Administration des Réseaux (SAMOVAR), Institut Mines-Télécom [Paris] (IMT)-Télécom SudParis (TSP)-Institut Mines-Télécom [Paris] (IMT)-Télécom SudParis (TSP), Health Research Institute (HRI), University of Limerick (UL), and Bahria University
Subjects: Smart contract, Leadership and Management, Computer science, 0211 other engineering and technologies, Health Informatics, Digital identity, 02 engineering and technology, Telehealth, Computer security, computer.software_genre, Article, Identity management, [INFO.INFO-SI]Computer Science [cs]/Social and Information Networks [cs.SI], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Ethereum, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], Blockchain, Health Information Management, 0202 electrical engineering, electronic engineering, information engineering, eHealth, 021110 strategic, defence & security studies, Authentication, Health Policy, Hhealthcare, healthcare, Service provider, 3. Good health, Identity management system, Medicine, Decentralized identity, 020201 artificial intelligence & image processing, computer
Abstract: COVID-19 has made eHealth an imperative. The pandemic has been a true catalyst for remote eHealth solutions such as teleHealth. Telehealth facilitates care, diagnoses, and treatment remotely, making them more efficient, accessible, and economical. However, they have a centralized identity management system that restricts the interoperability of patient and healthcare provider identification. Thus, creating silos of users that are unable to authenticate themselves beyond their eHealth application’s domain. Furthermore, the consumers of remote eHealth applications are forced to trust their service providers completely. They cannot check whether their eHealth service providers adhere to the regulations to ensure the security and privacy of their identity information. Therefore, we present a blockchain-based decentralized identity management system that allows patients and healthcare providers to identify and authenticate themselves transparently and securely across different eHealth domains. Patients and healthcare providers are uniquely identified by their health identifiers (healthIDs). The identity attributes are attested by a healthcare regulator, indexed on the blockchain, and stored by the identity owner. We implemented smart contracts on an Ethereum consortium blockchain to facilities identification and authentication procedures. We further analyze the performance using different metrics, including transaction gas cost, transaction per second, number of blocks lost, and block propagation time. Parameters including block-time, gas-limit, and sealers are adjusted to achieve the optimal performance of our consortium blockchain.
Published: 2021
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8. Event-driven ECG classification using an open-source, LC-ADC based non-uniformly sampled dataset

Author: Deepu John, Maryam Saeed, Qingyuan Wang, Antoine Frappe, Benoit Larras, Olev Martens, Barry Cardiff, University College Dublin [Dublin] (UCD), Tallinn University of Technology (TTÜ), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Microélectronique Silicium - IEMN (MICROELEC SI - IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Schlumberger Foundation, Science Foundation Ireland, SFI: 18/CRT/6183, Irish Research Council, This work is supported by 1) JEDAI project under the Chist-Era Program, 2)Schlumberger Foundation’s Faculty for the Future Program 3) Irish ResearchCouncil under the New Foundations Scheme and 4) Science FoundationIreland through the SFI Centre for Research Training in Machine Learning(18/CRT/6183), ANR-19-CHR3-0005,JEDAI,Event Driven Artificial Intelligence Hardware for Biomedical Sensors(2019), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), and Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA)
Subjects: Artificial neural network, Artificial neural networks, business.industry, Computer science, 020208 electrical & electronic engineering, Event-driven data, Signal compression, Cardiac arrhythmia, Pattern recognition, 02 engineering and technology, Converters, Reduction (complexity), [SPI]Engineering Sciences [physics], Signal-to-noise ratio, ComputingMethodologies_PATTERNRECOGNITION, Cardiac arrhythmia classification, Distortion, 0202 electrical engineering, electronic engineering, information engineering, Wearable sensors, ComputerSystemsOrganization_SPECIAL-PURPOSEANDAPPLICATION-BASEDSYSTEMS, Artificial intelligence, Quantization (image processing), business, LC-ADC
Abstract: The open-source event-driven ECG dataset is available at https://github.com/jedaiproject/Open-Source-Event-Driven-ECG-Dataset; International audience; In this article, non-uniformly sampled electrocardiogram (ECG) signals obtained from level-crossing analog-to-digital converters (LC-ADCs) are analyzed for event-driven classification and compression performance. The signal compression results show that it is important to assess the distortion in event-driven signals when simulating LC-ADC models, especially at lower resolutions and larger quantization steps. The effects of varying the LC-ADC parameters for the application of cardiac arrhythmia classifiers are also assessed using an artificial neural network (ANN) and the MIT-BIH Arrhythmia Database. In comparison with uniformly-sampled data, it is possible to achieve comparable classification accuracy at a much lower complexity with event-driven ECG signals. The results show the best event-driven model achieves over 97% accuracy with 79% reduction in ANN complexity with signal-to-distortion ratio (S/D)≥21dB. For S/D
Published: 2021
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9. Giant Magnetoelectric Coupling and Magnetic-Field-Induced Permanent Switching in a Spin Crossover Mn(III) Complex

Author: Grace G. Morgan, Xiaxin Ding, Vivien Zapf, Hai-Ping Cheng, Jie-Xiang Yu, Shalinee Chikara, Conor T. Kelly, Franziska Weickert, Elzbieta Trzop, Vibe B. Jakobsen, Emiel Dobbelaar, Eric Collet, University College Dublin [Dublin] (UCD), Los Alamos National Laboratory (LANL), University of Florida [Gainesville] (UF), Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), The scientific work by V.S.Z., H.P.C. and J.Y. was funded by the Center for Molecular Magnetic Quantum Materials (M2QM), an Energy Frontier Research Center funded by the U.S. Depart-ment of Energy, Office of Science, Basic Energy Sciences under Award DE SC0019330. G.G.M. would like to thank Science Foundation Ireland (SFI) for support via an Investigator Project Award (19/FFO/6909). V.B.J. was supported by the Irish Re-search Council GOIPG/2016/73 fellowship. Travel grants for V.B.J.’s research visits to LANL and IPR were funded by Augusti-nus Fonden (grant no. 18-0338), Oticon Fonden (grant no. 17-3813), Reinholdt W. Jorck og Hustrus Fond (grant no. 18-JI-0573), P.A. Fiskers Fond, A.P. Møller og Hustru Chastine Mc-Kinney Møllers Fond til almene Formaal and Christian og Ot-tilia Brorsons Rejselegat for yngre videnskabsmænd og -kvinder. C.T.K was supported by the Irish Research Council GOIPG/2018/2510 and UCD Advance PhD Scheme Supple-mental Award. The NHMFL experimental facility at LANL is funded by the U.S. National Science Foundation through Coop-erative Grant No. DMR-1157490, the State of Florida, and the U.S. Department of Energy., and Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS]Physics [physics], Phase transition, Field (physics), Condensed matter physics, 010405 organic chemistry, Chemistry, Magnetoelectric effect, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Magnetic field, Inorganic Chemistry, Polarization density, Spin crossover, Phase (matter), [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Spin-½
Abstract: International audience; We investigate giant magnetoelectric coupling at a Mn spin crossover in [MnL]BPh (L = (3,5-diBr-sal)323) with a field-induced permanent switching of the structural, electric, and magnetic properties. An applied magnetic field induces a first-order phase transition from a high spin/low spin (HS-LS) ordered phase to a HS-only phase at 87.5 K that remains after the field is removed. We observe this unusual effect for DC magnetic fields as low as 8.7 T. The spin-state switching driven by the magnetic field in the bistable molecular material is accompanied by a change in electric polarization amplitude and direction due to a symmetry-breaking phase transition between polar space groups. The magnetoelectric coupling occurs due to a γη coupling between the order parameter γ related to the spin-state bistability and the symmetry-breaking order parameter η responsible for the change of symmetry between polar structural phases. We also observe conductivity occurring during the spin crossover and evaluate the possibility that it results from conducting phase boundaries. We perform ab initio calculations to understand the origin of the electric polarization change as well as the conductivity during the spin crossover. Thus, we demonstrate a giant magnetoelectric effect with a field-induced electric polarization change that is 1/10 of the record for any material.
Published: 2021
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10. PI Regulation of a Reaction-Diffusion Equation with Delayed Boundary Control

