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2. Communication practices in asylum seekers reception centres: from information precarity to voluntary return

Author

1st Annual CESSMIR Conference: Needs and Care Practices for Refugees and Migrants (17-19-09-2018: CESSMIR, Gent University), Van Neste-Gottignies, Amandine, Mistiaen, Valériane Marie, 1st Annual CESSMIR Conference: Needs and Care Practices for Refugees and Migrants (17-19-09-2018: CESSMIR, Gent University), Van Neste-Gottignies, Amandine, and Mistiaen, Valériane Marie

Abstract

This presentation studies the relation of communication constructed between the Belgian Federal Agency for the Reception of Asylum Seekers (Fedasil) and asylum seekers during the reception period. This research is the continuation of a previous study (Van Neste-Gottignies and Mistiaen, forthcoming 2018) revealing that Fedasil communication to asylum seekers is hardly visible. Asylum seekers are found to experience ‘information precarity’ (Wall et al. 2015). Although the ‘invisibility’ of reception discourses seems to prevail, there is an exception: communication regarding voluntary return programmes. This article aims to understand more deeply how and why this communication is predominant. We adopted a multi-site approach that combines various survey methods conducted between 2014 and 2017 with Corpus Linguistics tools. Our main finding lies in the differentiation of treatments according to asylum seekers’ country of origin. These differences seem to match the representation of the ‘legitimate refugee’ versus the ‘illegitimate refugee’., info:eu-repo/semantics/nonPublished

Published
2018

3. Un nouveau modèle de rétrodiffusion radar semi-empirique pour les sols nus : le modèle de Baghdadi

Author

Choker, M., Baghdadi, N., Zribi, Mehrez, El Hajj, M., Paloscia, S., Verhoest, N.E.C., Lievens, H., Baup, Frédéric, Mattia, F., Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d'études spatiales de la biosphère (CESBIO), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), CNR FIRENZE ITA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), GENT UNIVERSITY LABORATORY OF HYDROLOGY AND WATER MANAGEMENT GHENT BELB-9000, Belgium, GENT UNIVERSITY LABORATORY OF HYDROLOGY AND WATER MANAGEMENT GHENT BEL, and CNR ISSIA BARI ITA

Subjects
MODEL, SOIL, [SDE]Environmental Sciences, BACKSCATTERING, RADAR
Abstract

International audience; The aim of this paper is to develop a new semi-empirical radar backscattering model (Baghdadi model) based on the Dubois model using a wide dataset of SAR data and experimental soil measurements for bare soil surfaces in HH, VV and HV polarizations. This dataset contains radar data in L-, C- and X-bands, with incidence angles ranged between 18° and 57°. The proposed model uses a formulation of radar signals based on physical principles that were validated in numerous studies. In comparison to Dubois model, results obtained with the new model are more accurate. The bias and the RMSE decrease for both HH and VV polarizations. The RMSE decreases from 3.8 dB to 2.0 dB for HH and from 2.8 dB to 1.9 dB for VV. In addition, the high over- and under-estimations of radar backscattering coefficients observed with the Dubois model according to soil moisture, surface roughness and radar incidence angle are clearly eliminated with the new model. Based on the same type of expression as that used for HH and VV, a radar signal in HV polarization was also proposed.

Published
2017

5. The Multifaceted Inhibitory Effects of an Alkylquinolone on the Diatom Phaeodactylum tricornutum

Author

Peter G. Kroth, Dávid Szamosvári, Benjamin Bailleul, Alexandra Peltekis, Bernard Lepetit, Adrien Lapointe, Thomas Böttcher, Frederike Stock, Michaela Prothiwa, Wim Vyverman, Lachlan Dow, University Hospital Rostock, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Gent University, Department of Biology, University of Konstanz, Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Project: 715579,PhotoPHYTOMICS, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
cytochromes, Chloroplasts, Mitochondrion, Thylakoids, 01 natural sciences, Biochemistry, Adenosine Triphosphate, Marine bacteriophage, diatom–bacteria interactions, N-OXIDES, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Plastids, ComputingMilieux_MISCELLANEOUS, MARINE ALTEROMONAS SP, Full Paper, biology, Chemistry, Full Papers, Mitochondria, 3. Good health, diatom-bacteria interactions, Molecular Medicine, cytochromes diatom-bacteria interactions photosynthesis quinolone respiration, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 010402 general chemistry, Photosynthesis, PHOTOSYSTEM-II, QUINOLONES, ddc:570, Phaeodactylum tricornutum, Plastid, Molecular Biology, Diatoms, 4-Quinolones, photosynthesis, QUANTUM YIELD, 010405 organic chemistry, fungi, Organic Chemistry, PSEUDOMONAS-AERUGINOSA, Biology and Life Sciences, biology.organism_classification, Electron transport chain, 0104 chemical sciences, reaction mechanisms, Cytochrome b6f Complex, Diatom, quinolones, Bacteria
Abstract

The mechanisms underlying interactions between diatoms and bacteria are crucial to understand diatom behaviour and proliferation, and can result in far‐reaching ecological consequences. Recently, 2‐alkyl‐4‐quinolones have been isolated from marine bacteria, both of which (the bacterium and isolated chemical) inhibited growth of microalgae, suggesting these compounds could mediate diatom–bacteria interactions. The effects of several quinolones on three diatom species have been investigated. The growth of all three was inhibited, with half‐maximal inhibitory concentrations reaching the sub‐micromolar range. By using multiple techniques, dual inhibition mechanisms were uncovered for 2‐heptyl‐4‐quinolone (HHQ) in Phaeodactylum tricornutum. Firstly, photosynthetic electron transport was obstructed, primarily through inhibition of the cytochrome b 6 f complex. Secondly, respiration was inhibited, leading to repression of ATP supply to plastids from mitochondria through organelle energy coupling. These data clearly show how HHQ could modulate diatom proliferation in marine environments., Double trouble: In the light, 2‐heptyl‐4‐quinolone (HHQ) primarily blocks photosynthetic electron flow at the cytochrome b 6 f complex in the diatom P. tricornutum. In darkness, HHQ inhibits mitochondrial respiration, resulting in a decreased ATP supply, which ultimately leads to a decreased electric field strength in the thylakoid membranes inside the chloroplast of diatoms.

Published
2020

6. N-Acyl Homoserine Lactone Derived Tetramic Acids Impair Photosynthesis in Phaeodactylum tricornutum

Author

Benjamin Bailleul, Ewout Ruysbergh, Koen Sabbe, Assaf Vardi, Sven Mangelinckx, Bernard Lepetit, Frederike Stock, Simon Backx, Peter G. Kroth, Shiri Graff van Creveld, Willem Stock, Lander Blommaert, Norbert De Kimpe, Wim Vyverman, Lachlan Dow, Anne Willems, Michail Syrpas, Universiteit Gent = Ghent University [Belgium] (UGENT), Laboratory of Protistology & Aquatic Ecology, University of Konstanz, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Faculty of Science, Department of Biochemistry and Microbiology, Laboratory of Microbiology, Gent University, Department of Biology, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Photosystem II, Homoserine, Photosynthetic efficiency, Photosynthesis, 01 natural sciences, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, 4-Butyrolactone, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phaeodactylum tricornutum, ComputingMilieux_MISCELLANEOUS, Diatoms, biology, 010405 organic chemistry, food and beverages, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Pyrrolidinones, 0104 chemical sciences, Quorum sensing, 030104 developmental biology, N-Acyl homoserine lactone, chemistry, 13. Climate action, Molecular Medicine, Bacteria
Abstract

Marine bacteria contribute substantially to nutrient cycling in the oceans and can engage in close interactions with microalgae. Many microalgae harbor characteristic satellite bacteria, many of which participate in N-acyl homoserine lactone (AHL) mediated quorum sensing. In the diffusion-controlled phycosphere, AHLs can reach high local concentrations, with some of them transforming into tetramic acids, compounds with a broad bioactivity. We tested a representative AHL, N-(3-oxododecanoyl) homoserine lactone, and its tetramic acid rearrangement product on the diatom Phaeodactylum tricornutum. While cell growth and photosynthetic efficiency of photosystem II were barely affected by the AHL, exposure to its tetramic acid rearrangement product had a negative effect on photosynthetic efficiency and led to growth inhibition and cell death in the long term, with a minimum inhibitory concentration between 20 and 50 μΜ. These results strengthen the view that AHLs may play an important role in shaping the outcome of microalgae-bacteria interactions.

Published
2019

7. Description of a new Agraecina species from Tunisia (Araneae Liocranidae), with a review of all species of the genus

Author

Abir Boubakri, Julien Pétillon, Mohamed Sghaïer Achouri, Robert Bosmans, Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), Terrestrial Ecology Unit, Gent University, Belgium, Universiteit Gent = Ghent University [Belgium] (UGENT), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Universiteit Gent = Ghent University (UGENT), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université Tunis El Manar (UTM), Ghent University [Belgium] (UGENT), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Tunisia, Arthropoda, Wunderlich, 010607 zoology, Zoology, 010603 evolutionary biology, 01 natural sciences, Genus, Arachnida, Animalia, Animals, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Taxonomy, geography, Spider, geography.geographical_feature_category, biology, Liocranidae, Spiders, Biodiversity, biology.organism_classification, Salt marsh, [SDE]Environmental Sciences, Araneae, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution
Abstract

International audience; While Liocranidae is a family encompassing 283 species distributed in 32 genera (World Spider Catalog 2019), the genus Agraecina Simon, 1932 currently counts only six described species: Agraecina canariensis Wunderlich, 1992 from the Canaries, A. cristriani (Georgescu, 1989) from Romania, A. hodna Bosmans, 1999 from Algeria, A. lineata (Simon, 1878) from Europe and Kazakhstan, A. rutilia (Simon, 1897) from Sierrra Leone, and A. scupiensis Deltshev, 2016 from Macedonia. During an ecological survey in the north of Tunisia, a new Agraecina species was discovered and is described here. Spiders were collected using pitfall traps in a salt marsh.

Published
2020

8. Interdisciplinary science to support North Sea marine management: lessons learned and future demands

Author

V. Van Lancker, E. Balian, B. De Witte, Karline Soetaert, Michael Elliott, T.A.G.P. van Dijk, H.J. Lindeboom, Francisco Hernandez, Vanessa Stelzenmüller, S. Van Gaever, D. Cox, Geneviève Lacroix, Henning Reiss, Silvana N.R. Birchenough, Steven Degraer, Jan Reubens, S. Le Bot, Gent University, Department of Biology, Department of Physcis and Astronomy, University of Amsterdam [Amsterdam] (UvA), University of Hull, Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie et évolution, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Netherlands Institute of Ecology (NIOO-KNAW)

Subjects
0106 biological sciences, Sociology of scientific knowledge, Open science, Aquatic Ecology and Water Quality Management, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Interdisciplinary science, Environmental monitoring, Natural science, 14. Life underwater, North sea, Environmental planning, business.industry, Science-policy-stakeholder communication, 010604 marine biology & hydrobiology, Citizen journalism, System knowledge, Aquatische Ecologie en Waterkwaliteitsbeheer, Society-driven research, Integrated knowledge bases, Knowledge base, 13. Climate action, Sustainability, [SDE]Environmental Sciences, business, Science-based management
Abstract

(IF 2.39; Q1); International audience; The expected increase of maritime activities in the North Sea and the growing awareness of its natural environmental value require enhanced science-based environmental advice for more efficient and effective marine management. The North Sea Open Science Conference organised by the Royal Belgian Institute of Natural Sciences and the Belgian Biodiversity Platform in 2016 aimed to take stock of the present-day scientific knowledge on the North Sea ecosystem, its interactions with human activities and its management. The conference was structured along three themes: (1) ‘the scientific backbone of the North Sea ecosystem: adequacy of the knowledge base?’, (2) ‘A new era in environmental monitoring and assessment: what is at stake?’, and (3) ‘Sustainability: one for all, all for one?’. Focusing on ‘open science’, we welcomed about 200 participants from around the North Sea with different backgrounds and interests in environmental sciences. The participants were challenged to reflect on current and future challenges for the North Sea management and, in particular, to explore possible nature-friendly solutions for addressing these challenges during a series of introductory oral (69) and poster (59) presentations, and World Café and Fish Bowl participatory sessions. The participants agreed on six main actions to (1) provide a solid scientific base for marine management decisions; (2) develop society-driven research; (3) increase interdisciplinary science; (4) recognise the need for system knowledge; (5) improve communication, knowledge exchange, and collective implementation of scientific knowledge; and (6) build integrated knowledge bases. For each of these, concrete action points were identified, and this review gives the most important and relevant ones for creating the knowledge base and managerial framework for a sustainable North Sea.

