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15 results on '"ANRT, France."'

1. Learning-Enhanced Adaptive Robust GNSS Navigation in Challenging Environments

Author

Yi Ding, Paul Chauchat, Gael Pages, Philippe Asseman, Département Electronique, Optronique et Signal (DEOS), Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO), Airbus Operation S.A.S., Airbus [France], Institut d'Électronique et des Technologies du numéRique (IETR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Airbus SAS and ANRT, France, Cifre [2019/1073], Airbus (FRANCE), Institut Supérieur de l'Aéronautique et de l'Espace - ISAE-SUPAERO (FRANCE), and CentraleSupélec (FRANCE)

Subjects
Control and Optimization, GNSS, Mechanical Engineering, Biomedical Engineering, Computer Science Applications, Human-Computer Interaction, Machine Learning, [SPI]Engineering Sciences [physics], Artificial Intelligence, Control and Systems Engineering, machine learning for robot control, Localization, probability and statistical methods, Traitement du signal et de l'image, Computer Vision and Pattern Recognition, Robust Statistics
Abstract

International audience; Global Navigation Satellite System (GNSS) is the widely used technology when it comes to outdoor positioning. But it has severe limitations with regard to safety-critical applications involving unmanned autonomous systems. Namely, the positioning performance degrades in harsh propagation environment such as urban canyons. In this letter we propose a new algorithm for GNSS navigation in challenging environments based on robust statistics. M-estimators showed promising results in this context, but are limited by some fixed hyper-parameters. Our main idea is to adapt this parameter, for the Huber cost function, to the current environment in a data-driven manner. Doing so, we also present a simple yet efficient way of learning with satellite data, whose number may vary over time. Focusing the learning problem on a single parameter enables to efficiently learn with a lightweight neural network. The generalization capability and the positioning performance of the proposed method are evaluated in multiple contexts scenarios (open-sky, trees, urban and urban canyon), with two distinct GNSS receivers, and in an airplane ground inspection scenario. The maximum positioning error is reduced by up to 68% with respect to M-estimators.

Published
2022

2. Assessment of fungal and thermo-alkaline post-treatments of solid digestate in a recirculation scheme to increase flexibility in feedstocks supply management of biogas plants

Author

Aude Bertrandias, Julie Jimenez, Ulysse Brémond, Nicolas Bernet, Denis Loisel, Jean-Philippe Steyer, Hélène Carrère, Air Liquide, Centre de Recherche Claude-Delorme, Paris-Saclay, France., Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and National Research and Technology Association (ANRT, France) PhD grant (reference CIFRE N° 2016/0617)

Subjects
020209 energy, 02 engineering and technology, Raw material, 7. Clean energy, Methane, Solid digestate recirculation, chemistry.chemical_compound, Biogas, Anaerobic digestion, 0202 electrical engineering, electronic engineering, information engineering, 0601 history and archaeology, Organic matter, Fungal post-treatment, 2. Zero hunger, chemistry.chemical_classification, 060102 archaeology, Renewable Energy, Sustainability and the Environment, [SDE.IE]Environmental Sciences/Environmental Engineering, 06 humanities and the arts, Pleurotus ostreatus, Biodegradation, Thermo-alkaline post-treatment, Pulp and paper industry, chemistry, Solid-state fermentation, Agricultural biogas plant, Digestate, Environmental science
Abstract

Agricultural biogas plants can suffer occasional feedstock shortages (poor harvest, storage …) and recirculation of solid digestate (SD) into digester has been identified as a simple way to offset methane production loss from these situations. Calculations show that recirculation of SD could offset for losses in plant methane production by up to 2.4%. In that context, two post-treatments were evaluated to enhance residual potential methane of agricultural SD. Effect of fungal solid state fermentation (SSF) of SD on subsequent methane production has never been explored before. It was hypothesized that: (i) ligninolytic fungi would be able to specifically use the complex fraction of SD for their growth and (ii) energy generation from the subsequent anaerobic digestion of the colonized SD will be enhanced. However, experiments showed that thermo-alkaline treatment of SD (used as alkalinization and sterilization process) and a high spawn level (20% w/w) were necessary to perform fungal SSF. Besides, the observed fungal activities on SD did not target specifically the most complex fractions. This led to uncontrolled organic matter losses and subsequent decreases of biodegradability and methane yield of SD (up to 50%). Therefore, fungal SSF of SD before its recirculation into biogas plants appeared not to be a viable option. Only thermo-alkaline treatment (CaO 2% w/w and 121 °C 30 min) enhanced methane yield of SD by 13% and decreased its complex fraction by 25%. Further studies on optimization of this post-treatment may enhance efficiency of SD recirculation strategy to offset plant methane production losses.