Author: Christophe Prieur, Hugo Lhachemi, Emmanuel Trélat, University College Dublin [Dublin] (UCD), GIPSA - Infinite Dimensional Dynamics (GIPSA-INFINITY), GIPSA Pôle Automatique et Diagnostic (GIPSA-PAD), Grenoble Images Parole Signal Automatique (GIPSA-lab), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Grenoble Alpes (UGA), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Control And GEometry (CaGE ), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under grant number 16/RC/3872 and is co-funded under the European Regional Development Fund and byI-Form industry partners., Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lyapunov function, 0209 industrial biotechnology, 1-D reaction-diffusion equation, Partial Differential Equations (PDEs), 1-D Reaction-diffusion equation, PID controller, Boundary (topology), 02 engineering and technology, Systems and Control (eess.SY), Electrical Engineering and Systems Science - Systems and Control, Setpoint, Tracking error, symbols.namesake, 020901 industrial engineering & automation, Control theory, Neumann trace, Reaction–diffusion system, FOS: Mathematics, FOS: Electrical engineering, electronic engineering, information engineering, [INFO.INFO-SY]Computer Science [cs]/Systems and Control [cs.SY], Electrical and Electronic Engineering, Mathematics - Optimization and Control, Delay boundary control, Mathematics, Computer Science Applications, PI regulation control, Control and Systems Engineering, Optimization and Control (math.OC), Time derivative, symbols, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Numerical stability
Abstract: The general context of this work is the feedback control of an infinite-dimensional system so that the closed-loop system satisfies a fading-memory property and achieves the setpoint tracking of a given reference signal. More specifically, this paper is concerned with the Proportional Integral (PI) regulation control of the left Neumann trace of a one-dimensional reaction-diffusion equation with a delayed right Dirichlet boundary control. In this setting, the studied reaction-diffusion equation might be either open-loop stable or unstable. The proposed control strategy goes as follows. First, a finite-dimensional truncated model that captures the unstable dynamics of the original infinite-dimensional system is obtained via spectral decomposition. The truncated model is then augmented by an integral component on the tracking error of the left Neumann trace. After resorting to the Artstein transformation to handle the control input delay, the PI controller is designed by pole shifting. Stability of the resulting closed-loop infinite-dimensional system, consisting of the original reaction-diffusion equation with the PI controller, is then established thanks to an adequate Lyapunov function. In the case of a time-varying reference input and a time-varying distributed disturbance, our stability result takes the form of an exponential Input-to-State Stability (ISS) estimate with fading memory. Finally, another exponential ISS estimate with fading memory is established for the tracking performance of the reference signal by the system output. In particular, these results assess the setpoint regulation of the left Neumann trace in the presence of distributed perturbations that converge to a steady-state value and with a time-derivative that converges to zero. Numerical simulations are carried out to illustrate the efficiency of our control strategy., Comment: Preprint
Published: 2021
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11. Virtual Avatars as Children Companions : For a VR-based Educational Platform: How Should They Look Like?

Author: Thiaville, Elsa, Normand, Jean-Marie, Kenny, Joe, Ventresque, Anthony, Science Foundation Ireland (SFI Lero), École Centrale de Nantes (ECN), 3D interaction with virtual environments using body and mind (Hybrid), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-MEDIA ET INTERACTIONS (IRISA-D6), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-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 Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-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 Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre de recherche nantais Architectures Urbanités (CRENAU ), Ambiances, Architectures, Urbanités (AAU), École Centrale de Nantes (ECN)-École nationale supérieure d'architecture de Nantes (ENSA Nantes)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Grenoble (ENSAG ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-École Centrale de Nantes (ECN)-École nationale supérieure d'architecture de Nantes (ENSA Nantes)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Grenoble (ENSAG ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA), Zeeko [Dublin], 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)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR]
Abstract: International audience; Virtual Reality (VR) has the potential of becoming a game changer in education, with studies showing that VR can lead to better quality of and access to education. One area that is promising, especially for young children, is the use of Virtual Companions that act as teaching assistants and support the learners' educational journey in the virtual environment. However, as it is the case in real life, the appearance of the virtual companions can be critical for the learning experience. This paper studies the impact of the age, gender and general appearance (human-or robot-like) of virtual companions on 9-12 year old children. Our results over two experiments (n=24 and n=13) tend to show that children have a bigger sense of Spatial Presence, Engagement and Ecological Validity when interacting with a human-like Virtual Companion of the Same Age and of a Different Gender.
Published: 2020