Published
2019

9. Using chemical language to shape future marine health

Author

Philippe Potin, Georg Pohnert, Michael Steinke, Fabrice Not, Ylenia Carotenuto, Erik Selander, Mahasweta Saha, Uwe John, Thomas Wichard, Patrick Fink, Valerio Zupo, Elisa Berdalet, Wim Vyverman, Tilmann Harder, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), University of Bremen, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Gent University, Department of Biology, Institute for Inorganic and Analytical Chemistry, Biological Sciences, University of Essex, German Research Foundation, Ministerio de Economía y Competitividad (España), and European Commission

Subjects
0106 biological sciences, HOST, 010504 meteorology & atmospheric sciences, COMMUNICATION, BIOFILM DISPERSAL, METABOLOMICS, 010603 evolutionary biology, 01 natural sciences, METABOLITES, CUES, Marine ecosystem, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Trophic level, Ecology, business.industry, Environmental resource management, Biology and Life Sciences, THREAT, LEPEOPHTHEIRUS-SALMONIS, SEA LICE, Chemical ecology, 13. Climate action, Earth and Environmental Sciences, Sustainability, Environmental science, FISHES, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

This article is an outcome of the EuroMarine Foresight Workshop on “Chemical ecology of marine interactions: the chemical language that shapes future marine health”, hosted by the University of Essex. Financial support for this event was provided by EuroMarine.-- 8 pages, 4 figures, 1 panel, “Infochemicals” (information‐conveying chemicals) dominate much of the underwater communication in biological systems. They influence the movement and behavior of organisms, the ecological interactions between and across populations, and the trophic structure of marine food webs. However, relative to their terrestrial equivalents, the wider ecological and economic importance of marine infochemicals remains understudied and a concerted, cross‐disciplinary effort is needed to reveal the full potential of marine chemical ecology. We highlight current challenges with specific examples and suggest how research on the chemical ecology of marine organisms could provide opportunities for implementing new management solutions for future “blue growth” (the sustainable use of ocean resources) and maintaining healthy marine ecosystems, M Saha acknowledges funding from the German Research Foundation (DFG) cluster of excellence “Future Ocean” for research grant CP1215, and the DFG under grant number SA 2571/2‐1. TW and GP acknowledge DFG for funding through CRC1127 ChemBioSys. EB received support from the CTM2014‐53818‐R (OstreoRisk) project funded by the Agencia Estatal de Investigación (AEI) and the Fondo Europeo de Desarrollo Regional (FEDER), and by the project CoCliME an ERA4CS Network (ERA‐NET) initiated by JPI Climate, and funded by EPA (IE), ANR (FR), BMBF (DE), UEFISCDI (RO), RCN (NO), and FORMAS (SE), with co‐funding by the European Union (grant agreement number 690462)

Published
2019

12. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum

Author

Rastogi, Achal, Vieira, Fabio Rocha Jimenez, Deton-Cabanillas, Anne-Flore, Veluchamy, Alaguraj, Cantrel, Catherine, Wang, Gaohong, Vanormelingen, Pieter, Bowler, Chris, Piganeau, Gwenael, Hu, Hanhua, Tirichine, Leïla, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie cellulaire et moléculaire des plantes (PCMP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Gent University, Department of Biology, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Hydrobiology - Chinese Academy of Sciences, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], [SDV.BID]Life Sciences [q-bio]/Biodiversity, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

13. Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications

Author

Nada Knežević, Anna Marja Aura, Baukje de Roos, María Teresa Garcia Conesa, Maria Rosário Bronze, Dragan Milenkovic, Arno Greyling, Tom Van de Wiele, Christine Morand, Aedin Cassidy, Jim Kaput, Ana Rodriguez-Mateos, Paul A. Kroon, Rikard Landberg, Eileen R. Gibney, Zohar Kerem, Claudine Manach, Francisco A. Tomás-Barberán, The Rowett Research Institute, University of Aberdeen, VTT Technical Research Centre of Finland (VTT), Instituto de Biologia Experimental e Tecnológica, Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), UCD Institute of Food and Health, University College Dublin (UCD), Unilever Research and Development, Vydiant, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Podravka d.d, Quadram Institute Bioscience, Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Nutritional Sciences, Mount Sinai Hospital (MSH), King’s College London, Center for Microbial Ecology and Technology (CMET), Gent University, Instituto de Biologia Experimental e Tecnológica (IBET), Centro de Edafologia y Biologia aplicada del Segura (CEBAS - CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Chalmers University of Technology [Gothenburg, Sweden], Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Mount Sinai Hospital [Toronto, Canada] (MSH), King‘s College London, Universiteit Gent = Ghent University [Belgium] (UGENT), University of East Anglia [Norwich] (UEA), Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universiteit Gent = Ghent University (UGENT), and de Roos, B.

Subjects
Agriculture and Food Sciences, 0301 basic medicine, and promotion of well-being, Food industry, Phytochemicals, Medicine (miscellaneous), Review, Gut flora, Cardiovascular, Oral and gastrointestinal, 0302 clinical medicine, Stakeholders, Cost action, Marketing, Cancer, 2. Zero hunger, Potential impact, education.field_of_study, Nutrition and Dietetics, biology, Dietary intake, Diet, Vegetarian, Cardiometabolic diseases, 3. Good health, Cardiovascular Diseases, Alimentation et Nutrition, HEALTH, Healthy diet Cardiometabolic diseases Inter-individual variability in responses Stakeholders Food industry, BIOMARKERS, Population, 030209 endocrinology & metabolism, Health Promotion, METABOLISM, 03 medical and health sciences, Vegetarian, Metabolic Diseases, Inter-individual variability in responses, Food and Nutrition, Humans, Obesity, 3.3 Nutrition and chemoprevention, education, Metabolic and endocrine, Nutrition, Healthy diet, 030109 nutrition & dietetics, Nutrition & Dietetics, business.industry, Prevention, Clinical study design, Prevention of disease and conditions, biology.organism_classification, Diet, Business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

Background A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a “one-size-fits-all approach” which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets. Purpose This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases., Key messages Individual differences in ADME (Absorption, Digestion, Metabolism and Excretion) is believed to underpin much of the inter-individual variation in responses.Recent developments in the area of food metabolome databases and fast improvements in innovative metabotyping technologies hold great promise for improved profiling of dietary intake, exposure to individual ingredients, foods and dietary patterns, as well as our ability to identify individual responsiveness.The food industry needs well-defined population clusters or targets in order to be able to design “personalized products”.There are indeed excellent industrial opportunities for foods that modulate gut microbiota, and thereby enable the delivery of food bioactive metabolites.It is currently not clear whether knowledge on individual nutrient needs, based on genetic or metagenomic data, would affect long-term dietary and health behaviours.Data to support the development of dietary recommendations may need to be generated by new n-of-1-based study designs in the future.

Published
2019

14. Future prospects for dissecting inter-individual variability in the absorption, distribution and elimination of plant bioactives of relevance for cardiometabolic endpoints

Author

Baukje de Roos, Francisco A. Tomás-Barberán, Tom Van de Wiele, Frederiek-Maarten Kerckhof, Claudine Manach, Rasha Noureldin M. Saleh, Christine Morand, Anne Marie Minihane, Rikard Landberg, Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Microbial Ecology and Technology (CMET), Gent University, Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, The Rowett Research Institute, University of Aberdeen, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Chalmers University of Technology [Gothenburg, Sweden], Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universiteit Gent = Ghent University [Belgium] (UGENT), Centro de Edafologia y Biologia aplicada del Segura (CEBAS - CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universiteit Gent = Ghent University (UGENT), University of East Anglia [Norwich] (UEA), and Landberg, R.

Subjects
0301 basic medicine, Agriculture and Food Sciences, Cardiometabolic, Future studies, BIOAVAILABILITY, Phytochemicals, Medicine (miscellaneous), Genomics, Computational biology, Review, Biology, Cardiovascular System, Inter-individual variation, 03 medical and health sciences, Metabolomics, Personalized nutrition, Plant bioactive compounds, Individual data, Genetic variation, CYP1A2 GENOTYPE, Medicine and Health Sciences, Food and Nutrition, Humans, Cost action, Microbiome, ADME, 2. Zero hunger, RISK, 030109 nutrition & dietetics, Nutrition and Dietetics, Diet, Vegetarian, CONSUMPTION, ASSOCIATION, 3. Good health, 030104 developmental biology, Biological Variation, Population, DEMETHYLASE, COMT GENOTYPE, Alimentation et Nutrition, Plants, Edible, VASCULAR FUNCTION, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, FLAVANONES, O-METHYLTRANSFERASE GENOTYPE
Abstract

Purpose The health-promoting potential of food-derived plant bioactive compounds is evident but not always consistent across studies. Large inter-individual variability may originate from differences in digestion, absorption, distribution, metabolism and excretion (ADME). ADME can be modulated by age, sex, dietary habits, microbiome composition, genetic variation, drug exposure and many other factors. Within the recent COST Action POSITIVe, large-scale literature surveys were undertaken to identify the reasons and extent of inter-individual variability in ADME of selected plant bioactive compounds of importance to cardiometabolic health. The aim of the present review is to summarize the findings and suggest a framework for future studies designed to investigate the etiology of inter-individual variability in plant bioactive ADME and bioefficacy. Results Few studies have reported individual data on the ADME of bioactive compounds and on determinants such as age, diet, lifestyle, health status and medication, thereby limiting a mechanistic understanding of the main drivers of variation in ADME processes observed across individuals. Metabolomics represent crucial techniques to decipher inter-individual variability and to stratify individuals according to metabotypes reflecting the intrinsic capacity to absorb and metabolize bioactive compounds. Conclusion A methodological framework was developed to decipher how the contribution from genetic variants or microbiome variants to ADME of bioactive compounds can be predicted. Future study design should include (1) a larger number of study participants, (2) individual and full profiling of all possible determinants of internal exposure, (3) the presentation of individual ADME data and (4) incorporation of omics platforms, such as genomics, microbiomics and metabolomics in ADME and efficacy studies., Key messages Human intervention studies are typically too small and do not report data from individuals to allow investigations of relevant determinants of inter-individual variability in ADME and bioefficacy.For some plant food bioactive compounds (isoflavones and ellagitannins), particular metabolites are produced only in a subset of the population, i.e., among individuals with a specific metabotype.Microbiota is an important determinant of the ADME of many bioactive compounds but microbial gene annotation is often lacking and interference with background diet and temporal variability is high: microbial metabolism capacity is, therefore, difficult to predict.Genetic variability is considered an important determinant of the ADME of some bioactive compounds, but there is a large gap in knowledge for many families of plant bioactive compounds regarding biotransformation enzymes and transport proteins.Information on other determinants such as age, sex, and diet is too incomplete to make firm conclusions about their impact on the inter-individual variability for most compounds investigatedMetabotyping individuals appears as essential to increase our understanding and improve prediction of ADME and health effects of plant bioactive compounds. Yet successful stratification examples are scarce and if available (e.g., urolithins), validation studies in larger cohorts are still required.

Published
2019

15. SIMULATIONS OF OSMOTIC EVENTS IN VITRIFICATION OF EQUINE OOCYTES AND PORCINE EMBRYOS

Author

Henri Woelders, Florence Guignot, Nerea Ortiz-Escribano, Katrien Smits, Ann Van Soom, Animal Breeding and Genomics, Wageningen University and Research [Wageningen] (WUR), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Faculty of Veterinary Medicine - Faculteit Diergeneeskunde [UGhent, Belgium], Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Gent University, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Guignot, Florence

Subjects
0301 basic medicine, 030219 obstetrics & reproductive medicine, Chemistry, [SDV]Life Sciences [q-bio], General Medicine, Porcine embryos, General Biochemistry, Genetics and Molecular Biology, 3. Good health, [SDV] Life Sciences [q-bio], Andrology, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Vitrification, General Agricultural and Biological Sciences
Abstract

International audience; Abstracts / Cryobiology 85 (2018) 120e190

Published
2018

16. The Chara genome: Secondary complexity and implications for plant terrestrialization

Author

Guru V. Radhakrishnan, Pierre-Marc Delaux, Yutaka Suzuki, Jan de Vries, Sabine Zachgo, Sumio Sugano, Gernot Glöckner, Roman Skokan, Marcel Quint, Martin Hagemann, Elio Schijlen, Jesper Harholt, Kristian K. Ullrich, Hiroshi Kagoshima, Caren Chang, Tomoaki Nishiyama, Philipp Janitza, Luz Irina A. Calderón Villalobos, Dirk Becker, Peter Ulvskov, Asao Fujiyama, Navindra Tajeshwar, Stephane Rombauts, Hidetoshi Sakayama, Florian Maumus, Günter Theißen, Daniel Lang, Stanislav Vosolsobě, Atsushi Toyoda, Dieter Deforce, Sven B. Gould, Yves Van de Peer, Christophe Dunand, Yuji Kohara, John M. Clay, Kenneth G. Karol, Dominique Van Der Straeten, Fabian B. Haas, Assia Saltykova, Denis Saint-Marcoux, Filip Van Nieuwerburgh, Florian Rümpler, Henrik Buschmann, Liam Dolan, Jane A. Langdale, Aikaterini Symeonidi, Jiri Friml, Ramona Kern, Bruno Catarino, Lisa Vanderstraeten, Alexander J. Hetherington, Charles F. Delwiche, Mary J. Beilby, Rainer Hedrich, Holger Breuninger, Clémence Bonnot, Stefan A. Rensing, Per K.I. Wilhelmsson, Alexander Heyl, Jan Petrášek, Kanazawa University (KU), Kobe University, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Dalhousie University, Osnabrück University, Department of Plant Sciences, University of Oxford [Oxford], Université Jean Monnet [Saint-Étienne] (UJM), Université de Lyon (COMUE), Philipps University of Marburg, Universiteit Gent = Ghent University [Belgium] (UGENT), University of Würzburg, PGSB, Helmholtz-Zentrum München (HZM), Charles University in Prague, Partenaires INRAE, Institute of Agricultural and Nutritional Sciences, Martin-Luther-Universität Halle Wittenberg (MLU), Plant Physiology, Umeå University, Adelphi University, Department of Genetics, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Department of Molecular Signal Processing, Leibniz Institute for Plant Biochemistry, National Institute of Genetics (NIG), The University of Tokyo (UTokyo), Wageningen University and Research Centre (WUR), Scientific Institute for Public Health, Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Department of Cell and Developmental Biology, John Innes Centre [Norwich], New York Botanical Garden (NYBG), Department of Plant and Environmental Sciences, department of Plant, University of Cologne, University of Pretoria [South Africa], Institute of Science and Technology [Austria] (IST Austria), University of New South Wales [Sydney] (UNSW), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Carlsberg Group, Carlsberg Laboratory, Dynamique et Evolution des Parois cellulaires végétales, Université Fédérale Toulouse Midi-Pyrénées, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, MEXT & JSPS KAKENHI [17020008, 20017013, 22128008, 15H04413, 24370095, 22770083, 24570100, 15K07185, 221S0002], Hyogo Science and Technology Association, DFG [GO1825/4-1, CRC1208, VR 132/1-1, SFB 944, FOR964, SFB 924], MEYS CR project [LO1417], Carlsberg Foundation, Villum Foundation’s Young Investigator Programme, LRSV laboratory [ANR-10-LABX-41], Gent University, Research Foundation Flanders [G.0317.17N, PhD fellowship 1S17917N], ERC Advanced Grants [EVO500, ETAP, EDIP], Leibniz Association, and NSF [DEB-1020660, DEB-1036466, MCB1714993, DEB 1036506]

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], plant evolution, Protein Serine-Threonine Kinases, Physcomitrella patens, Genome, Chara, General Biochemistry, Genetics and Molecular Biology, charophyte, BIOS Applied Bioinformatics, 03 medical and health sciences, Plant Growth Regulators, Cell Wall, streptophyte, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, transcriptional regulation, Pentosyltransferases, Phragmoplastophyta, Charophyte, Phragmoplast, Phytohormones, Plant Evolution, Reactive Oxygen Species, Streptophyte, Transcriptional Regulation, Plastid, Gene, Plant Proteins, Plant evolution, reactive oxygen species, biology, fungi, food and beverages, biology.organism_classification, Biological Evolution, phytohormones, phragmoplast, 030104 developmental biology, Plant protein, Evolutionary biology, Chara braunii, Embryophyta, Transcriptome, Genome, Plant, Transcription Factors
Abstract

The draft genome of Chara braunii reveals many plant-like features important for colonization of land that evolved in charophytic algae and therefore prior to the earliest land plants. Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote. © 2018 Elsevier Inc.