Published
2020

3. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction: Sequence-structure characteristics of VHH domains

Author

Melarkode Vattekatte, Akhila, Shinada, Nicolas Ken, Narwani, Tarun, Noël, Floriane, Bertrand, Olivier, Meyniel, Jean-Philippe, Malpertuy, Alain, Gelly, Jean-Christophe, Cadet, Frédéric, De Brevern, Alexandre, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
Frameworks, Structural alphabet, [SDV]Life Sciences [q-bio], complementarity determining regions, Bioinformatics Keywords Secondary structure, Sequence structure relationship, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, secondary structure, Subjects Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], nanobodies, Antibodies
Abstract

International audience; Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only 3 CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with other important features, e.g. easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationships. In this study sequence, characteristics of VHH have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHHs showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

Published
2020

4. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Author

Melarkode Vattekatte, Akhila, Shinada, Nicolas Ken, Narwani, Tarun, Noël, Floriane, Bertrand, Olivier, Meyniel, Jean-Philippe, Malpertuy, Alain, Gelly, Jean-Christophe, Cadet, Frédéric, de Brevern, Alexandre, de Brevern, Alexandre G., Université de Paris - - Université de Paris2018 - ANR-18-IDEX-0001 - IDEX - VALID, Université Sorbonne Paris Cité - - USPC2011 - ANR-11-IDEX-0005 - IDEX - VALID, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], complementarity determining regions, Bioinformatics Keywords Secondary structure, secondary structure, Subjects Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], nanobodies, [SDV] Life Sciences [q-bio], frameworks, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, antibodies, structural alphabet, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, sequence structure relationship
Abstract

International audience; Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only 3 CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with other important features, e.g. easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationships. In this study sequence, characteristics of VHH have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHHs showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

Published
2020

5. A structural entropy index to analyse local conformations in intrinsically disordered proteins: IDP PBs

Author

Melarkode Vattekatte, Akhila, Narwani, Tarun Jairaj, Floch, Aline, Maljković, Mirjana, Bisoo, Soubika, Shinada, Nicolas, Kranjc, Agata, Gelly, Jean-Christophe, Srinivasan, Narayanaswamy, Mitić, Nenad, de Brevern, Alexandre, de Brevern, Alexandre G., Université de Paris - - Université de Paris2018 - ANR-18-IDEX-0001 - IDEX - VALID, Université Sorbonne Paris Cité - - USPC2011 - ANR-11-IDEX-0005 - IDEX - VALID, Institut National de la Transfusion Sanguine [Paris] (INTS), Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Belgrade, Faculty of Mathematics, Molecular Biophysics Unit, Indian Institute of Science, Discngine S.A.S [Paris], Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. c2013037147 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., Conseil Régional Ile de France. INTS (SESAME Grant)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
flexibility, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], rigidity, protein structures, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, structural alphabet, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, entropy, Condensed Matter::Disordered Systems and Neural Networks, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; Sequence – structure – function paradigm has been revolutionized by the discovery of disordered regions and disordered proteins more than two decades ago. While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. The definition of disordered regions is more complex as in these same X-ray structures; it is associated to the position of missing residues. Thus a continuum so seems to exist between rigidity, flexibility and disorder. However, it had not been precisely described. In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disordered proteins in our study.