12. ASVspoof 2019: A large-scale public database of synthesized, converted and replayed speech

Author: Hirokazu Kameoka, Hsin-Te Hwang, Driss Matrouf, Markus Becker, Quan Wang, Sahidullah, Ye Jia, Yu Zhang, Lauri Juvela, Hsin-Min Wang, Wen-Chin Huang, Zhen-Hua Ling, Yuan Jiang, Yi-Chiao Wu, Héctor Delgado, Massimiliano Todisco, Yu Tsao, Li-Juan Liu, Junichi Yamagishi, Jean-François Bonastre, Tomoki Toda, Nicholas Evans, Robert A. J. Clark, Kai Onuma, Yu-Huai Peng, Sébastien Le Maguer, Avashna Govender, Takashi Kaneda, Andreas Nautsch, Kong Aik Lee, Xin Wang, Srikanth Ronanki, Ville Vestman, Koji Mushika, Ingmar Steiner, Tomi Kinnunen, Fergus Henderson, Jing-Xuan Zhang, Kou Tanaka, Paavo Alku, Hitotsubashi University, University of Edinburgh, Eurecom [Sophia Antipolis], Speech Modeling for Facilitating Oral-Based Communication (MULTISPEECH), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Natural Language Processing & Knowledge Discovery (LORIA - NLPKD), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Eastern Finland, NEC Corporation, Aalto University, Academia Sinica, ADAPT Centre, Sigmedia Lab, EE Engineering, Trinity College Dublin, Google Inc [Mountain View], Research at Google, Hoya Corp., iFlytek Research, Nagoya City University [Nagoya, Japan], NTT Communication Science Laboratories, NTT Corporation, audEERING GmbH, Laboratoire Informatique d'Avignon (LIA), Avignon Université (AU)-Centre d'Enseignement et de Recherche en Informatique - CERI, The Centre for Speech Technology Research [Edinburgh] (CSTR), Southern University of Science and Technology (SUSTech), The work was partially supported by JST CREST Grant No. JPMJCR18A6 (VoicePersonae project), Japan, MEXT KAKENHI Grant Nos. (16H06302, 16K16096, 17H04687, 18H04120, 18H04112, 18KT0051), Japan, the VoicePersonae and RESPECT projects funded by the French Agence Nationale de la Recherche (ANR), the Academy of Finland (NOTCH project no. 309629), and Region Grand Est, France. entitled 'NOTCH: NOn-cooperaTive speaker CHaracterization'). The authors at the University of Eastern Finland also gratefully acknowledge the use of the computational infrastructures at CSC – the IT Center for Science, and the support of the NVIDIA Corporation the donation of a Titan V GPU used in this research. The numerical calculations of some of the spoofed data were carried out on the TSUBAME3.0 supercomputer at the Tokyo Institute of Technology. The work is also partially supported by Region Grand Est, France. The ADAPT centre (13/RC/2106) is funded by the Science Foundation Ireland (SFI)., National Institute of Informatics, EURECOM, Université de Lorraine, Dept Signal Process and Acoust, Trinity College Dublin, Google, USA, HOYA Corporation, IFLYTEK Co., Ltd., Nagoya University, AudEERING GmbH, Avignon Université, University of Science and Technology of China, Aalto-yliopisto, and Southern University of Science and Technology of China (SUSTech)
Subjects: Signal Processing (eess.SP), FOS: Computer and information sciences, Sound (cs.SD), ASVspoof challenge, biometrics, Computer Science - Cryptography and Security, voice conversion, Computer science, Speech synthesis, 02 engineering and technology, computer.software_genre, 01 natural sciences, Computer Science - Sound, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], text-to-speech synthesis, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Audio and Speech Processing (eess.AS), 0202 electrical engineering, electronic engineering, information engineering, Replay, Use case, media forensics, 010301 acoustics, Protocol (object-oriented programming), Text-to-speech synthesis, Database, presentation attack, ComputingMilieux_MANAGEMENTOFCOMPUTINGANDINFORMATIONSYSTEMS, Automatic speaker verification, Cryptography and Security (cs.CR), [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Electrical Engineering and Systems Science - Audio and Speech Processing, automatic speaker verification, Voice conversion, Spoofing attack, Biometrics, anti-spoofing, Reliability (computer networking), Database design, Theoretical Computer Science, replay, presentation attack detection, 0103 physical sciences, FOS: Electrical engineering, electronic engineering, information engineering, Electrical Engineering and Systems Science - Signal Processing, [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, [INFO.INFO-CV]Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], 020206 networking & telecommunications, Human-Computer Interaction, Physical access, computer, countermeasure, Software
Abstract: Automatic speaker verification (ASV) is one of the most natural and convenient means of biometric person recognition. Unfortunately, just like all other biometric systems, ASV is vulnerable to spoofing, also referred to as "presentation attacks." These vulnerabilities are generally unacceptable and call for spoofing countermeasures or "presentation attack detection" systems. In addition to impersonation, ASV systems are vulnerable to replay, speech synthesis, and voice conversion attacks. The ASVspoof 2019 edition is the first to consider all three spoofing attack types within a single challenge. While they originate from the same source database and same underlying protocol, they are explored in two specific use case scenarios. Spoofing attacks within a logical access (LA) scenario are generated with the latest speech synthesis and voice conversion technologies, including state-of-the-art neural acoustic and waveform model techniques. Replay spoofing attacks within a physical access (PA) scenario are generated through carefully controlled simulations that support much more revealing analysis than possible previously. Also new to the 2019 edition is the use of the tandem detection cost function metric, which reflects the impact of spoofing and countermeasures on the reliability of a fixed ASV system. This paper describes the database design, protocol, spoofing attack implementations, and baseline ASV and countermeasure results. It also describes a human assessment on spoofed data in logical access. It was demonstrated that the spoofing data in the ASVspoof 2019 database have varied degrees of perceived quality and similarity to the target speakers, including spoofed data that cannot be differentiated from bona-fide utterances even by human subjects., Accepted, Computer Speech and Language. This manuscript version is made available under the CC-BY-NC-ND 4.0. For the published version on Elsevier website, please visit https://doi.org/10.1016/j.csl.2020.101114
Published: 2020
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13. Local intracerebral inhibition of IRE1 by MKC8866 sensitizes glioblastoma to irradiation/chemotherapy in vivo

Author: Qingping Zeng, Raphael Pineau, Pierre-Jean Le Reste, Afshin Samali, Amandine Etcheverry, Adrienne M. Gorman, Juhi Samal, Aristotelis Chatziioannou, Jean Mosser, Nicolas Soriano, Eric Chevet, Marc Aubry, Stéphanie Lhomond, Gwénaële Jégou, John B. Patterson, Tony Avril, Konstantinos Voutetakis, Abhay Pandit, Chemistry, Oncogenesis, Stress and Signaling (COSS), Institut National de la Santé et de la Recherche Médicale (INSERM)-CRLCC Eugène Marquis (CRLCC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), CRLCC Eugène Marquis (CRLCC), Rennes Brain Cancer Team (REACT), University of Thessaly [Volos] (UTH), National University of Ireland [Galway] (NUI Galway), Fosun Orinove PharmaTech Inc.[Newbury Park, CA], Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), CHU Pontchaillou [Rennes], National Hellenic Research Foundation [Athens], Biosit : biologie, santé, innovation technologique (SFR UMS CNRS 3480 - INSERM 018), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), This work was funded by grants from the French National Cancer Institute (INCa, PLBIO2017, 2019, 2020), the Fondation pour la recherche Médicale (FRM, équipe labellisée 2018) to EC and EU H2020 MSCA ITN-675448 (TRAINERS) and MSCA RISE-734749 (INSPIRED) grants to AS, AC and EC. The work was also supported in part by research grant from Science Foundation Ireland (SFI), co-funded under the European Regional Development Fund under Grant number 13/RC/2073., BIOSIT H2P2 platform, BIOSIT Animal facility ARCHE (https://biosit.univ-rennes1.fr/), European Project: 675448,H2020,H2020-MSCA-ITN-2015,TRAIN-ERS(2015), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: 0301 basic medicine, Oncology, Cancer Research, medicine.medical_treatment, Disease, Injections, Intralesional, Mice, 0302 clinical medicine, Tumor Microenvironment, 0303 health sciences, Stress sensor, Brain Neoplasms, Combined Modality Therapy, Chemotherapy regimen, Neoadjuvant Therapy, Treatment efficacy, 3. Good health, Gene Expression Regulation, Neoplastic, Treatment Outcome, 030220 oncology & carcinogenesis, Immunocompetence, Craniotomy, medicine.medical_specialty, Morpholines, [SDV.CAN]Life Sciences [q-bio]/Cancer, IRE1, 03 medical and health sciences, Animal model, Drug Therapy, In vivo, Cell Line, Tumor, Internal medicine, medicine, Animals, Humans, Benzopyrans, 030304 developmental biology, Chemotherapy, Radiotherapy, business.industry, Gene Expression Profiling, medicine.disease, Xenograft Model Antitumor Assays, 030104 developmental biology, Unfolded protein response, Unfolded Protein Response, Tumor surgery, business, Glioblastoma, Endoplasmic reticulum
Abstract: Glioblastoma multiforme (GBM) is the most severe primary brain cancer. Despite an aggressive treatment comprising surgical resection and radio/chemotherapy patient’s survival post diagnosis remains short. A limitation for success in finding novel improved therapeutic options for such dismal disease partly lies in the lack of a relevant animal model that accurately recapitulates patient disease and standard of care. In the present study, we have developed a novel immunocompetent GBM model that includes tumor surgery and a radio/chemotherapy regimen resembling the Stupp protocol and we have used this model to test the impact of the pharmacological inhibition of the endoplasmic reticulum (ER) stress sensor IRE1, on treatment efficacy.
Published: 2020
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14. A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis

Author: Theodorou, Ilias, Courtin, Pascal, Palussière, Simon, Kulakauskas, Saulius, Bidnenko, Elena, Péchoux, Christine, Fenaille, François, Penno, Christophe, Mahony, Jennifer, Van Sinderen, Douwe, Chapot Chartier, Marie-Pierre, University College Cork (UCC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), INRA, Science Foundation Ireland (SFI) : Starting Investigator Research Grant (SIRG) 15/SIRG/3430, and Principal Investigator Award 450 13/IA/1953
Subjects: lactic acid bacteria, glycopolymer, bacteriophage, polysaccharide, [SDV]Life Sciences [q-bio], rhamnose, cell wall, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, rhamnan, biosynthesis, Gram-positive bacteria, glycosyltransferase, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: Corresponding authors :Douwe van Sinderen (d.vansinderen@ucc.ie) Marie-Pierre Chapot-Chartier (marie-pierre.chapot-chartier@inra.fr); International audience; In $Lactococcus\ lactis$, cell-wall polysaccharides (CWPSs) act as receptors for many bacteriophages, and their structural diversity among strains explains, at least partially, the narrow host range of these viral predators. Previous studies have reported that lactococcal CWPS consists of two distinct components, a variable chain exposed at the bacterial surface, named polysaccharide pellicle (PSP), and a more conserved rhamnan chain anchored to, and embedded inside, peptidoglycan. These two chains appear to be covalently linked to form a large heteropolysaccharide. The molecular machinery for biosynthesis of both components is encoded by a large gene cluster, named $cwps$. In this study, using a CRISPR/Cas-based method, we performed a mutational analysis of the $cwps$ genes. MALDI-TOF MS-based structural analysis of the mutant CWPS combined with sequence homology, transmission EM, and phage sensitivity analyses enabled us to infer a role for each protein encoded by the $cwps$ cluster. We propose a comprehensive CWPS biosynthesis scheme in which the rhamnan and PSP chains are independently synthesized from two distinct lipid-sugar precursors and are joined at the extracellular side of the cytoplasmic membrane by a mechanism involving a membrane-embedded glycosyltransferase with a GT-C fold. The proposed scheme encompasses a system that allows extracytoplasmic modification of rhamnan by complex substituting oligo-/polysaccharides. It accounts for the extensive diversity of CWPS structures observed among lactococci and may also have relevance to the biosynthesis of complex rhamnose-containing CWPSs in other Gram-positive bacteria.
Published: 2019
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15. Recent Advances in Matrix Partitioning for Parallel Computing on Heterogeneous Platforms

Author: Ashley DeFlumere, Brett A. Becker, Alexey Lastovetsky, Olivier Beaumont, Lionel Eyraud-Dubois, Thomas Lambert, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Reformulations based algorithms for Combinatorial Optimization (Realopt), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), School of Computer Science and Informatics [Dublin], University College Dublin [Dublin] (UCD), Wellesley College, This publication has emanated from research conducted with the financial support of Science Foundation Ireland(SFI) under Grant Number 14/IA/2474. This work is partially supported by EU under the COST Program Action IC1305:Network for Sustainable Ultrascale Computing (NESUS), ANR-13-MONU-0007,SOLHAR,Solveurs pour architectures hétérogènes utilisant des supports d'exécution(2013), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Institut de Mathématiques de Bordeaux (IMB), and Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest
Subjects: Optimization, Optimization problem, Computer science, Recursive partitioning, 0102 computer and information sciences, 02 engineering and technology, 01 natural sciences, Matrix (mathematics), Load management, 0202 electrical engineering, electronic engineering, information engineering, Linear algebra, Discrete mathematics, 020203 distributed computing, Shape, Approximation algorithm, Load balancing (computing), Partitioning algorithms, Approximation algorithms, Kernel, Computational Theory and Mathematics, 010201 computation theory & mathematics, Hardware and Architecture, Signal Processing, Matrix partitioning, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract: The problem of partitioning dense matrices into sets of sub-matrices has received increased attention recently and is crucial when considering dense linear algebra and kernels with similar communication patterns on heterogeneous platforms. The problem of load balancing and minimizing communication is traditionally reducible to an optimization problem that involves partitioning a square into rectangles. This problem has been proven to be NP-Complete for an arbitrary number of partitions. In this paper, we present recent approaches that relax the restriction that all partitions be rectangles. The first approach uses an original mathematical technique to find the exact optimal partitioning. Due to the complexity of the technique, it has been developed for a small number of partitions only. However, even at a small scale, the optimal partitions found by this approach are often non-rectangular and sometimes non-intuitive. The second approach is the study of approximate partitioning methods utilizing recursive partitioning algorithms. In particular we use the work on optimal partitioning to improve pre-existing algorithms. In this paper we discuss the different perspectives this approach opens and present two algorithms, SNRPP which is a $\sqrt{\frac{3}{2}}$ approximation, and NRPP which is a $\frac{2}{\sqrt{3}}$ approximation. While sub-optimal, the NRRP approach works for an arbitrary number of partitions. We use the first exact approach to analyse how close to the known optimal solutions the NRRP algorithm is for small numbers of partitions.
Published: 2019
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16. Inhibition of IRE1 RNase activity modulates the tumor cell secretome and enhances response to chemotherapy

Author: Roisin M. Dwyer, Katarzyna Mnich, Qingping Zeng, Patrick Legembre, Aitor Almanza, Stephanie Greene, Anup M. Oommen, Adrienne M. Gorman, Eoghan P. McGrath, Susan E. Logue, Emma C. Madden, Brian Leuzzi, Patricia Cleary, Richard Jäger, John B. Patterson, Joanna Obacz, Florence Godey, Eric Chevet, Afshin Samali, National University of Ireland [Galway] (NUI Galway), Fosun Orinove PharmaTech Inc.[Newbury Park, CA], Chemistry, Oncogenesis, Stress and Signaling (COSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Eugène Marquis (CRLCC), Fosun Orinove PharmaTech Inc.[Jiangsu], University of Applied Sciences [Rheinbach], NUI Galway, Irish Government's Programme for Research in Third Level Institutions, Cycles 4 and 5, National Development Plan 2007-2013, Institut National du Cancer (INCa) [PLBIO 2017-148], Irish Cancer Society Scholarship [CRS11CLE], Thomas Crawford Hayes Funds of NUIG, Irish Research Council Employment Based Programme Scholarship Scheme [BPPG/2014/57], Irish Research Council Fellowship [GOIPD/2014/53], Breast Cancer Campaign grant [2010NovPR13, 2015MaySP550], Health Research Board [HRA-POR-2014-643], Belgium Grant [IAP 7/32], Science Foundation Ireland (SFI) grant - European Regional Development Fund [13/RC/2073], SFI Starting Investigator Grant [15/SIRG/3528], EU H2020 MSCA [ITN-675448, RISE-734749], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Jonchère, Laurent
Subjects: 0301 basic medicine, Programmed cell death, Paclitaxel, RNase P, Science, Mice, Nude, General Physics and Astronomy, Triple Negative Breast Neoplasms, [SDV.CAN]Life Sciences [q-bio]/Cancer, Protein Serine-Threonine Kinases, Article, General Biochemistry, Genetics and Molecular Biology, Cell Line, 03 medical and health sciences, chemistry.chemical_compound, [SDV.CAN] Life Sciences [q-bio]/Cancer, RNA interference, Cell Line, Tumor, ddc:570, Antineoplastic Combined Chemotherapy Protocols, Endoribonucleases, Animals, Humans, Medicine, Enzyme Inhibitors, lcsh:Science, Multidisciplinary, business.industry, Gene Expression Profiling, Endoplasmic reticulum, HEK 293 cells, General Chemistry, Xenograft Model Antitumor Assays, 3. Good health, Gene Expression Regulation, Neoplastic, CXCL1, HEK293 Cells, 030104 developmental biology, chemistry, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Cancer research, Unfolded protein response, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Female, RNA Interference, lcsh:Q, business
Abstract: Triple-negative breast cancer (TNBC) lacks targeted therapies and has a worse prognosis than other breast cancer subtypes, underscoring an urgent need for new therapeutic targets and strategies. IRE1 is an endoplasmic reticulum (ER) stress sensor, whose activation is predominantly linked to the resolution of ER stress and, in the case of severe stress, to cell death. Here we demonstrate that constitutive IRE1 RNase activity contributes to basal production of pro-tumorigenic factors IL-6, IL-8, CXCL1, GM-CSF, and TGFβ2 in TNBC cells. We further show that the chemotherapeutic drug, paclitaxel, enhances IRE1 RNase activity and this contributes to paclitaxel-mediated expansion of tumor-initiating cells. In a xenograft mouse model of TNBC, inhibition of IRE1 RNase activity increases paclitaxel-mediated tumor suppression and delays tumor relapse post therapy. We therefore conclude that inclusion of IRE1 RNase inhibition in therapeutic strategies can enhance the effectiveness of current chemotherapeutics., IRE1/XBP-1 activation has a major role in Triple negative breast cancer (TNBC). Here, the authors show that inhibition of IRE1’s RNase activity attenuates autocrine and paracrine signaling of pro-tumorigenic cytokines and synergizes with paclitaxel to confer potent anti-tumor effects in TNBC.
Published: 2018
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17. Performance analysis of AO-OFDM-CDMA with advanced 2D-hybrid coding for amplifier-free LR-PONs