Published
2018

17. Free-boundary extension of the SIESTA code and its application to the Wendelstein 7-X stellarator

Author

Peraza Rodríguez, Hugo Alberto, Sánchez Fernández, Luis Raúl, Geiger, Joachim, Reynolds Barredo, José Miguel, Noterdaeme, Jean-Marie, Gent University, UC3M. Departamento de Física, and Universidad Carlos III de Madrid. Departamento de Física

Subjects
Plasma fusion, Wendelstein 7-X stellarator, Plasmas de fusión, SIESTA, Stellarators, Física del plasma, Física, Fusión nuclear, Scalable Iterative Equilibrium Solver for Toroidal Application
Abstract

Erasmus Mundus, FUSION Ideal magnetohydrodynamics (MHD) codes are of utmost importance to analyse equilibria of different experiments. The well known VMEC code (Variational Moments Equilibrium Code) does the three-dimensional ideal MHD analysis assuming nested magnetic surfaces. SIESTA (Scalable Iterative Equilibrium Solver for Toroidal Applications) is a code that takes a step further than VMEC, relying on VMEC’s solution, it computes the ideal MHD equilibrium solution of a given problem, without the assumption of nested magnetic surfaces. This results in the possible development of magnetic islands and stochastic regions. SIESTA, as was originally conceived, has a limiting aspect: it would only solve the equilibrium inside of the last closed flux surface (LCFS) found by VMEC. This condition implies that the results obtained for equilibria where there are possible instabilities or perturbations close to the LCFS are not well computed since SIESTA leaves the LCFS untouched. In this work a free-plasma-boundary version of SIESTA is developed in order to overcome this original limitation. The approach used consists of extending the analysis domain given by VMEC, in such a way that the vacuum region, or at least the most important part of it, is within the analysis volume of SIESTA. This requires the extension of the numerical analysis mesh guaranteeing the continuity of the metric elements on the mesh; a good approximation of the magnetic field solution in all the volume, and a pressure solution which couples with the magnetic field. The new version of SIESTA is applied to the specific case of the Wendelstein 7-X stellarator, at the IPP Greifswald (Germany), making comparisons with previous studies of equilibria showing the development of neoclassical bootstrap currents which cause the divertor island chain to shift its position. The previous studies were carried out with the VMEC-EXTENDER code combination, which is the general tool for ideal MHD equilibrium studies used in IPP. While their method is not self consistent, in the sense that it is a combination of the results of two difeferent codes, it has shown to be correct for the vacuum case and has been tested to be close to the experiment. Ideale Magnetohydrodynamische (MHD) codes zijn enorm belangrijk voor de anlayse van evenwichten van verschillende experimenten. De bekende VMEC code doet de driedimensionale ideale MHD analyse, gebruik makende van de aanname van in elkaar passende fluxoppervlakken. SIESTA (Scalable Iterative Equilibrium Solver for Toroidal Applications) is een code die een stap verder dan VMEC neemt. De code berekent het ideale MHD evennwicht zonder deze aanname van in elkaar passende fluxoppervlakken, startende van de oplossing van VMEC. Een resultaat hiervan is de mogelijke ontwikkeling van magnetische eilanden en stochastische regio’s. SIESTA, volgens het oorspronkelijke ontwerp, had echter één limitatie: De code loste enkel evenwichten op binnen het laatste gesloten fluxoppervlak (’Last Closed Flux Surface’, LCFS), bepaald door VMEC. Deze voorwaarde heeft als gevolg dat de resultaten voor evenwichten met mogelijke instabiliteiten dicht bij de LCFS niet goed berekend worden aangezien SIESTA de LCFS niet kan verplaatsen. In dit werk werd een vrije plasmawand versie van SIESTA ontwikkeld om deze limitatie te overkomen. Deze strategie die we hier gebruiken bestaat uit het uitbreiden van het analysedomein van VMEC, zodat de vacuumregio, of op zijn minst het belangrijke deel ervan, binnen het analysisvolume van SIESTA valt. Hiervoor was het nodig om het analysemaas uit te breiden om de continuiteit van de metrische elementen te garanderen en om een goede benadering van het de oplossing van het magnetische veld in het volume te bekomen, alsook voor de druk die gekoppeld is met die van het magnetische veld. Deze nieuwe versie van SIESTA werd dan toegepast op een specifieke configuratie van de Wendelstein 7-X stellarator, gesitueerd aan het IPP Greifswald, om te kunnen vergelijken met een vorige studie. Bij deze studie werd de ontwikkeling van de ’bootstrap’ stromen zichtbaar, die ervoor zorgen dat het de divertoreilandsketen van positie verschuift. Ze was uitgevoerd met de VMEC-EXTENDER codecombinatie, die een algemeen gereedschap is voor ideale MHD evenwichtsstudies. Hoewel hun methode niet zelf consistent is, waarbij bedoeld wordt dat het een combinatie is van resultaten van twee verschillende codes, werd nu aangetoond dat het toch correct is voor het vauumgeval, en dicht bij experimentele waarnemimgen ligt. Los códigos de magnetohidrodinámica (MHD) ideal son de primordial importancia para realizar análisis de equilibrios de diferentes experimentos de fusión nuclear. El código VMEC (Variational Moments Equilibrium Code), bien conocido en la comunidad de investigadores en física de plasmas, realiza análisis tri-dimensionales de equilibrios de MHD ideal asumiendo superficies magnéticas anidadas. SIESTA (Scalable Iterative Equilibrium Solver for Toroidal Applications) es un código que va un paso más allá que VMEC, respaldándose en la solución de VMEC, SIESTA calcula la solución de equilibrio de MHD ideal para un problema dado, sin la suposición de superficies magnéticas anidadas. Esto resulta en el posible desarrollo de islas magnéticas y regiones estocásticas. SIESTA, en su versión original, posee un aspecto limitante: solo podía resolver el equilibrio dentro de la última superficie cerrada (LCFS, por sus siglas en inglés) encontrada por VMEC. Esta condición implica que los resultados obtenidos para equilibrios donde pueden existir inestabilidades o perturbaciones cerca de la LCFS no están bien calculados debido a que SIESTA no modifica la LCFS. En este trabajo se desarrolla una versión de SIESTA con frontera de plasma libre para sobrepasar esta limitación original. El planteamiento consiste en extender el dominio de análisis dado por VMEC, de modo tal que la región de vacío —o al menos la parte más importante de ella— se encuentre dentro del volumen de análisis de SIESTA. Esto requiere la extensión de la malla de análisis numérico garantizando la continuidad de los elementos métricos de la mala; una buena aproximación del campo magnético en todo el volumen, y una solución de la presion que se acople a el campo magnético. La nueva versión de SIESTA se aplica al caso específico del stellerator Wendelstein 7-X , en el IPP de Greifswald (Alemania), realizando comparaciones con estudios previos de equilibrios que muestran el desarrollo de corrientes neoclásicas bootstrap, las cuales causan que la cadena de islas magnéticas asociadas al divertor cambien su posición. Los estudios previos se realizaron con la combinación de códigos VMEC-EXTENDER, que es la herramienta general utilizada en el IPP Greifswald para estudios de equilibrios de MHD ideal. Si bien es cierto que su método no es auto-consistente, en cuanto a que es la combinación de los resultados de dos códigos diferentes, ha demostrado ser válido para el caso de vacío y se ha comprobado su aproximación a los resultados experimentales. Programa Oficial de Doctorado en Plasmas y Fusión Nuclear Presidente: José Ramón Martín Solís.- Secretario: Per Helander.- Vocal: Hendrik Rogier

Published
2017

18. The sensitivity of gas hydrate reservoirs to climate change: Perspectives from a new combined model for permafrost-related and marine settings

Author

Marc De Batist, Thomas Mestdagh, Jeffrey Poort, Renard Centre of Marine Geology, Gent University, Evolution et Modélisation des Bassins Sédimentaires (EMBS), Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Universiteit Gent = Ghent University (UGENT)

Subjects
010504 meteorology & atmospheric sciences, Earth science, Clathrate hydrate, Climate change, Permafrost, 010502 geochemistry & geophysics, 01 natural sciences, Methane, Modelling, chemistry.chemical_compound, Deglaciation, Gas hydrate, 14. Life underwater, Geomorphology, 0105 earth and related environmental sciences, Marine, Global warming, 15. Life on land, chemistry, 13. Climate action, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Greenhouse gas, General Earth and Planetary Sciences, Hydrate, Geology
Abstract

International audience; Gas hydrate reservoirs store large quantities of gas in sediments on continental margins, in deep lakes, and in continental and relic sub-shelf permafrost. The gas hydrate structure is only stable at sufficiently low temperature and high pressure, and may therefore collapse under changing climatic conditions. If a temperature rise or pressure drop (e.g. through falling sea level) is effective enough to dissociate hydrate deposits, methane (the most common gas component in hydrates and a potent greenhouse gas) is released from the hydrate structure and may eventually enter into the atmosphere. This may generate a positive feedback effect, as resulting enhanced greenhouse gas levels would additionally warm the atmosphere and hence maintain or reinforce hydrate dissociation. The significance of this mechanism has been debated over the past decades, often within the framework of geologically rapid Quaternary climatic oscillations and present-day climate warming. An extensive set of studies has addressed the climate-sensitivity of gas hydrate reservoirs in various study areas and geological settings, and by means of various approaches. No real consensus has yet been reached on the matter. In this study, we seek to evaluate the sensitivity of gas hydrate reservoirs to changes in global climate from a more general perspective, by firstly reviewing the available literature, and secondly developing a new numerical model to quantify gas hydrate destabilization under changing environmental conditions. Qualities of the model include the wide applicability to both marine and permafrost-related hydrate reservoirs and the integrative approach, combining existing hydrate formation models with a dissocation model that accounts for the consumption of latent heat during hydrate dissociation. To determine which settings are most vulnerable, and to acquire insight into the extent, fashion and rates of hydrate dissociation, we apply the model to four distinct types of hydrate reservoirs across a hypothetic high-latitude continental margin under two specific cases of climate change: the last deglaciation following the Last Glacial Maximum and present-day climate warming. The simulations indicate that hydrates on the upper continental slope and in association with thin, sub-shelf permafrost are most sensitive to the imposed climatic variations, whereas deepwater and onshore permafrost-related reservoirs react in a more stable way. However, the deep (i.e. at several tens to hundreds of meters subsurface depth) stratigraphic-type hydrates considered in this study constitute by far the largest fraction of the global gas hydrate volume, but dissociate on slow timescales of thousands to hundreds of thousands of years, even in the most sensitive environments. In contrast, shallow (i.e. at, or a few meters below the surface or seafloor) structural-type hydrates are able to respond to climatic variations on sub-millennial timescales, but the volumes of gas they may release are probably insignificant to the global carbon cycle and climate. Quaternary and present-day climate change do affect the stability of gas hydrate reservoirs, but at long timescales where hydrate volumes are large, and on short timescales where hydrate volumes are small. Consequently, gas hydrates dissociate to an extent that is too small or at a pace that is too slow to create a strong positive feedback effect. While the release of methane from the disintegration of gas hydrates is observed on different margins today, it is not likely to have played a leading role in Quaternary climatic variations or to become a significant process in the coming centuries as a result of present-day rising temperatures.

Published
2017

19. Herd-level animal management factors associated with the occurrence of bovine neonatal pancytopenia in calves in a multi-country study

Author

Dirk U. Pfeiffer, Matthijs Schouten, Richard Booth, Sarne De Vliegher, Piet Deprez, Gerdien van Schaik, Carola Sauter-Louis, Jacqueline M. Cardwell, Jörg Henning, Anja Smolenaars, Raphaël Guatteo, Ingrid den Uijl, Jozef Laureyns, Alexander Stoll, Aurélien Madouasse, Simon Nusinovici, Mirjam Nielen, Bryony A. Jones, Christine Fourichon, Clinic for Ruminants with Ambulatory and Herd Health Services at the Centre for Clinical Veterinary Medicine, Ludwig Maximilians University of Munich, Veterinary Epidemiology, Economics & Public Health Group, Royal Veterinary College - University of London, Institute of Epidemiology, Helmholtz Centre Munich, School of Veterinary Science, University of Bristol [Bristol], Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University [Utrecht], GD Animal Health Service, UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Department of Internal Medicine and Clinical Biology of Large Animals, Faculty of Veterinary Medicine, Ghent University [Belgium] (UGENT), Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Gent University, Department of Pathology and Infectious Diseases, Royal Veterinary College, Universiteit Gent = Ghent University [Belgium] (UGENT), and dFAH AVR

Subjects
0301 basic medicine, Questionnaires, Veterinary medicine, Physiology, Pancytopenia, [SDV]Life Sciences [q-bio], lcsh:Medicine, COLOSTRUM, 0403 veterinary science, Leukocytopenia, Belgium, Risk Factors, CLASS-I, Germany, Medicine and Health Sciences, Medicine, Public and Occupational Health, lcsh:Science, Breast Milk, Netherlands, Mammals, DAMAGE, Vaccines, Multidisciplinary, ALLOANTIBODIES, Vaccination, Disease Management, Agriculture, 04 agricultural and veterinary sciences, Ruminants, Animal husbandry, Vaccination and Immunization, Body Fluids, Professions, Infectious Diseases, Milk, Veterinary Diseases, Research Design, Vertebrates, VACCINATION, France, Anatomy, Research Article, Veterinary Medicine, Livestock, Infectious Disease Control, 040301 veterinary sciences, Immunology, Cattle Diseases, Breast milk, Research and Analysis Methods, Veterinarians, Beverages, 03 medical and health sciences, Bovines, Journal Article, Animals, Veterinary Sciences, Nutrition, Survey Research, business.industry, lcsh:R, Case-control study, Organisms, Biology and Life Sciences, Odds ratio, HEMORRHAGIC DIATHESIS, Newborn, Diet, 030104 developmental biology, Animals, Newborn, Case-Control Studies, People and Places, Amniotes, ANTIBODIES, Multivariate Analysis, Herd, Colostrum, Population Groupings, Veterinary Science, Cattle, lcsh:Q, Preventive Medicine, business, Demography, BNP
Abstract

Since 2007, mortality associated with a previously unreported haemorrhagic disease has been observed in young calves in several European countries. The syndrome, which has been named 'bovine neonatal pancytopenia' (BNP), is characterised by thrombocytopenia, leukocytopenia and a panmyelophthisis. A herd-level case-control study was conducted in four BNP affected countries (Belgium, France, Germany and the Netherlands) to identify herd management risk factors for BNP occurrence. Data were collected using structured face-to-face and telephone interviews of farm managers and their local veterinarians. In total, 363 case farms and 887 control farms were included in a matched multivariable conditional logistic regression analysis. Case-control status was strongly associated with the odds of herd level use of the vaccine PregSure r BVD (PregSure, Pfizer Animal Health) (matched adjusted odds ratio (OR) 107.2; 95% CI: 41.0-280.1). This was also the case for the practices of feeding calves colostrum from the calf's own dam (OR 2.0; 95% CI: 1.1-3.4) or feeding pooled colostrum (OR 4.1; 95% CI: 1.9-8.8). Given that the study had relatively high statistical power and represented a variety of cattle production and husbandry systems, it can be concluded with some confidence that no other herd level management factors are competent causes for a sufficient cause of BNP occurrence on herd level. It is suggested that genetic characteristics of the dams and BNP calves should be the focus of further investigations aimed at identifying the currently missing component causes that together with PregSure vaccination and colostrum feeding represent a sufficient cause for occurrence of BNP in calves.