Published
2020

6. Living concrete: Democratizing living walls

Author

Gilles Lecomte, Benjamin Riley, Valéry Malécot, Isabelle Dubois-Brugger, Hervé Lequay, François de Larrard, Modèles et simulations pour l'Architecture et le Patrimoine (MAP), Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Lafarge Centre de Recherche [Lyon] (Lafarge LCR Lyon), Lafarge, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), French Government, ANRT, France (French National Association of Research and Technology) through its CIFRE (systemof industrial agreements for training through research) program, LafargeHolcim, France, UMR-3495 MAP-ARIA laboratory (Models and Simulations for Architecture, Urbanism and Landscape Applications and Research in Computer Science for Architecture) of the CNRS, France (research unit of the French National Center for Scientific Research) at ENSAL, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)

Subjects
Conservation of Natural Resources, Architectural engineering, Environmental Engineering, 010504 meteorology & atmospheric sciences, Population, 010501 environmental sciences, 01 natural sciences, Irrigation water, [SPI.MAT]Engineering Sciences [physics]/Materials, 11. Sustainability, Environmental Chemistry, Construction system innovation, Fertilizers, education, Waste Management and Disposal, 0105 earth and related environmental sciences, education.field_of_study, Living concrete, Construction Materials, [SDE.IE]Environmental Sciences/Environmental Engineering, Green infrastructure, Pollution, Living wall technologies, [SDE.ES]Environmental Sciences/Environmental and Society, Transplantation, Constructability, Green wall integrated systems, Cost analysis, Environmental science, Facade, Cost of living, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Living walls can help bring nature to urban canyons. However, contemporary living walls are cost prohibitive and made of materials with shorter life spans than their buildings. High cost often restricts their use to luxury applications promoting ecological symbolism rather than impactful propagation of urban nature. This study shows an approach to lowering living wall costs and increasing their use by integrating them into the building's structure. Existing living wall systems are hung like curtains from a building's façade; they are made as light as possible to reduce the weight they superimpose. Their lighter materials, e.g., felts and plastics, limit their life cycle. Conversely, combining the living function with the exterior envelope will match a living wall's life cycle to its building, and cost diminishes by eliminating a living wall's secondary support structure. This study focuses on concrete construction, a typology needing ecological evolution. Chosen for its ubiquity, durability, affordability, and plasticity, concrete was tested as a potential growing medium for plants. The result of the study is a new living concrete material and system aimed at advancing biophilic design in cities facing shifting climates and population densification. Presented are a new cast-in-place living wall system, a new concrete and its mechanical properties, verification of constructability, identification of plants suitable to cementitious environments, indoor germination and growth, full-scale tests of a new construction methodology, how concrete's chemical composition affects irrigation water, outdoor germination and perenniality, and a cost analysis showing a 50% reduction to the installed cost of living walls. Cost savings include plants grown from seed-in-situ (eliminating raising plants in a nursery and transplantation), and not using fertilizer (eliminating chemicals and a fertigation system). This study shows how rethinking the current living wall paradigm could shift the industry toward solutions to democratize living walls via lower cost and permanence.

Published
2019

7. The Autophagic Flux Inhibitor Bafilomycine A1 Affects the Expression of Intermediary Metabolism-Related Genes in Trout Hepatocytes

Author

Sarah Séité, Tracy Pioche, Nicolas Ory, Elisabeth Plagnes-Juan, Stéphane Panserat, Iban Seiliez, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Evonik Rexim, Evonik Nutrition and care, and The authors acknowledge Evonik Industries and Agence National de la Recherche et de la Technologie (ANRT, France) for the scholarship to SS (CIFRE Ph.D. Research Grant)

Subjects
0301 basic medicine, autophagy, Physiology, hépatocyte, autophagie, lcsh:Physiology, 03 medical and health sciences, 0302 clinical medicine, métabolisme intermédiaire, poisson, Physiology (medical), Gene expression, Biologie animale, medicine, hepatocyte, 14. Life underwater, Original Research, Animal biology, fish, biology, lcsh:QP1-981, Endoplasmic reticulum, [SDV.BA]Life Sciences [q-bio]/Animal biology, Autophagy, intermediary metabolism, biology.organism_classification, Cell biology, ER stress, gene expression, Trout, 030104 developmental biology, medicine.anatomical_structure, Hepatocyte, Unfolded protein response, stress environnemental, Flux (metabolism), 030217 neurology & neurosurgery, Intracellular, expression des gènes
Abstract