Author: Iyad Dayoub, Hichem Mrabet, Sofien Mhatli, Elias Giacoumidis, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), COMmunications NUMériques - IEMN (COMNUM - IEMN), Institut d’Électronique, de Microélectronique et de Nanotechnologie - Département Opto-Acousto-Électronique - UMR 8520 (IEMN-DOAE), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France)-Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), School of Electronic Engineering [Dublin] (Dublin City University (DCU)), SERCOM Laboratory, Université de Carthage - University of Carthage, Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France)-Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), The work of Dr. Elias Giacoumidis was emanated from EU Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant agreement no. 713567 and in part by a research grant from Science Foundation Ireland (SFI) and is co-funded under the European Regional Development Fund under Grant No. 13/RC/2077., European Project: 713567,H2020,H2020-MSCA-COFUND-2015,EDGE(2016), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), and Institut National des Sciences Appliquées (INSA)
Subjects: optical modulation, Code division multiple access, Orthogonal frequency-division multiplexing, Computer science, OFDM modulation, 02 engineering and technology, passive optical networks, Passive optical network, Atomic and Molecular Physics, and Optics, Subcarrier, code division multiple access, Amplitude modulation, QAM, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], [SPI]Engineering Sciences [physics], 020210 optoelectronics & photonics, 0202 electrical engineering, electronic engineering, information engineering, Electronic engineering, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, Forward error correction, Electrical and Electronic Engineering, Quadrature amplitude modulation, error statistics
Abstract: International audience; All‐optical orthogonal frequency division multiplexing (AO‐OFDM) and optical code‐division multiple‐access system (OCDMA) are combined in the first analytical model, which considers subcarrier hopping by means of advanced two‐dimensional (2D) hybrid‐coded (2D‐HC) signature. The model incorporates probabilistic subcarrier overlapping, multiple‐access interferences and is tested, for the first time, over amplifier‐free long‐reach passive optical networks (LR‐PONs) using cost‐effective intensity modulations and direct detection. For the upstream direction at 40 Gb/s, AO‐OFDM‐OCDMA outperforms a ‘classical’ multi‐channel OCDMA system for low received powers and any number of simultaneous users. In comparison to conventional 1D Walsh–Hadamard, 1D prime code and 2D prime hop system, coding with 2D‐HC can improve the performance of AO‐OFDM‐CDMA, thus allowing a higher number of simultaneous users in LR‐PON without optical amplification. From numerical simulations, the authors show that 16‐quadrature amplitude modulation (16‐QAM) AO‐OFDM‐CDMA with 45 users has comparable performance to conventional multi‐channel 16‐QAM coherent optical OFDM in the downstream direction and up to 58 km with 1:45 split ratio, without employing complex coherent technology. Similarly, based on the feasibility of physical implementation configuration, a budget power calculation is performed showing 108 km as maximum reachability distance for 40 Gb/s QAM signal, 1:64 split ratio when considering standard forward‐error‐correction.
Published: 2018
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18. Dietary conjugated linoleic acid-enriched cheeses influence the levels of circulating n-3 highly unsaturated fatty acids in humans

Author: Anne Ferlay, Maria Rosaria Melis, Maria Cristina Mele, Lina Cordeddu, Elisabetta Murru, Margherita Addis, Yves Chilliard, M. Coakley, Catherine Stanton, Erika Desogus, G. Piredda, Gianfranca Carta, Giorgio Cannelli, Sebastiano Banni, R.P. Ross, Claudia Manca, Hastimansooreh Ansar, Dipartimento Scienze Biomediche, Università degli studi 'G. d'Annunzio' Chieti-Pescara [Chieti-Pescara] (Ud'A), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Teagasc Agriculture and Food Development Authority (Teagasc), APC Microbiome Ireland, University College Cork (UCC), Servizio per la Ricerca nei Prodotti di Origine Animale, AGRIS sardegna, Fondazione Policlinico Universitario Agostino Gemelli, EU Project QLK1-2002-02362, INNOVA.RE-WP 2.3-P.O.R.-F.E.S.R., Science Foundation Ireland (SFI), SFI/12/RC/2273, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, Male, Conjugated, Conjugated linoleic acid, [SDV]Life Sciences [q-bio], Peroxisome proliferator-activated receptor, fromage, ruminant, Highly unsaturated fatty acids (HUFA), lcsh:Chemistry, Plasma, chemistry.chemical_compound, Linseed oil, Cheese, Ruminant, fatty acids (FA), Linoleic Acids, Conjugated, Food science, lcsh:QH301-705.5, Spectroscopy, Omega-3, 2. Zero hunger, chemistry.chemical_classification, biology, Chemistry, Fatty Acids, clinical trial, General Medicine, Peroxisome, Cheese intake, 3. Good health, Computer Science Applications, conjugated linoleic acids (CLA), Clinical trial, Linoleic Acids, Female, Adult, cheese, highly unsaturated fatty acids (HUFA), plasma, food.ingredient, Alpha (ethology), n-3 fatty acid, Catalysis, Article, Inorganic Chemistry, 03 medical and health sciences, food, acide gras n 3, Settore MED/41 - ANESTESIOLOGIA, Fatty Acids, Omega-3, Humans, PPAR alpha, Physical and Theoretical Chemistry, Molecular Biology, micromass, Conjugated linoleic acids (CLA), 030109 nutrition & dietetics, Organic Chemistry, Lipid metabolism, Fatty acids (FA), biology.organism_classification, acide linoléique, Diet, lcsh:Biology (General), lcsh:QD1-999
Abstract: n-3 highly unsaturated fatty acids (n-3 HUFA) directly and indirectly regulate lipid metabolism, energy balance and the inflammatory response. We investigated changes to the n-3 HUFA score of healthy adults, induced by different types and amounts of conjugated linoleic acid (CLA)-enriched (ENCH) cheeses consumed for different periods of time, compared to dietary fish oil (FO) pills (500 mg, each containing 100 mg of eicosapentaenoic and docosahexaenoic acids&mdash, EPA+DHA) or &alpha, linolenic acid (ALA)-rich linseed oil (4 g, containing 2 g of ALA). A significant increase in the n-3 HUFA score was observed, in a dose-dependent manner, after administration of the FO supplement. In terms of the impact on the n-3 HUFA score, the intake of ENCH cheese (90 g/day) for two or four weeks was equivalent to the administration of one or two FO pills, respectively. Conversely, the linseed oil intake did not significantly impact the n-3 HUFA score. Feeding ENCH cheeses from different sources (bovine, ovine and caprine) for two months improved the n-3 HUFA score by increasing plasma DHA, and the effect was proportional to the CLA content in the cheese. We suggest that the improved n-3 HUFA score resulting from ENCH cheese intake may be attributed to increased peroxisome proliferator-activated receptor alpha (PPAR-&alpha, ) activity. This study demonstrates that natural ENCH cheese is an alternative nutritional source of n-3 HUFA in humans.
Published: 2018
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19. TILLING by Sequencing (TbyS) for targeted genome mutagenesis in crops