Published
2017

20. Sustainable production of biologically active molecules of marine based origin

Author

Eric Causse, Catherine Majella Collins, Edward McHugh, Alysson Wagner Fernandes Duarte, Spiros N. Agathos, Renata Manconi, Lara Durães Sette, Wim Vyverman, Luis M. Botana, Daniel J. Walsh, Susete Pinteus, Clayton Jeffryes, Gumersindo Feijoo, Marta Leirós, Fernando Suzigan Nobre, Juan A. Rubiolo, Rui Pedrosa, Angela Bisio, Ivan A. Laptev, Fernando Carlos Pagnocca, Fabio D. Ledda, Roberto Pronzato, Patrick Murray, Ifeloju O Owoyemi, Paula Perez-Lopez, Annick Verween, Sergei Sineoky, Mario Marchi, Siobhan Moane, André Horta, Céline C. Allewaert, Tanya Beletskaya, Olivier P. Thomas, Celso Alves, Ma Teresa Moreira, Shannon Applied Biotechnology, Limerick Institute of Technology, Department of Applied Science, Metabolomique Marine Environnementale, Institut de Chimie de Nice (ICN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institute of Computing [Campinas] (UNICAMP), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Algae Health, Claregalway Corporate Park, GREENSEA, Greensea, Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela [Spain] (USC ), Department Farmacologia, University of Santiago de Compostela, GIRM, Instituto Politécnico de Leiria, Bioengineering Group (GEBI), Université Catholique de Louvain = Catholic University of Louvain (UCL), Gent University, Department of Biology, Genetika, State Research Institute for Genetics and Selection of Industrial Microorganisms, Universita degli studi di Genova, Dipartimento di Scienze della Natura e del Territorio, and University of Sassari

Subjects
SCENEDESMUS-OBLIQUUS, Aquatic Organisms, EICOSAPENTAENOIC ACID, Natural resource economics, Bioengineering, Biology, 01 natural sciences, 12. Responsible consumption, 03 medical and health sciences, Resource (project management), ALGA SPHAEROCOCCUS-CORONOPIFOLIUS, NATURAL-PRODUCTS, LIFE-CYCLE ASSESSMENT, ALGA SPHAEROCOCCUS-CORONOPIFOLIUS, SPONGE FASCIOSPONGIA-CAVERNOSA, NATURAL-PRODUCTS, OXIDATIVE STRESS, PHAEODACTYLUM-TRICORNUTUM, EICOSAPENTAENOIC ACID, BROMINATED DITERPENES, SCENEDESMUS-OBLIQUUS, BIODIESEL PRODUCTION, 14. Life underwater, OXIDATIVE STRESS, PHAEODACTYLUM-TRICORNUTUM, Molecular Biology, BIODIESEL PRODUCTION, Exploitation of natural resources, 030304 developmental biology, Sustainable development, 0303 health sciences, Scope (project management), [SDE.IE]Environmental Sciences/Environmental Engineering, 010405 organic chemistry, Ecology, General Medicine, SPONGE FASCIOSPONGIA-CAVERNOSA, Marine Biology (journal), Natural resource, 0104 chemical sciences, Europe, Product (business), LIFE-CYCLE ASSESSMENT, 13. Climate action, Sustainability, BROMINATED DITERPENES, Biotechnology
Abstract

International audience; The marine environment offers both economic and scientific potential which are relatively untapped from a biotechnological point of view. These environments whilst harsh are ironically fragile and dependent on a harmonious life form balance. Exploitation of natural resources by exhaustive wild harvesting has obvious negative environmental consequences. From a European industry perspective marine organisms are a largely underutilised resource. This is not due to lack of interest but due to a lack of choice the industry faces for cost competitive, sustainable and environmentally conscientious product alternatives. Knowledge of the biotechnological potential of marine organisms together with the development of sustainable systems for their cultivation, processing and utilisation are essential. In 2010, the European Commission recognised this need and funded a collaborative RTD/SME project under the Framework 7-Knowledge Based Bio-Economy (KBBE) Theme 2 Programme ‘Sustainable culture of marine microorganisms, algae and/or invertebrates for high value added products’. The scope of that project entitled ‘Sustainable Production of Biologically Active Molecules of Marine Based Origin’ (BAMMBO) is outlined. Although the Union is a global leader in many technologies, it faces increasing competition from traditional rivals and emerging economies alike and must therefore improve its innovation performance. For this reason innovation is placed at the heart of a European Horizon 2020 Strategy wherein the challenge is to connect economic performance to eco performance. This article provides a synopsis of the research activities of the BAMMBO project as they fit within the wider scope of sustainable environmentally conscientious marine resource exploitation for high-value biomolecules.

Published
2013

21. Stability of Constant Retrial Rate Systems with NBU Input

Author

Konstantin Avrachenkov, Bart Steyaert, Ruslana Nekrasova, Evsey Morozov, Models for the performance analysis and the control of networks (MAESTRO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institute of Applied Mathematical Research [Petrozavodsk], Russian Academy of Sciences [Moscow] (RAS)-Petrozavodsk State University [Petrozavodsk], Universiteit Gent = Ghent University (UGENT), and Gent University

Subjects
Statistics and Probability, Discrete mathematics, Class (set theory), 021103 operations research, Applied Mathematics, General Mathematics, 0211 other engineering and technologies, 02 engineering and technology, Queueing system, Expression (computer science), Poisson distribution, 01 natural sciences, Stability (probability), Exponential function, 010104 statistics & probability, symbols.namesake, Stability conditions, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], symbols, Applied mathematics, 0101 mathematics, Constant (mathematics), Mathematics
Abstract

International audience; We study the stability of a single-server retrial queueing system with constant retrial rate, general input and service processes. First, we present a review of some relevant recent results related to the stability criteria of similar systems. Sufficient stability conditions were obtained by (Avrachenkov and Morozov, 2014), which hold for a rather general retrial system. However, only in case of Poisson input an explicit expression is provided; otherwise one has to rely on simulation. On the other hand, the stability criteria derived by (Lillo, 1996) can be easily computed, but only hold for the case of exponential service times. We present new sufficient stability conditions, which are less tight than the ones obtained by (Avrachenkov and Morozov, 2010), but have an analytical expression under rather general assumptions. A key assumption is that interarrival times belongs to the class of new better than used (NBU) distributions. We illustrate the accuracy of the condition based on this assumption (in comparison with known conditions when possible) for a number of non-exponential distributions.

Published
2016

22. Sufficient Stability Conditions for Multi-class Constant Retrial Rate Systems

Author

Bart Steyaert, Evsey Morozov, Konstantin Avrachenkov, Models for the performance analysis and the control of networks (MAESTRO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institute of Applied Mathematical Research [Petrozavodsk], Russian Academy of Sciences [Moscow] (RAS)-Petrozavodsk State University [Petrozavodsk], Universiteit Gent = Ghent University (UGENT), and Gent University

Subjects
0211 other engineering and technologies, Joins, 02 engineering and technology, Management Science and Operations Research, 01 natural sciences, 010104 statistics & probability, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], Control theory, Applied mathematics, 0101 mathematics, Mathematics, Constant retrial rate, Queueing theory, 021103 operations research, Probabilistic logic, Computer Science Applications, Exponential function, Computer Science::Performance, Stability conditions, Regenerative approach, Computational Theory and Mathematics, Transmission (telecommunications), Stability condition, Retrial systems, Orbit (control theory), Constant (mathematics), Multi-class systems
Abstract

International audience; We study multi-class retrial queueing systems with Poisson inputs, general service times, and an arbitrary numbers of servers and waiting places. A class-i blocked customer joins orbit i and waits in the orbit for retrial. Orbit i works like a single-server ·/M/1 queueing system with exponential retrial time regardless of the orbit size. Such retrial systems are referred to as retrial systems with constant retrial rate. Our model is motivated by several telecommunication applications, such as wireless multi-access systems, optical networks and transmission control protocols, but represents independent theoretical interest as well. Using a regenerative approach, we provide sufficient stability conditions which have a clear probabilistic interpretation. We show that the provided sufficient conditions are in fact also necessary, in the case of a single-server system without waiting space and in the case of symmetric classes. We also discuss a very interesting case, when one orbit is unstable, whereas the rest of the system is stable.

Published
2016

23. A Hotspot of Amoebae Diversity: 8 New Naked Amoebae Associated with the Planktonic Bloom-forming Cyanobacterium Microcystis

Author

Van Wichelen, Jeroen, D 'hondt, Sofie, Claeys, Myriam, Vyverman, Wim, Berney, Cédric, Bass, David, Vanormelingen, Pieter, Gent University, Department of Biology, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and The Natural History Museum [London] (NHM)

Subjects
harmful algal blooms, Europe, Naked amoebae, Microcystis, 18S rDNA, [SDV.BA]Life Sciences [q-bio]/Animal biology, morphology, grazing
Abstract

International audience; The colonies of Microcystis, one of the most common bloom-forming cyanobacteria worldwide, harbor a diverse community of microorganisms. Among these, naked amoebae feeding on Microcystis cells can strongly influence natural Microcystis population dynamics. In this study, we investigated the species diversity of these amoebae based on 26 Microcystis-associated amoebae (MAA) strains from eutrophied water bodies in Belgium and elsewhere in western Europe. A detailed morphological characterization in combination with 18S rDNA (SSU) phylogenies revealed the presence of no less than 10 species. Nine of these belonged to the known genera Vannella (2 species), Korotnevella (2), Copromyxa (2), Vexillifera (1), Cochliopodium (1) and the recently described Angulamoeba (1). Only two were previously described, the others were new to science. One taxon could not be assigned to a known genus and is here described as Schoutedamoeba gen. n., representing a new variosean lineage. The discovery of so many new species from only one very specific habitat (Microcystis colonies) from a rather restricted geographical area indicates that the diversity of planktonic naked amoebae is much higher than previously appreciated and that only a tiny fraction of the total diversity of naked amoebae is currently known.

Published
2016

24. Optimizing on-line RPLCxRPLC-MS for both peak capacity enhancement and matrix effect reduction. Application to the separation of peptides

Author

Sarrut, Morgan, Heinisch, Sabine, Bussy, Agnès, Chromatography & Hyphenated Techniques - Chromatographie et techniques couplées, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), University of Leuven, VUB - Vrije Universteit Brussel, and Gent University

Subjects
[CHIM.ANAL] Chemical Sciences/Analytical chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

25. Development of Supercritical Fluid Chromatography Methods with Mass Spectrometry and U.V. Detection for the Characterization of Fast Pyrolysis Bio Oils

Author

Crepier, Julien, Le Masle, Agnès, Charon, Nadège, Heinisch, Sabine, Bussy, Agnès, IFP Energies nouvelles (IFPEN), Chromatography & Hyphenated Techniques - Chromatographie et techniques couplées, Institut des Sciences Analytiques (ISA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Leuven, VUB - Vrije Universteit Brussel, and Gent University

Subjects
[CHIM.ANAL] Chemical Sciences/Analytical chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

26. Algorithm Selection for Combinatorial Search Problems: A Survey

Author

Lars Kotthoff, Ian Miguel, University of St Andrews, Ian Gent, University of St Andrews, and EPSRC

Subjects
FOS: Computer and information sciences, Artificial Intelligence (cs.AI), Artificial Intelligence, Computer Science - Artificial Intelligence, problem solving, search, machine learning and discovery, Computer Science, Artificial Intelligence, Problem Solving
Abstract

The Algorithm Selection Problem is concerned with selecting the best algorithm to solve a given problem on a case-by-case basis. It has become especially relevant in the last decade, as researchers are increasingly investigating how to identify the most suitable existing algorithm for solving a problem instead of developing new algorithms. This survey presents an overview of this work focusing on the contributions made in the area of combinatorial search problems, where Algorithm Selection techniques have achieved significant performance improvements. We unify and organise the vast literature according to criteria that determine Algorithm Selection systems in practice. The comprehensive classification of approaches identifies and analyses the different directions from which Algorithm Selection has been approached. This paper contrasts and compares different methods for solving the problem as well as ways of using these solutions. It closes by identifying directions of current and future research.