Autophagy is an evolutionarily conserved process of cellular self-eating which emerged these last years as a major adaptive metabolic response to various stresses such as fasting, hypoxia, or environmental pollutants. However, surprisingly very few data is currently available on its role in fish species which are directly exposed to frequent environmental perturbations. Here, we report that the treatment of fasted trout hepatocytes with the autophagy inhibitor Bafilomycine A1 lowered the mRNA levels of many of the gluconeogenesis-related genes and increased those of genes involved in intracellular lipid stores. Concurrently, intracellular free amino acid levels dropped and the expression of the main genes involved in the endoplasmic reticulum (ER) stress exhibited a sharp increase in autophagy inhibited cells. Together these results highlight the strong complexity of the crosstalk between ER, autophagy and metabolism and support the importance of considering this function in future studies on metabolic adaptation of fish to environmental stresses.

Published
2019

8. A structural entropy index to analyse local conformations in intrinsically disordered proteins

Author

Nicolas K. Shinada, Alexandre G. de Brevern, Nenad S. Mitić, Melarkode Vattekatte Akhila, Mirjana Maljković, Agata Kranjc, Tarun Jairaj Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Soubika Bisoo, Aline Floch, Institut National de la Transfusion Sanguine [Paris] (INTS), Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Belgrade, Faculty of Mathematics, Molecular Biophysics Unit, Indian Institute of Science, Discngine S.A.S [Paris], Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. c2013037147 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., Conseil Régional Ile de France. INTS (SESAME Grant)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), and Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP)

Subjects
Physics, 0303 health sciences, Structural entropy, Local conformation, Protein Conformation, 030302 biochemistry & molecular biology, Intrinsically disordered proteins, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Condensed Matter::Disordered Systems and Neural Networks, Intrinsically Disordered Proteins, flexibility, 03 medical and health sciences, Generalized entropy index, Protein structure, rigidity, Structural Biology, protein structures, Entropy (information theory), structural alphabet, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Structural alphabet, Statistical physics, entropy, 030304 developmental biology
Abstract

International audience; Sequence – structure – function paradigm has been revolutionized by the discovery of disordered regions and disordered proteins more than two decades ago. While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. The definition of disordered regions is more complex as in these same X-ray structures; it is associated to the position of missing residues. Thus a continuum so seems to exist between rigidity, flexibility and disorder. However, it had not been precisely described. In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disordered proteins in our study.

Published
2020

9. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Author

Frédéric Cadet, Nicolas K. Shinada, Olivier Bertrand, Floriane Noël, Alexandre G. de Brevern, Alain Malpertuy, Jean-Christophe Gelly, Jean-Philippe Meyniel, Tarun Jairaj Narwani, Akhila Melarkode Vattekatte, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
Bioinformatics, Computer science, [SDV]Life Sciences [q-bio], Structural alphabet, In silico, Bioinformatics Keywords Secondary structure, Discrete analysis, lcsh:Medicine, Complementarity determining region, Computational biology, Subjects Biochemistry, Biochemistry, Antibodies, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Secondary structure, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein secondary structure, Complementarity determining regions, 030304 developmental biology, 0303 health sciences, Heavy chain, Frameworks, General Neuroscience, lcsh:R, 030302 biochemistry & molecular biology, General Medicine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Template, Complementarity (molecular biology), Sequence structure relationship, Nanobodies, General Agricultural and Biological Sciences
Abstract

Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

Published
2020

10. Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber

Author

M. Salomez, Jérôme Sainte-Beuve, Laurent Vaysse, Jutharat Intapun, Françoise Granet, Frédéric Bonfils, T. Vallaeys, Eric Dubreucq, Sylvain Santoni, Maeva Subileau, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ecologie des systèmes marins côtiers (Ecosym), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Prince of Songkla University, Société Michelin, National Association for Research and Technology (ANRT, France), National Institute of Higher Studies in Agricultural Sciences (Montpellier SupAgro, France), French Agricultural Research Centre for International Development (CIRAD, France), Manufacture Francaise des Pneumatiques Michelin (France), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Prince of Songkla University (PSU), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0301 basic medicine, K50 - Technologie des produits forestiers, para rubber (tree), Applied Microbiology and Biotechnology, chemistry.chemical_compound, hevea brasiliensis, Food science, 2. Zero hunger, latex, 000 - Autres thèmes, General Medicine, Biodiversity, Lactic acid, Actinobacteria, visual_art, Propriété technologique, visual_art.visual_art_medium, Aeration, Biotechnology, microbiologie végétale, F60 - Physiologie et biochimie végétale, Plant Exudates, 030106 microbiology, rubber, microbial communities, natural rubber, Biology, 03 medical and health sciences, Natural rubber, caoutchouc, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Propriété physicochimique, Coagulation, Bacteria, Flore microbienne, maturation, Fungi, biology.organism_classification, lactic acid bacteria, 030104 developmental biology, chemistry, Microbial population biology, Propriété mécanique, Pyrosequencing, Hevea, Hevea brasiliensis
Abstract

Aim: To characterize microbial communities present in natural rubber (NR) coagula from Hevea brasiliensis latex during maturation and identify microbial taxa (bacteria and fungi) having an impact on dry NR properties. Methods and Results: Microbial community dynamics in NR coagula maturated under controlled conditions were compared and related with the evolution of dry NR properties. The pyrosequencing of 16S (119 837 effective reads) and 18S (131 879 effective reads) rRNA gene regions was performed on 21 samples covering different maturation times and two aeration conditions. Results showed a relatively high bacterial richness (Chao1 estimates of 200–1000) associated with significant bacterial dynamics. Lactic acid bacteria (LAB) were dominant in the first days of maturation. Then, in aerobic conditions, development of Actinobacteria represented by the family Microbacteriaceae was associated with alkalinization of the samples and a higher sensitivity of NR to thermo-oxidation as evaluated by its plasticity retention index (PRI). In anaerobiosis, the reduced development of bacteria, mostly LAB present, was associated with improved NR properties (higher initial plasticity P0 and PRI). Conclusions: The involvement of micro-organisms in the evolution of dry NR properties during the maturation of NR coagula was confirmed. The importance of the structure and dynamics of microbial communities is specifically highlighted. Significance and Impact of the Study: Natural rubber is a key elastomer for the tyre industry and for a variety of other applications. The majority of raw NR is obtained by natural coagulation of H. brasiliensis latex under the activity of micro-organisms. An improved understanding of the microbial communities involved in the maturation of NR coagula may lead to an improvement in the production process of raw NR to provide a better consistency in NR quality. (Resume d'auteur)

Published
2018

11. Validity and sensitivity of the longitudinal asymmetry index to detect gait asymmetry using Microsoft Kinect data

Author

Justin Cobb, Victoria Manning, Jean Meunier, Franck Multon, Edouard Auvinet, The Sackler Trust, MSk Lab, Imperial College London, Analysis-Synthesis Approach for Virtual Human Simulation (MIMETIC), Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-MEDIA ET INTERACTIONS (IRISA-D6), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire Mouvement Sport Santé (M2S), École normale supérieure - Cachan (ENS Cachan)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut de génie biomédical [Montreal] (IGB), Université de Montréal (UdeM), This work was funded by the Wellcome Trust and EPSRC grant number 088844/Z/09/Z and the Association nationale de la recherche et de la technologie (ANRT) (France) for the Conventions Industrielles de Formation par la REcherche (CIFRE) 146/2009 funding., Université de Rennes 2 (UR2)-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), École normale supérieure - Cachan (ENS Cachan)-Université de Rennes (UR)-Université de Brest (UBO)-Université de Rennes 2 (UR2)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
Male, SYMMETRY, 01 natural sciences, 0302 clinical medicine, Gait (human), Reference Values, Image Processing, Computer-Assisted, Orthopedics and Sports Medicine, Computer vision, Asymmetry Index, Treadmill, Gait, media_common, 1106 Human Movement And Sports Science, Rehabilitation, [INFO.INFO-MM]Computer Science [cs]/Multimedia [cs.MM], Biomechanical Phenomena, Female, Gait analysis, Psychology, Sensitivity analysis, CRP, Life Sciences & Biomedicine, WALKING, STROKE, 0913 Mechanical Engineering, Adult, Correlation coefficient, media_common.quotation_subject, Biophysics, Motion capture, Asymmetry, Sensitivity and Specificity, 03 medical and health sciences, Gait asymmetry, Humans, Sensitivity (control systems), Simulation, Science & Technology, Kinect, business.industry, 010401 analytical chemistry, Neurosciences, Reproducibility of Results, 1103 Clinical Sciences, BILATERAL COORDINATION, 0104 chemical sciences, Orthopedics, OSTEOARTHRITIS, Exercise Test, Artificial intelligence, Neurosciences & Neurology, business, LENGTH DISCREPANCY, 030217 neurology & neurosurgery, Software, Sport Sciences
Abstract