Author: Abdelhafid Bendahmane, Galina Brychkova, Anishkumar P. K. Kumar, Peter Ryder, Abhimanyu Sarkar, Adnane Boualem, Manash Chatterjee, Charles Spillane, Peter C. McKeown, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Bench Bio Private Limited (BenchBio), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Metabolic Biology Department, John Innes Centre, Science Foundation Ireland (SFI) (02/IN.1/B49, 08/IN.1/B1931), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), John Innes Centre [Norwich], and Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0106 biological sciences, 0301 basic medicine, TILLING, [SDV]Life Sciences [q-bio], Genomics, Plant Science, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Genome editing, Genetic variation, Genetics, CRISPR, Molecular Biology, CRISPR/Cas9, 2. Zero hunger, Molecular breeding, fungi, food and beverages, TbyS, 030104 developmental biology, Induced variation, Mutagenesis, TILLINGby Sequencing, Agronomy and Crop Science, Functional genomics, 010606 plant biology & botany, Biotechnology
Abstract: TILLING (Targeting Induced Local Lesions in Genomes) by Sequencing (TbyS) refers to the application of high-throughput sequencing technologies to mutagenised TILLING populations as a tool for functional genomics. TbyS can be used to identify and characterise induced variation in genes (controlling traits of interest) within large mutant populations, and is a powerful approach for the study and harnessing of genetic variation in crop breeding programmes. The extension of existing TILLING platforms by TbyS will accelerate crop functional genomics studies, in concert with the rapid increase in genome editing capabilities and the number and quality of sequenced crop plant genomes. In this mini-review, we provide an overview of the growth of TbyS and its potential applications to crop molecular breeding.
Published: 2017
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20. Multi-language evaluation of exact solvers in graphical model discrete optimization

Author: George Katsirelos, David Allouche, Matthias Zytnicki, Simon de Givry, Barry O'Sullivan, Thomas Schiex, Barry Hurley, Insight Centre for Data Analytics, University College Cork (UCC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Science Foundation Ireland (SFI) [10/IN.1/I3032], and SFI [SFI/12/RC/2289]
Subjects: 0301 basic medicine, MaxSAT, Mathematical optimization, Optimization problem, Linear programming, 02 engineering and technology, 03 medical and health sciences, Artificial Intelligence, Discrete optimization, 0202 electrical engineering, electronic engineering, information engineering, Discrete Mathematics and Combinatorics, [INFO]Computer Science [cs], Graphical model, [MATH]Mathematics [math], Integer programming, Mathematics, Markov random field, Solver, 030104 developmental biology, Integer linear programming, Computational Theory and Mathematics, Benchmark (computing), Probability distribution, 020201 artificial intelligence & image processing, Weighted constraint satisfaction problem, Software
Abstract: International audience; By representing the constraints and objective function in factorized form, graphical models can concisely define various NP-hard optimization problems. They are therefore extensively used in several areas of computer science and artificial intelligence. Graphical models can be deterministic or stochastic, optimize a sum or product of local functions, defining a joint cost or probability distribution. Simple transformations exist between these two types of models, but also with MaxSAT or linear programming. In this paper, we report on a large comparison of exact solvers which are all state-of-the-art for their own target language. These solvers are all evaluated on deterministic and probabilistic graphical models coming from the Probabilistic Inference Challenge 2011, the Computer Vision and Pattern Recognition OpenGM2 benchmark, the Weighted Partial MaxSAT Evaluation 2013, the MaxCSP 2008 Competition, the MiniZinc Challenge 2012 & 2013, and the CFLib (a library of Cost Function Networks). All 3026 instances are made publicly available in five different formats and seven formulations. To our knowledge, this is the first evaluation that encompasses such a large set of related NP-complete optimization frameworks, despite their tight connections. The results show that a small number of evaluated solvers are able to perform well on multiple areas. By exploiting the variability and complementarity of solver performances, we show that a simple portfolio approach can be very effective. This portfolio won the last UAI Evaluation 2014 (MAP task).
Published: 2016
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21. Amorphous calcium carbonate based-microparticles for peptide pulmonary delivery

Author: Oliviero L. Gobbo, Carsten Ehrhardt, Anne Marie Healy, Frederic Tewes, Tewes, Frederic, Pharmacologie des anti-infectieux (PHAR), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), School of Pharmacy and Pharmaceutical Science [Dublin, Irlande], Trinity College Dublin, This publication has emanated from research conducted with the financial support of Science Foundation Ireland (SFI) under Grant Numbers 07/SRC/B1158 and SFI/12/RC/2275., Ingénierie de la vectorisation particulaire, Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), School of Pharmacy and Pharmaceutical Sciences and Institute of Neuroscience, School of Pharmacy and Pharmaceutical Science, and School of Pharmacy and Pharmaceutical Sciences [Dublin 2, Ireland]
Subjects: Calcitonin, Lung Diseases, Ammonium carbonate, Materials science, composite microparticle, Inorganic chemistry, biomimetic process, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Calcium Carbonate, chemistry.chemical_compound, Administration, Inhalation, Animals, Humans, General Materials Science, Peptidase inhibitor activity, Particle Size, Microparticle, Aerosols, Calcium formate, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, 021001 nanoscience & nanotechnology, Amorphous calcium carbonate, peptide, Rats, 3. Good health, 0104 chemical sciences, Bioavailability, Amorphous solid, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Calcium carbonate, chemistry, Chemical engineering, alpha 1-Antitrypsin, Nanoparticles, pulmonary inhalation, Peptides, 0210 nano-technology
Abstract: International audience; Amorphous calcium carbonate (ACC) is known to interact with proteins, for example, in biogenic ACC, to form stable amorphous phases. The control of amorphous/crystalline and inorganic/organic ratios in inhalable calcium carbonate microparticles may enable particle properties to be adapted to suit the requirements of dry powders for pulmonary delivery by oral inhalation. For example, an amorphous phase can immobilize and stabilize polypeptides in their native structure and amorphous and crystalline phases have different mechanical properties. Therefore, inhalable composite microparticles made of inorganic (i.e., calcium carbonate and calcium formate) and organic (i.e., hyaluronan (HA)) amorphous and crystalline phases were investigated for peptide and protein pulmonary aerosol delivery. The crystalline/amorphous ratio and polymorphic form of the inorganic component was altered by changing the microparticle drying rate and by changing the ammonium carbonate and HA initial concentration. The bioactivity of the model peptide, salmon calcitonin (sCT), coprocessed with alpha-1-antitrypsin (AAT), a model protein with peptidase inhibitor activity, was maintained during processing and the microparticles had excellent aerodynamic properties, making them suitable for pulmonary aerosol delivery. The bioavailability of sCT after aerosol delivery as sCT and AAT-loaded composite microparticles to rats was 4-times higher than that of sCT solution.
Published: 2015
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22. Differences in lactococcal cell wall polysaccharide structure are major determining factors in bacteriophage sensitivity