Published
2014

27. A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum

Author

Bentley, Michael J., Ó Cofaigh, Colm, Anderson, John B., Conway, Howard, Davies, Bethan, Graham, Alastair G.C., Hillenbrand, Claus-Dieter, Hodgson, Dominic A., Jamieson, Stewart S.R., Larter, Robert, Mackintosh, Andrew N., Smith, James A., Verleyen, Elie, Ackert, Robert, Bart, Philip J., Berg, Sonja, Brunstein, Daniel, Canals, Miquel, Colhoun, Eric A., Crosta, Xavier, Dickens, William A., Domack, Eugene, Dowdeswell, Julia, Dunbar, Robert, Ehrmann, Werner, Evans, Jeffrey, Favier, Vincent, Fink, David, Fogwill, Christopher J., Glasser, Neil F., Gohl, Karsten, Golledge, Nicholas R., Goodwin, Ian, Gore, Damian B., Greenwood, Sarah L., Hall, Brenda L., Hall, Kevin, Hedding, David W., Hein, Andrew S., Hocking, Emma P., Jakobsson, Martin, Johnson, Joanne S., Jomelli, Vincent, Jones, R. Selwyn, Klages, Johann P., Kristoffersen, Yngve, Kuhn, Gerhard, Leventer, Amy, Licht, Kathy, Lilly, Katherine, Lindow, Julia, Livingstone, Stephen J., Massé, Guillaume, Mcglone, Matt S., Mckay, Robert, Melles, Martin, Miura, Hideki, Mulvaney, Robert, Nel, Werner, Nitsche, Frank O., O'Brien, Philip E., Post, Alexandra L., Roberts, Stephen J., Saunders, Krystyna M., Selkirk, Patricia M., Simms, Alexander R., Spiegel, Cornelia, Stolldorf, Travis D., Sugden, David E., van Der Putten, Nathalie, van Ommen, Tas, Verfaillie, Deborah, Vyverman, Wim, Wagner, Bernd, White, Duanne A., Witus, Alexandra E., Zwartz, Dan, Department of Geography, Durham University, School of Oceanography [Seattle], University of Washington [Seattle], Biological and Biomedical Sciences, Glasgow Caledonian University (GCU), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Universiteit Gent = Ghent University (UGENT), Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), GRC Geociencies Marines, GRC, School of Environmental and Life Sciences, The University of Newcastle, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Space Research Institute of Austrian Academy of Sciences (IWF), Austrian Academy of Sciences (OeAW), College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Scott Polar Research Institute, University of Cambridge [UK] (CAM), Stanford University, Centre for glaciology, Department of Geography and Earth Sciences (DGES), Aberystwyth University-Aberystwyth University, Department of biomedical sciences, University of Prince Edward Island, University of Calgary, Department of Evolutionary Biology, Uppsala University, Institute for Biomechanics, Colgate University, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of integrative biology (Liverpool), University of Liverpool, Paul Scherrer Institute (PSI), NIFS, National Institute for Fusion Science (NIFS), Gent University, Department of Biology, Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], University of West London, Dpt Biological Sciences, Macquarie University, Macquarie University, Division of Migratory Birds - Northeast Region, US Fish and Wildlife Service, Lund University [Lund], UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Department of Geology and Geochemistry [Stockholm], Stockholm University, Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Panthéon-Sorbonne (UP1), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Protistology and Aquatic Ecology, Ghent University, Universiteit Gent = Ghent University [Belgium] (UGENT), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), and Earth and Climate

Subjects
Matematikk og naturvitenskap: 400::Geofag: 450::Kvartærgeologi, glasiologi: 465 [VDP], [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Modelling, Mathematics and natural scienses: 400::Geosciences: 450::Quaternary geology, glaciology: 465 [VDP], Quaternary, HISTORY, MASS-BALANCE, COLLAPSE, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, WEDDELL SEA EMBAYMENT, CONSTRAINTS, LEVEL CHANGE, Geology, RETREAT, Antarctic Ice Sheet, STREAM STABILITY, Glacial geology, ISOSTATIC-ADJUSTMENT, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Earth and Environmental Sciences, PENINSULA
Abstract

The Weddell Sea sector is one of the main formation sites for Antarctic Bottom Water and an outlet for about one fifth of Antarctica’s continental ice volume. Over the last few decades, studies on glacialegeological records in this sector have provided conflicting reconstructions of changes in ice-sheet extent and ice-sheet thickness since the Last Glacial Maximum (LGM at ca 23e19 calibrated kiloyears before present, cal ka BP). Terrestrial geomorphological records and exposure ages obtained from rocks in the hinterland of the Weddell Sea, ice-sheet thickness constraints from ice cores and some radiocarbon dates on offshore sediments were interpreted to indicate no significant ice thickening and locally restricted grounding-line advance at the LGM. Other marine geological and geophysical studies concluded that subglacial bedforms mapped on theWeddell Sea continental shelf, subglacial deposits and sediments over-compacted by overriding ice recovered in cores, and the few available radiocarbon ages from marine sediments are consistent with major ice-sheet advance at the LGM. Reflecting the geological interpretations, different icesheet models have reconstructed conflicting LGM ice-sheet configurations for the Weddell Sea sector. Consequently, the estimated contributions of ice-sheet build-up in the Weddell Sea sector to the LGM sealevel low-stand of w130 m vary considerably. In this paper, we summarise and review the geological records of past ice-sheet margins and past icesheet elevations in the Weddell Sea sector. We compile marine and terrestrial chronological data constraining former ice-sheet size, thereby highlighting different levels of certainty, and present two alternative scenarios of the LGM ice-sheet configuration, including time-slice reconstructions for post- LGM grounding-line retreat. Moreover, we discuss consistencies and possible reasons for inconsistencies between the various reconstructions and propose objectives for future research. The aim of our study is to provide two alternative interpretations of glacialegeological datasets on Antarctic Ice- Sheet History for the Weddell Sea sector, which can be utilised to test and improve numerical icesheet models

Published
2014
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28. Arabidopsis thaliana RNase H2 Deficiency Counteracts the Needs for the WEE1 Checkpoint Kinase but Triggers Genome Instability[C][W]

Author

Pooneh Kalhorzadeh, Charles I. White, Korbinian Schneeberger, Simon Amiard, Eva-Maria Willing, Toon Cools, Nancy De Winne, Lieven De Veylder, Geert De Jaeger, Zhubing Hu, Kris Gevaert, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Medical Protein Research, VIB-Gent University, Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT)-VIB, and White, Charles

Subjects
Cell cycle checkpoint, RNase P, Molecular Sequence Data, Ribonuclease H, Arabidopsis, Eukaryotic DNA replication, [SDV.GEN] Life Sciences [q-bio]/Genetics, Plant Science, Protein Serine-Threonine Kinases, Genes, Plant, Genomic Instability, Mutation Rate, Catalytic Domain, Hydroxyurea, Amino Acid Sequence, RNase H, Base Pairing, ComputingMilieux_MISCELLANEOUS, Research Articles, Genetics, Recombination, Genetic, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Base Sequence, Arabidopsis Proteins, Cell Biology, Cell Cycle Checkpoints, G2-M DNA damage checkpoint, Ribonucleotides, RNase MRP, Mutation, biology.protein, Origin recognition complex, Homologous recombination
Abstract

The WEE1 kinase is an essential cell cycle checkpoint regulator in Arabidopsis thaliana plants experiencing replication defects. Whereas under non-stress conditions WEE1-deficient plants develop normally, they fail to adapt to replication inhibitory conditions, resulting in the accumulation of DNA damage and loss of cell division competence. We identified mutant alleles of the genes encoding subunits of the ribonuclease H2 (RNase H2) complex, known for its role in removing ribonucleotides from DNA-RNA duplexes, as suppressor mutants of WEE1 knockout plants. RNase H2 deficiency triggered an increase in homologous recombination (HR), correlated with the accumulation of γ-H2AX foci. However, as HR negatively impacts the growth of WEE1-deficient plants under replication stress, it cannot account for the rescue of the replication defects of the WEE1 knockout plants. Rather, the observed increase in ribonucleotide incorporation in DNA indicates that the substitution of deoxynucleotide with ribonucleotide abolishes the need for WEE1 under replication stress. Strikingly, increased ribonucleotide incorporation in DNA correlated with the occurrence of small base pair deletions, identifying the RNase H2 complex as an important suppressor of genome instability.

Published
2014

29. Stability Analysis and Simulation of N-class Retrial System with Constant Retrial Rates and Poisson Inputs

Author

Evsey Morozov, Konstantin Avrachenkov, Bart Steyaert, Ruslana Nekrasova, Models for the performance analysis and the control of networks (MAESTRO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Petrozavodsk State University [Petrozavodsk], Gent University, Campus France, and Universiteit Gent = Ghent University (UGENT)

Subjects
Retrial system, Technology and Engineering, Real-time computing, Ocean Engineering, Management Science and Operations Research, Poisson distribution, Stability (probability), Retrial system, constant retrial rate, stability condition, regenerative approach, busy probability, multi-class system, stability condition, multi-class system, symbols.namesake, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], Applied mathematics, Queues, busy probability, Queue, Mathematics, Probabilistic logic, Exponential function, Computer Science::Performance, Stability conditions, symbols, regenerative approach, Orbit (control theory), Constant (mathematics), constant retrial rate
Abstract

In this paper, we study a new retrial queueing system with N classes of customers, where a class-i blocked customer joins orbit i. Orbit i works like a single-server queueing system with (exponential) constant retrial time (with rate [Formula: see text]) regardless of the orbit size. Such a system is motivated by multiple telecommunication applications, for instance wireless multi-access systems, and transmission control protocols. First, we present a review of some corresponding recent results related to a single-orbit retrial system. Then, using a regenerative approach, we deduce a set of necessary stability conditions for such a system. We will show that these conditions have a very clear probabilistic interpretation. We also performed a number of simulations to show that the obtained conditions delimit the stability domain with a remarkable accuracy, being in fact the (necessary and sufficient) stability criteria, at the very least for the 2-orbit M/M/1/1-type and M/Pareto/1/1-type retrial systems that we focus on.

Published
2014

30. Environmental evaluation of eicosapentaenoic acid production by Phaeodactylum tricornutum

Author

Sara González-García, Annick Verween, Patrick Murray, Maria Teresa Moreira, Paula Perez-Lopez, Céline C. Allewaert, Gumersindo Feijoo, Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela [Spain] (USC ), Gent University, Department of Biology, Shannon Applied Biotechnology, Limerick Institute of Technology, Department of Applied Science, and European Project: 265896,EC:FP7:KBBE,FP7-KBBE-2010-4,BAMMBO(2011)

Subjects
Environmental Engineering, Pilot Projects, Biology, engineering.material, Environment, chemistry.chemical_compound, Bioreactors, Nitrate, Biogas, Bioenergy, Microalgae, Environmental Chemistry, Phaeodactylum tricornutum, Nitrogen Compounds, Waste Management and Disposal, Diatoms, Waste management, biology.organism_classification, Pulp and paper industry, Pollution, 6. Clean water, Anaerobic digestion, chemistry, Eicosapentaenoic Acid, 13. Climate action, Biofuel, Biodiesel production, [SDE]Environmental Sciences, engineering, Fertilizer, Biotechnology
Abstract

International audience; Polyunsaturated fatty acids (PUFAs) play an important role in human health. Due to the increased market demand, the production of PUFAs from potential alternative sources such as microalgae is receiving increased interest.The aim of this study was to perform a life cycle assessment (LCA) of the biotechnological production of eicosapentaenoic acid (EPA) from the marine diatom Phaeodactylum tricornutum, followed by the identification of avenues to improve its environmental profile. The LCA tackles two production schemes of P. tricornutum PUFAs with an EPA content of 36%: lab and pilot scales.The results at lab scale show that both the electricity requirements and the production of the extraction agent (chloroform) have significant influence on the life cycle environmental performance of microalgal EPA production. An alternative method based on hexane was proposed to replace chloroform and environmental benefits were identified.Regarding the production of EPA at pilot scale, three main environmental factors were identified: the production of the nitrogen source required for microalgae growing, the transport activities and electricity requirements. Improvement alternatives were proposed and discussed concerning: a) the use of nitrogen based fertilizers, b) the valorization of the residual algal paste as soil conditioner and, c) the anaerobic digestion of the residual algal paste for bioenergy production.Encouraging environmental benefits could be achieved if sodium nitrate was substituted by urea, calcium nitrate or ammonium nitrate, regardless the category under assessment. In contrast, minor improvement was found when valorizing the residual algal paste as mineral fertilizer, due to its overall low content in N and P. Concerning the biogas production from the anaerobic digestion, the improvement on the environmental profile was also limited due to the discrepancy between the potential energy production from the algal paste and the high electricity requirements in the culturing and extraction stages.

Published
2014

31. AUREOCHROME1a-Mediated Induction of the Diatom-Specific Cyclin dsCYC2 Controls the Onset of Cell Division in Diatoms (Phaeodactylum tricornutum)

Author

Chris Bowler, Michiel Matthijs, Wim Vyverman, Peter G. Kroth, Dirk Inzé, Marie J. J. Huysman, Antonio Emidio Fortunato, Benjamin Schellenberger Costa, Rudy Vanderhaeghen, Lieven De Veylder, Hilde Van den Daele, Matthias Sachse, Christian Wilhelm, Angela Falciatore, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Biotechnology and Genetics [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Fachbereich Biologie [Konstanz], University of Konstanz, Dept Plant Biotechnol & Bioinformat, Dept Plant Syst Biol, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Universität Leipzig [Leipzig], Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Gent University, Department of Biology, Agency for Innovation by Science and Technology in Flanders (IWT-Vlaanderen), Research Foundation Flanders [G.0288.13], Federation of European Biochemical Societies (FEBS) organization, European Molecular Biology Organization (EMBO) organization [ASTF 93-2011], Agence Nationale de Recherche, Deutsche Forschungsgemeinschaft [FOR 1261 (Wi 764/19)], Human Frontier Science Program Young Investigator Grant [RGY0082/2010], Centre National de la Recherche Scientifique, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Universität Leipzig

Subjects
0106 biological sciences, Cell cycle checkpoint, Cell division, Light, Transcription, Genetic, [SDV]Life Sciences [q-bio], Cyclin A, PROTEIN, PROGRESSION, Plant Science, 01 natural sciences, SACCHAROMYCES-CEREVISIAE, Photosynthesis, Promoter Regions, Genetic, Research Articles, GENE-EXPRESSION, Cyclin, 0303 health sciences, biology, Cell cycle, Darkness, Cell biology, MARINE-PHYTOPLANKTON, Cell Division, Signal Transduction, HIGH LIGHT, Models, Biological, 03 medical and health sciences, ddc:570, Cyclins, YEAST, Phaeodactylum tricornutum, PLANT, Transcription factor, 030304 developmental biology, Diatoms, Cyclin-dependent kinase 1, PHOTOSYNTHESIS, fungi, Algal Proteins, Genetic Complementation Test, Biology and Life Sciences, PHOTOPROTECTION, Cell Biology, biology.organism_classification, Gene Expression Regulation, Protein Biosynthesis, Mutation, biology.protein, 010606 plant biology & botany
Abstract

Cell division in photosynthetic organisms is tightly regulated by light. Although the light dependency of the onset of the cell cycle has been well characterized in various phototrophs, little is known about the cellular signaling cascades connecting light perception to cell cycle activation and progression. Here, we demonstrate that diatom-specific cyclin 2 (dsCYC2) in Phaeodactylum tricornutum displays a transcriptional peak within 15 min after light exposure, long before the onset of cell division. The product of dsCYC2 binds to the cyclin-dependent kinase CDKA1 and can complement G1 cyclin-deficient yeast. Consistent with the role of dsCYC2 in controlling a G1-to-S light-dependent cell cycle checkpoint, dsCYC2 silencing decreases the rate of cell division in diatoms exposed to light-dark cycles but not to constant light. Transcriptional induction of dsCYC2 is triggered by blue light in a fluence rate-dependent manner. Consistent with this, dsCYC2 is a transcriptional target of the blue light sensor AUREOCHROME1a, which functions synergistically with the basic leucine zipper (bZIP) transcription factor bZIP10 to induce dsCYC2 transcription. The functional characterization of a cyclin whose transcription is controlled by light and whose activity connects light signaling to cell cycle progression contributes significantly to our understanding of the molecular mechanisms underlying light-dependent cell cycle onset in diatoms.