International audience; Gait asymmetry information is a key point in disease screening and follow-up. Constant Relative Phase (CRP) has been used to quantify within-stride asymmetry index, which requires noise-free and accurate motion capture, which is difficult to obtain in clinical settings. This study explores a new index, the Longitudinal Asymmetry Index (ILong) which is derived using data from a low-cost depth camera (Kinect). ILong is based on depth images averaged over several gait cycles, rather than derived joint positions or angles. This study aims to evaluate 1) the validity of CRP computed with Kinect, 2) the validity and sensitivity of ILong for measuring gait asymmetry based solely on data provided by a depth camera, 3) the clinical applicability of a posteriorly mounted camera system to avoid occlusion caused by the standard front-fitted treadmill consoles and 4) the number of strides needed to reliably calculate ILong. The gait of 15 subjects was recorded concurrently with a marker-based system (MBS) and Kinect, and asymmetry was artificially reproduced by introducing a 5cm sole attached to one foot. CRP computed with Kinect was not reliable. ILong detected this disturbed gait reliably and could be computed from a posteriorly placed Kinect without loss of validity. A minimum of five strides was needed to achieve a correlation coefficient of 0.9 between standard MBS and low-cost depth camera based ILong. ILong provides a clinically pragmatic method for measuring gait asymmetry, with application for improved patient care through enhanced disease, screening, diagnosis and monitoring.

Published
2016

12. Effectiveness of modified yeast cell wall extracts to reduce aflatoxin B1 absorption in dairy ewes

Author

Diego P. Morgavi, Alexandros Yiannikouris, Hamid Boudra, Stéphane Firmin, Unité de Recherches sur les Herbivores (URH), Institut National de la Recherche Agronomique (INRA), Alltech-France, Alltech Inc, Partenaires INRAE, and S. Firmin was supported by a doctoral fellowship (CIFRE 1058/2007) jointly financed by Alltech and Association Nationale de la Recherche Technique (ANRT, France). The authors greatly thank J. P. Jouany (INRA, Centre de Clermont-Theix, Saint Genes-Champanelle, France) for helpful discussions during the experimental set up, C. Mathevon and the staff of the animal experimental facilities of the INRA's Herbivores Research Unit for animal care, and D. Alvarez (INRA, Centre de Clermont-Theix, Saint Genes-Champanelle, France) for help in sample analysis.

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, aflatoxins, Aflatoxin, Aflatoxin B1, Time Factors, food science and technology, 040301 veterinary sciences, dairy and animal science, Agriculture, Dairy & Animal Science, Food Science & Technology, Urine, Absorption (skin), Biology, dairy sheep, Absorption, 0403 veterinary science, Excretion, Cell wall, Eating, 0404 agricultural biotechnology, Cell Wall, Yeasts, Genetics, Animals, Lactation, Food science, extract, paroie cellulaire, Feces, agriculture, 2. Zero hunger, Sheep, Body Weight, food and beverages, yeast cell wall, 04 agricultural and veterinary sciences, 040401 food science, Yeast, Diet, Dairying, Milk, Female, excretion, Animal Science and Zoology, Composition (visual arts), Food Science
Abstract