Author: Evguenii Vinogradov, Jennifer Mahony, Pascal Courtin, Thierry Grard, Irina Sadovskaya, Douwe van Sinderen, Stuart Ainsworth, Marie-Pierre Chapot-Chartier, Christian Cambillau, Yann Guérardel, Department of Microbiology, University College Cork (UCC), Université du Littoral Côte d'Opale (ULCO), Institute for Biological Science, National Research Council of Canada (NRC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biosciences Institute - Alimentary Pharmabiotic Centre - Department of Microbiology, Science Foundation Ireland (SFI) [08/IN.1/B1909], French ANR Project 'Lactophages' [ANR-11-BSV8-004-01], IR-RMN [Fr3050], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: host cell, genetic association, Operon, [SDV]Life Sciences [q-bio], Mutant, cell surface receptor, pentasaccharide, gene cluster, law.invention, Bacteriophage, bacteriophage, sensitivity analysis, Cell Wall, law, biochemical composition, bacterial genome, Lactococcus, Phage group, genetic variability, genetic complementation, Bacteriophages, bacterial polysaccharide, Genetics, Host cell surface, 0303 health sciences, Polysaccharides, Bacterial, cell wall polysaccharide, structure analysis, QR1-502, unclassified drug, Lactococcus lactis, Multigene Family, Host-Pathogen Interactions, Recombinant DNA, Receptors, Virus, paroi cellulaire, Research Article, Genotype, Molecular Sequence Data, host range, Biology, Microbiology, Host Specificity, 03 medical and health sciences, Virology, bacterium mutant, Gene, 030304 developmental biology, 030306 microbiology, nucleotide sequence, biology.organism_classification, bacterial strain, récepteurs de surface cellulaire, Genes, Bacterial, biosynthesis, bacterial cell wall
Abstract: Analysis of the genetic locus encompassing a cell wall polysaccharide (CWPS) biosynthesis operon of eight strains of Lactococcus lactis, identified as belonging to the same CWPS type C genotype, revealed the presence of a variable region among the strains examined. The results allowed the identification of five subgroups of the C type named subtypes C1 to C5. This variable region contains genes encoding glycosyltransferases that display low or no sequence homology between the subgroups. In this study, we purified an acidic polysaccharide from the cell wall of L. lactis 3107 (subtype C2) and confirmed that it is structurally different from the previously established CWPS of subtype C1 L. lactis MG1363. The CWPS of L. lactis 3107 is composed of pentasaccharide repeating units linked by phosphodiester bonds with the structure 6-α-Glc-3-β-Galf-3-β-GlcNAc-2-β-Galf-6-α-GlcNAc-1-P. Combinations of genes from the variable region of subtype C2 were introduced into a mutant of subtype C1 L. lactis NZ9000 deficient in CWPS biosynthesis. The resulting recombinant mutant synthesized a polysaccharide with a composition characteristic of that of subtype C2 L. lactis 3107 and not wild-type C1 L. lactis NZ9000. By challenging the recombinant mutant with various lactococcal phages, we demonstrated that CWPS is the host cell surface receptor of tested bacteriophages of both the P335 and 936 groups and that differences between the CWPS structures play a crucial role in determining phage host range., IMPORTANCE Despite the efforts of nearly 80 years of lactococcal phage research, the precise nature of the cell surface receptors of the P335 and 936 phage group receptors has remained elusive. This work demonstrates the molecular nature of a P335 group receptor while bolstering the evidence of its role in host recognition by phages of the 936 group and at least partially explains why such phages have a very narrow host range. The information generated will be instrumental in understanding the molecular mechanisms of how phages recognize specific saccharidic receptors located on the surface of their bacterial host.
Published: 2014
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23. Clustering User Trajectories to Find Patterns for Social Interaction Applications

Author: Reinaldo Braga, Ali Tahir, Michela Bertolotto, Hervé Martin, Laboratoire d'Informatique de Grenoble (LIG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF), School of Computer Science and Informatics [Dublin], University College Dublin [Dublin] (UCD), Spatio-temporal information systems (STEAMER), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF), Strategic Research Cluster grant (07/SRC/I1168) by the Science Foundation Ireland (SFI) under the National Development Plan, the IRCSET Ulysses program, the French Ministry of Higher Education and Research, the EGIDE program and the European Cooperation in Science and Technology (COST), and S. Di Martino, A. Peron and T. Tezuka
Subjects: Focus (computing), Social network, business.industry, Computer science, 02 engineering and technology, Time based, computer.software_genre, Social relation, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Global Positioning System, 020201 artificial intelligence & image processing, Data mining, Minimum bounding rectangle, business, Cluster analysis, computer, Virtual community
Abstract: International audience; Sharing of user data has substantially increased over the past few years facilitated by sophisticated Web and mobile applications, including social networks. For instance, users can easily register their trajectories over time based on their daily trips captured with GPS receivers as well as share and relate them with trajectories of other users. Analyzing user trajectories over time can reveal habits and preferences. This information can be used to recommend content to single users or to group users together based on similar trajectories and/or preferences. Recording GPS tracks generates very large amounts of data. Therefore clustering algorithms are required to efficiently analyze such data. In this paper, we focus on investigating ways of efficiently analyzing user trajectories and extracting user preferences from them. We demonstrate an algorithm for clustering user GPS trajectories. In addition, we propose an algorithm to correlate trajectories based on near points between two or more users. The obtained results provided interesting avenues for exploring Location-based Social Network (LBSN) applications.
Published: 2012
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24. Identifying single copy orthologs in Metazoa