Published
2013

32. Gas hydrate of Lake Baikal: Discovery and varieties

Author

Andrey Yu. Manakov, Lieven Naudts, Hitoshi Shoji, Jeffrey Poort, Shinya Nishio, A. V. Khabuev, Oleg Khlystov, Marc De Batist, Akihiro Hachikubo, G. V. Kalmychkov, O. V. Belousov, Limnologial Institute of the Siberian Division of the Russina, Chinese Academy of Sciences [Beijing] (CAS), Renard Centre of Marine Geology, Gent University, Kitami Institute, Institute of Technology, Technology Institute of Shimizu Corporation, Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Nikolaev Institute of Inorganic Chemistry, SB RAS, and Universiteit Gent = Ghent University (UGENT)

Subjects
010504 meteorology & atmospheric sciences, MIR submersible, Clathrate hydrate, Geochemistry, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Geology, 010502 geochemistry & geophysics, 01 natural sciences, Methane, Petroleum seep, chemistry.chemical_compound, Oceanography, chemistry, Gas, Gas hydrate, Sedimentary rock, Lake Baikal, Hydrate, Mud volcano, 0105 earth and related environmental sciences, Earth-Surface Processes, Seep
Abstract

International audience; This paper summarizes the results of recent gas-hydrate studies in Lake Baikal, the only fresh-water lake in the world containing gas hydrates in its sedimentary infill. We provide a historical overview of the different investigations and discoveries and highlight some recent breakthroughs in our understanding of the Baikal hydrate system. So far, 21 sites of gas hydrate occurrence have been discovered. Gas hydrates are of structures I and II, which are of thermogenic, microbial, and mixed origin. At the 15 sites, gas hydrates were found in mud volcanoes, and the rest six – near gas discharges. Additionally, depending on type of discharge and gas hydrate structure, they were visually different. Investigations using MIR submersibles allowed finding of gas hydrates at the bottom surface of Lake Baikal at the three sites.

Published
2013

33. Damage to white matter pathways in subacute and chronic spatial neglect: a group study and 2 single-case studies with complete virtual 'in vivo' tractography dissection

Author

Marilena Aiello, Massimo Silvetti, Francesco Tomaiuolo, Sheila Merola, Paolo Bartolomeo, Francesca Lecce, Fabrizio Doricchi, Michel Thiebaut de Schotten, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), 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), Natbrainlab, Department of Forensic and Neurodevelopmental Sciences, Institute of psychiatry-King‘s College London, Auxilium Vitae, Fondazione Santa Lucia IRCCS, Clinical and Behavioral Neurology - Neuroscienze e riabilitazione, IRCCS Fondazione Santa Lucia [Roma], Gent University, Department of Psychology, Catholic University, Dipartimento di Psicologia 39, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Universiteit Gent = Ghent University (UGENT), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), and Thiebaut De Schotten, Michel

Subjects
Male, FRONTAL-LOBE INFARCTION, Image Processing, VISUAL NEGLECT, cervello, Nerve Fibers, Myelinated, Functional Laterality, attenzione spaziale, materia bianca, CEREBRAL-ARTERY INFARCTION, User-Computer Interface, Computer-Assisted, Nerve Fibers, 0302 clinical medicine, Supramarginal gyrus, Leukoencephalopathies, Image Processing, Computer-Assisted, LEFT UNILATERAL NEGLECT, 05 social sciences, Superior longitudinal fasciculus, THALAMIC HEMORRHAGE, DIFFUSION-TENSOR MRI, Middle Aged, diffusion tensor imaging, stroke, Stroke, medicine.anatomical_structure, OF-THE-LITERATURE, Sensation Disorders, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Female, anatomy, human, spatial neglect, Adult, Aged, Diffusion Magnetic Resonance Imaging, Humans, Linear Models, Perceptual Disorders, Psychomotor Performance, Visual Fields, Psychology, Cognitive Neuroscience, Posterior parietal cortex, Inferior frontal gyrus, 050105 experimental psychology, White matter, Angular gyrus, 03 medical and health sciences, Cellular and Molecular Neuroscience, medicine, 0501 psychology and cognitive sciences, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], RIGHT-HEMISPHERE STROKE, Biology and Life Sciences, Inferior parietal lobule, STIMULUS-DRIVEN ATTENTION, HUMAN BRAIN-LESIONS, Settore M-PSI/02 - Psicobiologia e Psicologia Fisiologica, Myelinated, Neuroscience, 030217 neurology & neurosurgery, Diffusion MRI
Abstract

International audience; The exact anatomical localization of right hemisphere lesions that lead to left spatial neglect is still debated. The effect of confounding factors such as acute diaschisis and hypoperfusion, visual field defects, and lesion size may account for conflicting results that have been reported in the literature. Here, we present a comprehensive anatomical investigation of the gray- and white matter lesion correlates of left spatial neglect, which was run in a sample 58 patients with subacute or chronic vascular strokes in the territory of the right middle cerebral artery. Standard voxel-based correlates confirmed the role played by lesions in the posterior parietal cortex (supramarginal gyrus, angular gyrus, and temporal-parietal junction), in the frontal cortex (frontal eye field, middle and inferior frontal gyrus), and in the underlying parietal-frontal white matter. Using a new diffusion tensor imaging-based atlas of the human brain, we were able to run, for the first time, a detailed analysis of the lesion involvement of subcortical white matter pathways. The results of this analysis revealed that, among the different pathways linking parietal with frontal areas, damage to the second branch of the superior longitudinal fasciculus (SLF II) was the best predictor of left spatial neglect. The group study also revealed a subsample of patients with neglect due to focal lesion in the lateral-dorsal portion of the thalamus, which connects the premotor cortex with the inferior parietal lobule. The relevance of fronto-parietal disconnection was further supported by complete in vivo tractography dissection of white matter pathways in 2 patients, one with and the other without signs of neglect. These 2 patients were studied both in the acute phase and 1 year after stroke and were perfectly matched for age, handedness, stroke onset, lesion size, and for cortical lesion involvement. Taken together, the results of the present study support the hypothesis that anatomical disconnections leading to a functional breakdown of parietal-frontal networks are an important pathophysiological factor leading to chronic left spatial neglect. Here, we propose that different loci of SLF disconnection on the rostro-caudal axis can also be associated with disconnection of short-range white matter pathways within the frontal or parietal areas. Such different local disconnection patterns can play a role in the important clinical variability of the neglect syndrome.

Published
2012

34. COLD-WATER Coral carbonate mounds as palaeo-archives : the Plio-Pleistocene sediment record from the Challenger Mound (NE Atlantic)

Author

Thierens, M., Pirlet, H., Dorschel, B., Huvenne, V.A.I., Titschack, J., Stuut, J.B., Colin, Christophe, Browning, E., Tyrrell, S., Lee, J., Loutre, M.F., Vanhaecke, F., Henriet, J.P., Wheeler, A.J., School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Renard Centre of Marine Geology, Universiteit Gent = Ghent University [Belgium] (UGENT), Flanders Marine Institute, VLIZ, Southampton Geology & Geophysics, National Oceanography Centre (NOC), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Senckenberg am Meer, Abteilung für Meeresforschung, Marine Geology, Royal Netherlands Institute for Sea Research (NIOZ), Interactions et dynamique des environnements de surface (IDES), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut d'Astronomie et de Géophysique Georges Lemaître (UCL-ASTR), Université Catholique de Louvain = Catholic University of Louvain (UCL), Dpt of Analytical Chemistry, and Gent University

Subjects
[SDU.STU]Sciences of the Universe [physics]/Earth Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

35. Slug control in cabbage using nematode Phasmarhabditis hermaphrodita Schneider

Author

Grubišić, D., Gotlin Ćuljak, T., Stojnić, B., Brmež, M., Benković-Lalić T and Gent University

Subjects
fungi, Arion lusitanicus, cabbage, Deroceras reticulatum, slug control, Phasmarhabditis hermaphrodita
Abstract

Vegetable crops, more than other agricultural crops, suffer a great damages caused by slugs. Current control methods rely on chemical molluscicides that are often ineffective and harmful to non-target organisms, specially Carabids. Parasitic nematode Phasmarhabditis hermaphrodita parasites many slugs and snails and has been formulated as biological molluscicide. The main objectives of this investigation were to establish the effectiveness of P. hermaphrodita applied in recommended and in half the recommended rate (separate and in combination by half rate of metaldehyde), so as of metaldehyde and methiocarb, in standard rates, in slug control in greenhouse cabbage. Slug species determined in cabbage crop were Arion lusitanicus Mabille, 1868 and Deroceras reticulatum Müller, 1774. Investigation was conducted from March 30 to May 5 2010. Nematodes suspension was applied by watering can fitted with a rose. Pellets were broadcasted by hand. The percetage of slug damage per plant was recorded 7, 9, 16, 22, 30 and 37 days after treatment and data were subjected to ANOVA and Duncan's MRT (P=0.05). All treatments were significantly different from the control from the first week to 22 days after treatment. At the end of the experiment, significantly the best efficacy was obtained by the recommended dose of P. hermaphrodita. Treatments with half the recommended dose of P. hermaphrodita, separate and in combination by half rate of metaldehyde, and recommended rate of metaldehyde did not differ significantly. Methiocarb was significantly less effective than P. hermaphrodita and metaldehyde. The use of standard dose of P. hermaphrodita in greenhouse cabbage provide high protection from slugs to harvest and, what is of the great importance, as biological control agent is not harmful to non-target organisms.

Published
2012

36. The importance of the terrigenous fraction within a cold-water coral mound : A case study

Author

Christophe Colin, Hans Pirlet, Kris Latruwe, Frank Vanhaecke, Dominique Blamart, Anneleen Foubert, Norbert Frank, Rudy Swennen, Jean-Pierre Henriet, Veerle A.I. Huvenne, David Van Rooij, Mieke Thierens, Renard Centre of Marine Geology, Universiteit Gent = Ghent University (UGENT), Interactions et dynamique des environnements de surface (IDES), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Dpt of Analytical Chemistry, RCMG Ghent, Department of Earth and Environmental Sciences, K.U. Leuven, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Paléocéanographie (PALEOCEAN), Dpt of Geology & Geophysics, National Oceanography Centre (NOC), Gent University, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Subjects
010506 paleontology, Challenger Mound, EUROPEAN CONTINENTAL-MARGIN, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Cold-water coral mound, 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, LATE QUATERNARY SEDIMENTS, Sedimentary depositional environment, ROCKALL TROUGH, Geochemistry and Petrology, IRISH ICE-SHEET, Deglaciation, Glacial period, Sedimentology, North Altantic, 0105 earth and related environmental sciences, Terrigenous sediment, Porcupine Seabight, NORTHERN PORCUPINE SEABIGHT, Sediment, Geology, Last Glacial Maximum, HEINRICH LAYERS, Clay mineralogy, IODP EXP. 307, deep-sea corals, LAST GLACIAL MAXIMUM, 13. Climate action, Earth and Environmental Sciences, NE ATLANTIC, CARBONATE MOUND, Interglacial, Sr and Nd isotopes
Abstract

International audience; In the nineties, cold-water coral mounds were discovered in the Porcupine Seabight (NE Atlantic. west of Ireland). A decade later, this discovery led to the drilling of the entire Challenger cold-water coral mound (Eastern slope, Porcupine Seabight) during IODP Expedition 307. As more than 50% of the sediment within Challenger Mound consists of terrigenous material, the terrigenous component is equally important for the build-up of the mound as the framework-building corals. Moreover, the terrigenous fraction contains important information on the dynamics and the conditions of the depositional environment during mound development. In this study, the first in-depth investigation of the terrigenous sediment fraction of a cold-water coral mound is performed, combining clay mineralogy, sedimentology, petrography and Sr-Nd-isotopic analysis on a gravity core (MD01-2451G) collected at the top of Challenger Mound. Sr- and Nd-isotopic fingerprinting identifies Ireland as the main contributor of terrigenous material in Challenger Mound. Besides this, a variable input of volcanic material from the northern volcanic provinces (Iceland and/or the NW British Isles) is recognized in most of the samples. This volcanic material was most likely transported to Challenger Mound during cold climatic stages. In three samples, the isotopic ratios indicate a minor contribution of sediment deriving from the old cratons on Greenland, Scandinavia or Canada. The grain-size distributions of glacial sediments demonstrate that ice-rafted debris was deposited with little or no sorting, indicating a slow bottom-current regime. In contrast, interglacial intervals contain strongly current-sorted sediments, including reworked glacio-marine grains. The micro textures of the quartz-sand grains confirm the presence of grains transported by icebergs in interglacial intervals. These observations highlight the role of ice-rafting as an important transport mechanism of terrigenous material towards the mound during the Late Quaternary. Furthermore, elevated smectite content in the siliciclastic, glaciomarine sediment intervals is linked to the deglaciation history of the British-Irish Ice Sheet (BIIS). The increase of smectite is attributed to the initial stage of chemical weathering processes, which became activated following glacial retreat and the onset of warmer climatic conditions. During these deglaciations a significant change in the signature of the detrital fraction and a lack of coral growth is observed. Therefore, we postulate that the deglaciation of the BUS has an important effect on mound growth. It can seriously alter the hydrography, nutrient supply and sedimentation processes, thereby affecting both sediment input and coral growth and hence, coral mound development. (C) 2011 Elsevier B.V. All rights reserved.

Published
2011

37. The Istanbul consensus workshop on embryo assessment: proceedings of an expert meeting

Author

Santiago Munné, L.A. Scott, Alan R. Thornhill, Lisa Cowan, Gloria Calderón, David K. Gardner, Jonathan Van Blerkom, Thorir Hardarson, Daniel R. Brison, Johan Smitz, Thomas Ebner, Basak Balaban, James Catt, Etienne Van den Abbeel, Kersti Lundin, M. Cristina Magli, Dominique Royere, Sharon T. Mortimer, Joe Conaghan, David Mortimer, Assisted Reproduction Unit, American Hospital, Department of Reproductive medicine, St Marys Hospital, Instituo Valenciano de Infertilitad (IVI), Melbourne IVF, Pacific Fertility Centre, Victoria Fertility Centre, IVF Unit, Landes Frauen & Kinderklin, Department of Zoology, University of Melbourne, Fertilitetscentrum, Sahlgrenska University Hospital, SISMER, Oozoa Biomedical Inc, Reprogenetics, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Service de Médecine et Biologie de la Reproduction, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Fertility Centre of New England, Vrije Universiteit [Brussels] (VUB), Department of Molecular, Cellular & Developmental Biology, University of Colorado [Boulder], Rose Medicine Centre, Rose Mecicine Centre, Gent University Hospital, IBSA Institut Biochimique SA, Ferring International, Merck Serono SA, Alpha and ESHRE, Sahlgrenska University Hospital [Gothenburg], Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Brussel (VUB), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Department of Embryology and Genetics, Follicle Biology, and ProdInra, Archive Ouverte

Subjects
Minimum Data Set, medicine.medical_specialty, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], animal structures, assisted conception, Standardization, business.industry, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], Rehabilitation, Treatment outcome, Obstetrics and Gynecology, embryo, Embryo, Embryo grading, Embryo morphology, consensus meeting, Terminology, Reproductive Medicine, Current practice, embryonic structures, medicine, Medical physics, embryo assessment, business, oocyte
Abstract

Background: Many variations in oocyte and embryo grading make inter-laboratory comparisons extremely difficult. This paper reports the proceedings of an international consensus meeting on oocyte and embryo morphology assessment. Methods: Background presentations about current practice were given. Results: The expert panel developed a set of consensus points to define the minimumcriteria for oocyte and embryomorphology assessment. Conclusions: It is expected that the definition of common terminology and standardization of laboratory practice related to embryo morphology assessment will result in more effective comparisons of treatment outcomes. This document is intended to be referenced as a global consensus to allow standardized reporting of the minimum data set required for the accurate description of embryo development.

Published
2011

38. Intermolecular interaction studies using small volumes

Author

Bourry, David, Sinnaeve, Davy, Gheysen, Katelijne, Fritzinger, Bernd, Vandenborre, Gianni, van Damme, Els J M, Wieruszeski, Jean-Michel, Lippens, Guy, Ampe, Christophe, Martins, José C, Department of organic Chemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Molecular Biotechnology, 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), Department of Biochemistry, Department of Medical Protein Research, VIB-Gent University, Ghent University [Belgium] (UGENT), 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), Universiteit Gent = Ghent University (UGENT), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Universiteit Gent = Ghent University (UGENT)-VIB

Subjects
Phosphatidylinositol 4,5-Diphosphate, Profilins, Magnetic Resonance Spectroscopy, Molecular Structure, Polysaccharides, Lectins, Temperature, Humans, Reference Standards, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ligands, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience; We present the use of 1-mm room-temperature probe technology to perform intermolecular interaction studies using chemical shift perturbation methods and saturation transfer difference (STD) spectroscopy using small sample volumes. The use of a small sample volume (5-10 µl) allows for an alternative titration protocol where individual samples are prepared for each titration point, rather than the usual protocol used for a 5-mm probe setup where the ligand is added consecutively to the solution containing the protein or host of interest. This allows for considerable economy in the consumption and cost of the protein and ligand amounts required for interaction studies. For titration experiments, the use of the 1-mm setup consumes less than 10% of the ligand amount required using a 5-mm setup. This is especially significant when complex ligands that are only available in limited quantities, typically because they are obtained from natural sources or through elaborate synthesis efforts, need to be investigated. While the use of smaller volumes does increase the measuring time, we demonstrate that the use of commercial small volume probes allows the study of interactions that would otherwise be impossible to address by NMR.

Published
2011

39. Screening of Genes Encoding Adhesion Factors and Biofilm Formation in Staphylococcus aureus Isolates from Poultry

Author

Mostafa Nemati, Katleen Hermans, Luc Devriese, Freddy Haesebrouck, Dominiek Maes, Pathology, Bacteriology and Avian Diseases, Universiteit Gent = Ghent University [Belgium] (UGENT), Bacteriology, Ilam university, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, and Gent University

Subjects
Staphylococcus aureus, Meticillin, 040301 veterinary sciences, Virulence, Drug resistance, Biology, medicine.disease_cause, Microbiology, Bacterial genetics, 0403 veterinary science, 03 medical and health sciences, Food Animals, medicine, Animals, Adhesins, Bacterial, 0303 health sciences, General Immunology and Microbiology, 030306 microbiology, Biofilm, Life Sciences, 04 agricultural and veterinary sciences, Gene Expression Regulation, Bacterial, Staphylococcal Infections, Bacterial adhesin, Genes, Bacterial, Biofilms, Animal Science and Zoology, MSCRAMM, Chickens, medicine.drug
Abstract

Staphylococcus aureus isolates recovered from poultry between 1970 and 1972 (90 old isolates) and in 2006 (81 recent isolates) were screened for the presence of bap, icaA and icaD genes associated with biofilm formation, and for bbp, cna, ebpS, eno, fib, fnbA, fnbB, clfA and clfB genes that encode microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Most of the old isolates were collected from broiler breeders affected by staphylococcal tenosynovitis and arthritis, whilst nearly all recent isolates were derived from the nose and cloaca of healthy broilers. Ten recent isolates belonged to the animal-associated methicillin-resistant S. aureus (MRSA) ST398. All isolates were positive for clfA, clfB, eno and fnbA, and were negative for bap and bbp. All recent isolates were also positive for ebpS and cna, and all old isolates were positive for fib. The average number of genes encoding adhesins and biofilm-associated proteins in both groups was eight per isolate. All MRSA ST398 isolates in this study were positive for icaD, cna, ebpS, eno, fnbA, fnbB, clfA and clfB. No relevant differences were found between the presence of adhesin and biofilm formation genes in old and recent S. aureus isolates or in isolates from healthy compared with diseased chickens. From this study, there is no indication that the presence of these genes has changed over time and no specific association could be found between the presence of certain MSCRAMM or biofilm genes in poultry S. aureus isolates and the isolate's capacity to cause disease.

Published
2009

40. Differential response of phytoplankton to additions of nitrogen, phosphorus and iron in Lake Tanganyika

Author

Luc André, Wim Vyverman, Laurent Y. Alleman, Jean-Pierre Descy, Aaike De Wever, D. Langlet, Christine Cocquyt, Koenraad Muylaert, Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre for Energy and Environment (CERI EE), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Web Scale Trustworthy Collaborative Service Systems (COAST), 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 Networks, Systems and Services (LORIA - NSS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Gent University, Department of Biology, Research Institute for Nature and Forest (INBO), K.U. LEUVEN, Section de Pétrographie-Minéralogie-Géochimie, Musée royal de l'Afrique centrale, École des Mines de Douai (Mines Douai EMD), Institut Mines-Télécom [Paris] (IMT), CERM, University of Liege, Institute of Chemistry, CERM, Royal Museum for Central Africa [Tervuren] (RMCA), Limnology Unit - Department of Biology, Universiteit Gent = Ghent University [Belgium] (UGENT), Domein van Bouchout, National Botanic Garden of Belgium, Laboratory of Protistology and Aquatic Ecology, University of Gent, Centre for Energy and Environment (CERI EE - IMT Nord Europe), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Nord Europe), 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), and 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)

Subjects
0106 biological sciences, Cyanobacteria, 010504 meteorology & atmospheric sciences, biology, 010604 marine biology & hydrobiology, Phosphorus, [SDV]Life Sciences [q-bio], fungi, chemistry.chemical_element, Aquatic Science, biology.organism_classification, 01 natural sciences, Nitrogen, 6. Clean water, Nutrient, chemistry, Productivity (ecology), [SDU]Sciences of the Universe [physics], Environmental chemistry, Phytoplankton, Botany, Green algae, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Hydrobiology
Abstract

SUMMARY 1. In order to evaluate limitation of different phytoplankton groups by inorganic nutrients, multiple nutrient enrichment bioassays using the addition of iron (Fe) and the combined addition of nitrogen and phosphorus (NP) were carried out in the north and the south of Lake Tanganyika during the rainy and dry seasons in 2003 and 2004. 2. Nutrient additions resulted in an increase in phytoplankton growth rate relative to control treatments in all experiments. HPLC pigment data and epifluorescence microscopy counts indicated differential stimulation of the dominant phytoplankton groups. Iron additions mainly stimulated prokaryotic picophytoplankton, while enrichments with nitrogen and phosphorus stimulated green algae and in some cases diatoms. Extended incubation (3 days) indicated co-limitation of Fe and NP, in particular for picocyanobacteria.

Published
2007

41. Building on the concept for marine biological valuation with respect to translating it to a practical protocol: Viewpoints derived from a joint ENCORA-MARBEF initiative

Author

Derous, S., Austen, M., Claus, S., Daan, N., Dauvin, Jean-Claude, Deneudt, K., Depestele, J., Desroy, N., Heessen, H., Hostens, K., Marboe, A.H., Lescrauwaet, A.K., Moreno, M., Moulaert, I., Paelinckx, D., Rabaut, M., Rees, H., Ressurreição, A., Roff, J., Talhadas Santos, P., Speybroeck, J., Willem, E., Stienen, M., Tatarek, A., Hofstede R., Ter, Vincx, M., Zarzycki, T., Degraer, S., Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), Synthèses sélective organique et produits naturels (SSOPN), Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Gent University, Department of Biology, and Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord])

Subjects
ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2007

42. Porcupine Basin and Rockall Trough, off Western Ireland, September 7 - 11, 2001: Cruise Report MD123-Géosciences Leg 2, part GEOMOUND

Author

van Rooij, David, Blamart, Dominique, Unnithan, Vikram, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Renard Centre for Marine Geology (RCMG). Gent University, Belgium, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment
Published
2001

43. Terrestrial and submarine evidence for the extent and timing of the Last Glacial Maximum and the onset of deglaciation on the maritime-Antarctic and sub-Antarctic islands

Author

Hodgson, Dominic A., Graham, Alastair G.C., Roberts, Stephen J., Bentley, Michael J., Cofaigh, Colm Ó, Verleyen, Elie, Vyverman, Wim, Jomelli, Vincent, Favier, Vincent, Brunstein, Daniel, Verfaillie, Deborah, Colhoun, Eric A., Saunders, Krystyna M., Selkirk, Patricia M., Mackintosh, Andrew, Hedding, David W., Nel, Werner, Hall, Kevin, McGlone, Matt S., Van der Putten, Nathalie, Dickens, William A., Smith, James A., Natural Environment Research Council (NERC), Biological and Biomedical Sciences, Glasgow Caledonian University (GCU), Protistology and Aquatic Ecology, Ghent University, Universiteit Gent = Ghent University [Belgium] (UGENT), Gent University, Department of Biology, Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Geography, Ghent University, Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Earth and Climate

Subjects
TIERRA-DEL-FUEGO, MARION-ISLAND, Sub-Antarctica, Antarctic ice sheet, [SDE.MCG]Environmental Sciences/Global Changes, Climate, NEW-ZEALAND, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, FALKLAND-ISLANDS, SOUTHERN INDIAN-OCEAN, ENVIRONMENTAL-CHANGE, Quaternary, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, 910 Geography & travel, 550 Earth sciences & geology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, MACQUARIE-ISLAND, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Deglaciation, Global and Planetary Change, CLIMATE-CHANGE, Biology and Life Sciences, Geology, Maritime Antarctica glaciation, HEARD ISLAND, [SDU]Sciences of the Universe [physics], [SDE]Environmental Sciences, KERGUELEN-ISLANDS
Abstract

This paper is the maritime and sub–Antarctic contribution to the Scientific Committee for Antarctic Research (SCAR) Past Antarctic Ice Sheet Dynamics (PAIS) community Antarctic Ice Sheet reconstruction. The overarching aim for all sectors of Antarctica was to reconstruct the Last Glacial Maximum (LGM) ice sheet extent and thickness, and map the subsequent deglaciation in a series of 5000 year time slices. However, our review of the literature found surprisingly few high quality chronological constraints on changing glacier extents on these timescales in the maritime and sub–Antarctic sector. Therefore, in this paper we focus on an assessment of the terrestrial and offshore evidence for the LGM ice extent, establishing minimum ages for the onset of deglaciation, and separating evidence of deglaciation from LGM limits from those associated with later Holocene glacier fluctuations. Evidence included geomorphological descriptions of glacial landscapes, radiocarbon dated basal peat and lake sediment deposits, cosmogenic isotope ages of glacial features and molecular biological data. We propose a classification of the glacial history of the maritime and sub–Antarctic islands based on this assembled evidence. These include: (Type I) islands which accumulated little or no LGM ice; (Type II) islands with a limited LGM ice extent but evidence of extensive earlier continental shelf glaciations; (Type III) seamounts and volcanoes unlikely to have accumulated significant LGM ice cover; (Type IV) islands on shallow shelves with both terrestrial and submarine evidence of LGM (and/or earlier) ice expansion; (Type V) Islands north of the Antarctic Polar Front with terrestrial evidence of LGM ice expansion; and (Type VI) islands with no data. Finally, we review the climatological and geomorphological settings that separate the glaciological history of the islands within this classification scheme.

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44. Phase 2 study of the antitumour activity and safety of simlukafusp alfa (FAP-IL2v) combined with atezolizumab in patients with recurrent and/or metastatic cervical squamous cell carcinoma.

Author

Verlingue L, Italiano A, Prenen H, Guerra Alia EM, Tosi D, Perets R, Lugowska I, Moiseyenko V, Gumus M, Arslan C, Lindsay CR, Deva S, Taus Á, Oaknin A, Rottey S, Cicin I, Goksu SS, Smolin A, Roselló-Keränen S, Habigt C, Marbach D, Boetsch C, Dejardin D, Sleiman N, Evers S, Richard M, Ardeshir C, Charo J, Kraxner A, Teichgräber V, Keshelava N, and Dziadziuszko R