Author: Detlev Arendt, Tobias Doerks, Peer Bork, Christopher J. Creevey, Jean Muller, Julie D. Thompson, Animal & Grassland Research and Innovation Centre, Teagasc - The Agriculture and Food Development Authority (Teagasc), European Molecular Biology Laboratory [Heidelberg] (EMBL), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de diagnostic génétique, CHU Strasbourg, Max-Delbrück-Centre for Molecular Medicine, This work was funded by the EURASNET grant (European Union FP6 Programme, Contract number LSH-2004-1.1.5-3)(http://www.eurasnet.info/). CJC wishes to acknowledge current support from the Science Foundation Ireland (SFI) Stokes Lectureship Programme (Reference number: 07/SK/B1236A)(http://www.sfi.ie), European Project: 32894,EURASNET, European Union, Science Foundation Ireland, LSH-2004-1.1.5-3, 07/SK/B1236A, Autard, Delphine, and European Alternative Splicing Network of Excellence - EURASNET - 32894 - OLD
Subjects: Most recent common ancestor, Gene Dosage, Genome, MESH: Gene Dosage, 0302 clinical medicine, Gene Duplication, Databases, Genetic, MESH: Animals, Biology (General), MESH: Phylogeny, Genome Evolution, Expressed sequence, Phylogeny, MESH: Databases, Genetic, MESH: Evolution, Molecular, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Expressed Sequence Tags, Genetics, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Phylogenetic analysis, Ecology, Phylogenetic tree, MESH: Genomics, Genome project, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computational Theory and Mathematics, Multigene Family, Modeling and Simulation, Gene Classes, Research Article, Genome evolution, QH301-705.5, Computational biology, single copy (1-to-1) orthologs, Biology, MESH: Expressed Sequence Tags, Evolution, Molecular, Molecular Genetics, 03 medical and health sciences, Cellular and Molecular Neuroscience, Phylogenetics, Animals, Humans, MESH: Genome, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, MESH: Humans, Metazoa, Computational Biology, Comparative Genomics, Cardiovascular and Metabolic Diseases, MESH: Multigene Family, Gene Function, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract: The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived., Author Summary The correct identification of single copy (1-to-1) orthologs is crucial for functional classification of genes and for phylogenetic studies of groups of organisms, including the Metazoa. Nevertheless, despite the recent increase in the number of genomes and short sequence read datasets (e.g. ESTs) from the Metazoa, we know little about their completeness and how useful they may be for phylogenetic studies. Here we describe a novel approach for the identification of single copy gene families at any hierarchical level and demonstrate its effectiveness by identifying a set of over one thousand gene families that have been in single copy since the last common ancestor of the Metazoa. By comparing our orthologs to those predicted by other datasets we show that our procedure identifies a significantly larger set of single copy orthologs in the Metazoa. We then use this dataset to assess 24 metazoan genomes and 61 metazoan EST datasets for their completeness. We thus identify the underlying error rate in genome annotation and suggest a mechanism for assessing the quality of genomes and EST datasets in terms of their suitability for phylogenetic studies.
Published: 2011
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25. Parasite and host assemblages: embracing the reality will improve our knowledge of parasite transmission and virulence

Author: Mark J. F. Brown, Thierry Rigaud, Marie-Jeanne Perrot-Minnot, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), School of Biological Sciences, Royal Holloway [University of London] ( RHUL ), Department of Zoology, Trinity College Dublin, Work supported by a Research Frontiers Programme grant from Science Foundation Ireland (SFI, grant 05-RFP-EEB0040)., ANR BLAN07-3_183300,ANR BLAN07-3_183300, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Royal Holloway [University of London] (RHUL), and ANR BLAN07-3_183300
Subjects: 0106 biological sciences, [ SDV.MP.PAR ] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, multi-parasitized hosts, media_common.quotation_subject, Ecology (disciplines), Virulence, interspecies transmission, Biology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Competition (biology), Host-Parasite Interactions, Interspecies transmission, 03 medical and health sciences, Parasitic Diseases, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Animals, Parasite hosting, Parasites, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Review Articles, 030304 developmental biology, General Environmental Science, media_common, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, General Immunology and Microbiology, Ecology, Transmission (medicine), Host (biology), General Medicine, Biological Evolution, Obligate parasite, immune system, Evolutionary biology, multi-host parasites, intrahost competition, epidemiology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 10 pages; International audience; Interactions involving several parasite species (multi-parasitized hosts) or several host species (multi-host parasites) are the rule in nature. Only a few studies have investigated these realistic, but complex, situations from an evolutionary perspective. Consequently, their impact on the evolution of parasite virulence and transmission remains poorly understood. The mechanisms by which multiple infections may influence virulence and transmission include the dynamics of intrahost competition, mediation by the host immune system and an increase in parasite genetic recombination. Theoretical investigations have yet to be conducted to determine which of these mechanisms are likely to be key factors in the evolution of virulence and transmission. In contrast, the relationship between multi-host parasites and parasite virulence and transmission has seen some theoretical investigation. The key factors in these models are the trade-off between virulence across different host species, variation in host species quality and patterns of transmission. The empirical studies on multi-host parasites suggest that interspecies transmission plays a central role in the evolution of virulence, but as yet no complete picture of the phenomena involved is available. Ultimately, determining how complex host-parasite interactions impact the evolution of host-parasite relationships will require the development of cross-disciplinary studies linking the ecology of quantitative networks with the evolution of virulence.
Published: 2010
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26. The transmembrane semaphorin Sema6A controls cerebellar granule cell migration

Author: Kevin J. Mitchell, Cécile Haumaitre, Géraldine Kerjan, Hajime Fujisawa, Sylvie Schneider-Maunoury, Alain Chédotal, Jackie Dolan, Neurobiologie des processus adaptatifs (NPA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Smurfit Institute of Genetics, Trinity College Dublin, Laboratoire de Biologie du Développement (LBD), Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The 21st Century Center of Excellence Program, Division of Biological Science, Nagoya University Graduate School of Science, A.C. is supported by the Fondation pour la Recherche sur le Cerveau (FRC), the Schlumberger Foundation and the Association pour la Recherche sur le Cancer (ARC). K.J.M is a Science Foundation Ireland (SFI) Investigator. This work was supported by SFI grant 01/F.1/B006 to K.J.M, and grants from the 21st Century COE Program, and from the Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Agency (JST) to H.F., Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cerebellum, Time Factors, granule cell migration, Phalloidine, cerebellum development, Semaphorins, Mice, Cell Movement, Tubulin, Cricetinae, granule cell layer, Basic Helix-Loop-Helix Transcription Factors, Cells, Cultured, In Situ Hybridization, Neurons, Sema6A, Microscopy, Video, General Neuroscience, Granule (cell biology), Cell Polarity, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Cell Differentiation, Dextrans, Immunohistochemistry, medicine.anatomical_structure, CXCL3, transmembrane semaphorin protein, developing axons, Neurite, Cell Adhesion Molecules, Neuronal, Blotting, Western, Green Fluorescent Proteins, Biotin, Mice, Transgenic, Biology, Cricetulus, Semaphorin, Glial Fibrillary Acidic Protein, medicine, Contactin 2, Animals, Cell Proliferation, Analysis of Variance, Calcium-Binding Proteins, ACM, Granule cell, Oligodendrocyte, Mice, Inbred C57BL, Animals, Newborn, Bromodeoxyuridine, nervous system, Calcium-Calmodulin-Dependent Protein Kinases, Vesicular Glutamate Transport Protein 2, Axon guidance, Neuroscience, Calcium-Calmodulin-Dependent Protein Kinase Type 4
Abstract: The transmembrane semaphorin protein Sema6A is broadly expressed in the developing nervous system. Sema6A repels several classes of developing axons in vitro and contributes to thalamocortical axon guidance in vivo. Here we show that during cerebellum development, Sema6A is selectively expressed by postmitotic granule cells during their tangential migration in the deep external granule cell layer, but not during their radial migration. In Sema6A-deficient mice, many granule cells remain ectopic in the molecular layer where they differentiate and are contacted by mossy fibers. The analysis of ectopic granule cell morphology in Sema6a-/- mice, and of granule cell migration and neurite outgrowth in cerebellar explants, suggests that Sema6A controls the initiation of granule cell radial migration, probably through a modulation of nuclear and/or soma translocation. Finally, the analysis of mouse chimeras suggests that this function of Sema6A is primarily non-cell-autonomous.
Published: 2005
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14. A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis

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23. Clustering User Trajectories to Find Patterns for Social Interaction Applications

24. Identifying single copy orthologs in Metazoa

25. Parasite and host assemblages: embracing the reality will improve our knowledge of parasite transmission and virulence

26. The transmembrane semaphorin Sema6A controls cerebellar granule cell migration

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