Abstract

Background: Simlukafusp alfa (FAP-IL2v) is an immune cytokine engineered to selectively promote immune responses in the tumour microenvironment. We evaluated the antitumour activity and safety of FAP-IL2v plus atezolizumab in recurrent and/or metastatic cervical squamous cell carcinoma (SCC) in a phase 2 basket study (NCT03386721)., Methods: Patients with confirmed metastatic, persistent or recurrent cervical SCC who had progressed on ≥1 anti-cancer therapy and had measurable disease were enrolled. FAP-IL2v 10 mg was administered once every 3 weeks (Q3W) or once weekly (QW) for 4 weeks then once every 2 weeks (Q2W) with the corresponding Q3W or Q2W atezolizumab regimens. The primary endpoint was objective response rate by investigator assessment., Findings: Forty-eight patients were enrolled (Q3W: n = 47; QW/Q2W: n = 1). Among 45 response evaluable patients, objective responses occurred in 12 patients (27%; CI 16.0-41.0), including 3 complete and 9 partial responses. Responses occurred in 6/19 PD-L1 positive patients (32%; 95% CI 15.4-54.0) and 5/24 PD-L1 negative patients (21%; 95% CI 9.2-35.6). Median duration of response was 13.3 months (95% CI 7.6-NE). Median progression-free survival was 3.7 months (95% CI 3.3-9.0). Adverse events (AEs) were consistent with the known safety profile of each drug. AEs leading to withdrawal of either agent occurred in 6 patients (13%). Pronounced expansion and activation of natural killer and CD8 T cells in peripheral blood and increased tumour infiltration and inflammation were observed., Interpretation: FAP-IL2v plus atezolizumab is clinically active and has manageable safety in patients with recurrent and/or metastatic cervical SCC., Funding: F. Hoffmann-La Roche Ltd., Competing Interests: Declaration of interests L. Verlingue reports grants from Bristol-Myers Squibb; royalties or licenses from RESOLVED; payment or honoraria from Bristol-Myers Squibb; leadership or fiduciary role as CEO of RESOLVED; stock or stock options from RESOLVED; as part of the Drug Development Department (DITEP) of Gustave Roussy and Early Phase Unit of Centre Léon Bérard, L. Verlingue reports being Principal/Sub-Investigator of clinical trials for AbbVie, Adaptimmune, Aduro Biotech, Agios Pharmaceuticals, Amgen, argenx, Arno Therapeutics, Astex Pharmaceuticals, AstraZeneca, AVEO pharmaceuticals, Basilea Pharmaceutica, Bayer, BBB Technologies, BeiGene, Blueprint Medicines, Boehringer Ingelheim, Boston Pharmaceuticals, Bristol-Myers Squibb, Celgene Corporation, Chugai Pharmaceutical Co., Clovis Oncology, Cullinan-Apollo, Daiichi Sankyo, Debiopharm, Eisai, Eli Lilly, Exelixis, Faron Pharmaceuticals, F. Hoffmann-La Roche, Forma Therapeutics, GamaMabs Pharma, Genentech, GlaxoSmithKline, H3 Biomedicine, ImCheck Therapeutics, Innate Pharma, Institut De Recherche Pierre Fabre, Iris Servier, Janssen Pharmaceuticals, Kura Oncology, Kyowa Kirin, Loxo Oncology, Lytix Biopharma, Medimmune, Menarini Ricerche, Merck Sharpe & Dohme, Merrimack Pharmaceuticals, Merus, Millennium Pharmaceuticals, Molecular Partners, Nanobiotix, Nektar Therapeutics, Novartis, Octimet Oncology, Oncoethix, Oncopeptides, Orion Pharma, Ose Pharma, Pfizer, PharmaMar, Pierre Fabre, Medicament, Sanofi, Seattle Genetics, SOTIO, Servier, Syros Pharmaceuticals, Taiho Pharma, Tesaro, and Xencor; research grants from AstraZeneca, Bristol-Myers Squibb, Boehringer Ingelheim, Janssen Pharmaceuticals, Merck Sharpe & Dohme, Novartis, Onxeo, Pfizer, Roche, and Sanofi; non-financial support (drug supplied) from AstraZeneca, Bayer, Bristol-Myers Squibb, Boehringer Ingelheim, Medimmune, Merck Sharpe & Dohme, NH TherAGuiX, Onxeo, and Pfizer. H. Prenen reports payment or honoraria for presentations from Amgen, AstraZeneca, Bayer, Roche, and Sanofi; support for attending meetings from AstraZeneca, Bayer, and Roche; personal fees for participation on a Data Safety Monitoring Board or Advisory Board for Biocartis and Cureteq. E. M. Guerra Alia reports personal consulting fees for AstraZeneca, Clovis Oncology, GlaxoSmithKline, Merck Sharpe & Dohme, PharmaMar, and Roche; payment or honoraria from AstraZeneca (personal), Clovis Oncology, GlaxoSmithKline, Merck Sharpe & Dohme, and PharmaMar; personal payment for expert testimony from AstraZeneca, Clovis Oncology, GlaxoSmithKline, Merck Sharpe & Dohme, PharmaMar, and Roche; personal support for attending meetings and/or travel from AstraZeneca and GlaxoSmithKline. R. Perets reports personal consulting fees for 1Etx, Galmed Therapeutics, and Gilboa Therapeutics; payment or honoraria from Merck Sharpe & Dohme; support for attending meetings and/or travel from Pfizer. I Lugowska reports grants or contracts from Agenus and Roche; personal payment or honoraria from Bristol-Myers Squibb, Novartis, and Merck Sharpe & Dohme; support for attending a meeting and/or travel from ESMO; other financial interests or non-financial interests from Clinnote. A. Taus reports payment or honoraria from AstraZeneca, Bristol-Myers Squibb, GlaxoSmithKline, Merck Sharpe & Dohme, Pfizer, Roche, Sanofi, and Takeda. A. Oaknin reports institutional funding from AbbVie, Advaxis, Aeterna Zentaris, Amgen, Aprea Therapeutics, Bristol-Myers Squibb, Clovis Oncology, Eisai, Immunogen, Merck Sharpe & Dohme, Millennium Pharmaceuticals, PharmaMar, Regeneron Pharmaceuticals, Roche, and Tesaro; personal fees for participation on an Advisory Board from Agenus, AstraZeneca, Clovis Oncology, Corcept Therapeutics, Deciphera Pharmaceuticals, Eisai, EMD Serono, Genmab, GlaxoSmithKline, ImmunoGen, Itheos, Merck Sharpe & Dohme, Mersana Therapeutics, Novocure, OneXerna Therapeutics, PharmaMar, Regeneron, Roche, Sattucklabs, Seagen, and Sutro Biopharm. S. Goksu reports institutional payment or honoraria from Bristol-Myers Squibb, Merck Sharpe & Dohme, Novartis, and Pfizer; participation on a Data Safety Monitoring Board or Advisory Board from Novartis and Pfizer. S. Roselló-Keränen reports personal payment or honoraria for presentations from Amgen, Merck Sharpe & Dohme, and Servier; personal fees for participation on an Advisory Board from Pierre Fabre and Sirtex. R. Dziadziuszko reports personal consulting fees from AstraZeneca, Bristol-Myers Squibb, Merck Sharpe & Dohme, Pfizer, Novartis, Roche, and Takeda; payment or honoraria from AstraZeneca, Amgen, Pfizer, Novartis, Roche, and Takeda; support for attending meetings and or travel from Pfizer; receipt of equipment, materials, drugs, medical writing, gifts, or other services from Novartis and Pfizer. C. Habigt is a Roche employee with stock options. D. Marbach is a Roche employee. C. Boetsch is a Roche employee with stock options. D. Dejardin is a Roche employee with patents/stocks. N. Sleiman is a Roche employee. S. Evers is a former Roche employee and current shareholder. M. Richard is a Roche employee with stock options. C. Ardeshir is a Roche employee and shareholder. J. Charo is a Roche employee with patents/stocks. A. Kraxner is a Roche employee with stocks and stock options. V. Teichgräber is a Roche employee with stock options. N. Keshelava is a Roche employee with stock options. A. Italiano, D. Tosi, V. Moiseyenko, M. Gumus, C. Arslan, C. Lindsay, S. Deva, S. Rottey, I. Cicin, and A. Smolin have no disclosures to report., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Published
2024
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45. Effects of per- and polyfluoroalkyl substances on the liver: Human-relevant mechanisms of toxicity.

Author

Maerten A, Callewaert E, Sanz-Serrano J, Devisscher L, and Vinken M

Abstract

Per- and polyfluoroalkyl substances (PFAS) are abundantly used in a plethora of products with applications in daily life. As a result, PFAS are widely distributed in the environment, thus providing a source of exposure to humans. The majority of human exposure to PFAS is attributed to the human diet, which encompasses drinking water. Their chemical nature grants persistent, accumulative and toxic properties, which are currently raising concerns. Over the past few years, adverse effects of PFAS on different organs have been repeatedly documented. Numerous epidemiological studies established a clear link between PFAS exposure and liver toxicity. Likewise, effects of PFAS on liver homeostasis, lipid metabolism, bile acid metabolism and hepatocarcinogenesis have been reported in various in vitro and in vivo studies. This review discusses the role of PFAS in liver toxicity with special attention paid to human relevance as well as to the mechanisms underlying the hepatotoxic effects of PFAS. Future perspectives and remaining knowledge gaps were identified to enhance future PFAS risk assessment., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Published
2024
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46. Approaching ramp lesions from the different world of posterior knee compartment: A review of evidence with a proposal of a new classification and treatment.

Author

Keyhani S, Mirahmadi A, Maleki A, Vosoughi F, Verdonk R, LaPrade RF, Landreau P, and Movahedinia M

Abstract

Ramp lesions (RLs) are peripheral lesions that occur in the posterior part of the medial meniscus or where it attaches to the joint capsule. The classification of the medial meniscus RLs has been the focus of numerous studies and publications. This review provides an overview of RL's current classification and treatment options in anterior cruciate ligament deficient knees. The study also aims to present a more practical classification system for RLs to assist in treatment decision-making. For the first time, we also presented a new surgical treatment for incomplete inferior and double-complete RL based on the posterior knee arthroscopy that provides direct access to the posterior meniscal borders, enabling effective treatment and stronger biomechanical repair., Level of Evidence: Level V., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Journal of Experimental Orthopaedics published by John Wiley & Sons Ltd on behalf of European Society of Sports Traumatology, Knee Surgery and Arthroscopy.)

Published
2024
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47. Auditory-motor synchronization in developmental coordination disorder: Effects on interlimb coordination during walking and running.

Author

Goetschalckx M, Feys P, Rameckers E, Moens B, Leman M, and Moumdjian L

Subjects
Humans, Child, Male, Female, Psychomotor Performance physiology, Gait physiology, Walking physiology, Running physiology, Motor Skills Disorders physiopathology
Abstract

Developmental coordination disorder (DCD) presents challenges in motor control. DCD affects tasks such as walking and running and is characterized by poor interlimb coordination and increased spatiotemporal variability compared to typically developing children (TDC). While auditory rhythm synchronization has shown to have benefits for gait performance in adults, its impact on children with DCD during walking and running remains unclear. This study investigated auditory-motor synchronization and interlimb coordination during walking and running in children with and without DCD. Twenty-one DCD and 23 TDC participants aged 8-12 years walked and ran to two different auditory metronomes (discrete and continuous). Synchronization consistency was the primary outcome, with interlimb coordination and spatiotemporal variability as secondary outcomes. Results showed that children with DCD exhibited significantly lower synchronization consistency than TDC, particularly during running. The metronome structure did not influence synchronization ability. Additionally, interlimb coordination differed significantly between DCD and TDC during running and was not impacted by auditory-motor synchronization. Spatiotemporal variability was higher in DCD during both walking and running than in TDC, and accentuated during running. Variability of cadence was influenced by the use of continuous metronomes, which may offer potential benefits in reducing cadence variability., (© 2024 The Author(s). Annals of the New York Academy of Sciences published by Wiley Periodicals LLC on behalf of The New York Academy of Sciences.)

Published
2024
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48. Hidden gems: Scattered knowledge hampered freshwater jellyfish research over the past one-and-a-half centuries.

Author

Lüskow F, Bezio N, Caputo L, Chi X, Dumont HJ, Karunarathne KD, López-González PJ, Mańko MK, Marchessaux G, Suzuki KS, and Pakhomov EA

Abstract

Freshwater jellyfish (= limnic medusa-budding hydrozoans, FWJ) are a small group of cnidarians found on all continents except Antarctica in temperate to tropical latitudes. Members of this group belong primarily to three genera: Astrohydra , Craspedacusta , and Limnocnida . While Astrohydra and Limnocnida are typically restricted to the islands of Japan, Africa, and the Indian subcontinent, one species or potential species complex, Craspedacusta sowerbii , became globally invasive. Despite research going back about one-and-a-half centuries, little is known about their phylogeny and ecology compared to marine jellyfish. Recent species distribution modelling, however, showed that by 2050, C. sowerbii will potentially extend their distribution ranges due to global warming to high-latitude ecosystems and be present (medusa stage) for an extended time in the seasonal limnic production cycle. An increase in their relative ecological importance with temporal and spatial spreading is hypothesised. Only recently, it has been shown that the trophic roles of polyps and medusae and their prey overlap with other ecosystem members. In addition, medusa behaviour may cause trophic cascades and alter vertical nutrient distributions. However, polyps and other benthic life cycle stages are understudied. In globally, changing freshwater ecosystems that may become more accommodating for FWJ, an improved understanding of their population biology and ecosystem ecology is urgently needed. In this integrative review, we, therefore, explore reasons for the hampered historical research progress, contrast developments with those of marine cnidarians, compile and publish alongside an extensive and unprecedented literature database, and formulate avenues for future directions in FWJ research., Competing Interests: The authors declare that there is no conflict of interest., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Published
2024
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49. Protocol for a Validation Study of an Ontology of Administrable Dose Forms of Medicinal Products.

Author

Roumier J, Vander Stichele RH, van Nimwegen D, and Kalra D

Subjects
Humans, Pharmaceutical Preparations, Natural Language Processing, Vocabulary, Controlled, Systematized Nomenclature of Medicine
Abstract

Administrable dose form can be obtained after (no-)transformation from pharmaceutical dose form. Building on the creation of a small ontology of 428 pharmaceutical dose forms from EDQM to support alignment with other dose form ontologies (SNOMED-CT, RxNorm), the present study is focused on a simple ontology of 308 administrable dose forms, 27 Intended Sites and an intermediary level of 65 dose form groupers. The ontology was created after 432 pharmaceutical dose forms, 65 combined pharmaceutical dose forms and 73 combined terms were linked by EDQM to administrable dose forms during the UNICOM project. The article describes these resources, the resulting ontology, the differences between its top-level concepts and the source's. It presents the protocol for a validation study through expert review, as a preparation for use case studies.

Published
2024
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50. How do we make progress in phenotyping patients with lower urinary tract such as overactive bladder and underactive detrusor, including using urine markers and microbiome data, to personalize therapy? ICI-RS 2023-Part 2.

Author

Finazzi Agrò E, Rosato E, Wagg A, Sinha S, Fede Spicchiale C, Serati M, Mancini V, de Rijk M, Tarcan T, Wein A, Abrams P, and Bou Kheir G

Subjects
Humans, Microbiota, Lower Urinary Tract Symptoms physiopathology, Lower Urinary Tract Symptoms diagnosis, Lower Urinary Tract Symptoms microbiology, Urodynamics, Urinary Bladder, Overactive physiopathology, Urinary Bladder, Overactive microbiology, Urinary Bladder, Overactive diagnosis, Phenotype, Biomarkers urine, Precision Medicine, Urinary Bladder, Underactive physiopathology, Urinary Bladder, Underactive diagnosis
Abstract

Introduction: Overactive bladder (OAB) and underactive bladder (UAB) could be associated with metabolic syndrome, affective disorders, sex hormone deficiency, changes in urinary microbiota, functional gastrointestinal disorders, or autonomic nervous system dysfunction., Objectives: The aim of this Think Tank was to provide a guide on how to investigate OAB and/or detrusor underactivity (DU) patients to better clarify the underlying pathophysiology and possibly personalize the treatment., Methods: A compendium of discussion based on the current evidence related to phenotyping patients with OAB or DU using urodynamic tests, functional neuro-imaging, urinary markers, and microbiome., Results and Conclusions: The article emphasizes the critical significance of adopting a comprehensive yet tailored approach to phenotyping patients with lower urinary tract (LUT) symptoms, such as OAB and UAB. The intricate interplay between the LUT and various factors, metabolic, neurological, psychological, and gastrointestinal can define unique LUT profiles, enabling personalized therapies to replace the one-size-fits-all approach., (© 2024 Wiley Periodicals LLC.)

Published
2024
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