International audience; This study investigated the effect of a modified yeast cell wall extract preparation (YCW) on the excretion of aflatoxin B1 (AFB1) and aflatoxin M1 (AFM1) in feces, urine, and milk of dairy ewes fed an aflatoxin-contaminated diet. Sixteen ewes in mid-lactation were assigned to 4 treatment groups: control, AF (60 mu g of AFB1/kg of feed), YCW (2 g/kg of feed), and AF+YCW. The trial consisted of a short-term (3-d) exposure period followed by a long-term (21-d) exposure period. At the end of each exposure period, milk, urine, and feces were collected over 72 h. The treatments did not affect feed intake, milk production, milk composition, or body weight. The presence of AFM1 was detected in all matrices, whereas AFB1 was only present in feces. Daily excretion was higher following long-term exposure and reached 26.9 mu g of AFB1/d in feces, 37.2 mu g of AFM1/d in feces, and 10.7 mu g of AFM1/d in urine. Supplementation with YCW was effective in increasing aflatoxin excretion in feces in the long-term exposure (up to 156% increase). The effect was accompanied by a trend of decreasing urinary excretion of AFM1. In contrast, the addition of YCW to the contaminated diet did not affect the transfer of aflatoxins from feed to milk under the present experimental conditions with low-producing ewes. The transfer rates of AFM1 in milk ranged from 0.24 to 0.54%. In conclusion, feed supplementation with YCW reduced the absorption of AFB1 and increased the elimination of AFB1 and AFM1 in ewe feces. Yeast cell wall extract could be used to protect ruminants from chronic exposure to aflatoxins present in feeds.

Published
2011

13. Guidelines in the experimental validation of a 3D heat and fluid flow model of keyhole laser welding

Author

Mikhaël Balabane, Philippe Masson, Mickael Courtois, Muriel Carin, Sadok Gaied, Institut de Recherche Dupuy de Lôme (IRDL), Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS), Université Paris 13 (UP13), and ArcelorMittal Global RandD and ANRT (France)

Subjects
fluid flow, Level set method, Acoustics and Ultrasonics, Computer science, 02 engineering and technology, 01 natural sciences, experimental validation, heat transfer, 0103 physical sciences, Fluid dynamics, Fluid queue, 010302 applied physics, Jet (fluid), Computer simulation, Laser beam welding, [CHIM.MATE]Chemical Sciences/Material chemistry, Mechanics, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, numerical simulation, keyhole, Heat transfer, laser welding, 0210 nano-technology, Keyhole
Abstract

During the past few years, numerous sophisticated models have been proposed to predict in a self-consistent way the dynamics of the keyhole, together with the melt pool and vapor jet. However, these models are only partially compared to experimental data, so the reliability of these models is questionable. The present paper aims to propose a more complete experimental set-up in order to validate the most relevant results calculated by these models. A complete heat transfer and fluid flow three-dimensional (3D) model is first proposed in order to describe laser welding in keyhole regimes. The interface is tracked with a level set method and fluid flows are calculated in liquid and gas. The mechanisms of recoil pressure and keyhole creation are highlighted in a fusion line configuration chosen as a reference. Moreover, a complete validation of the model is proposed with guidelines on the variables to observe. Numerous comparisons with dedicated experiments (thermocouples, pyrometry, high-speed camera) are proposed to estimate the validity of the model. In addition to traditional geometric measurements, the main variables calculated, temperatures, and velocities in the melt pool are at the center of this work. The goal is to propose a reference validation for complex 3D models proposed over the last few years.

Published
2016

14. Time course and amplitude of DNA methylation in the shoot apical meristem are critical points for bolting induction in sugar beet and bolting tolerance between genotypes

Author

Claude Joseph, Claire Hébrard, Franck Brignolas, Clément Lafon-Placette, Marc Lefebvre, Alain Delaunay, Daniel Hagège, Steve Barnes, Marie-Véronique Trap-Gentil, Stéphane Maury, Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), Institut National de la Recherche Agronomique (INRA), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), SES Vanderhave, Partenaires INRAE, SES-VanderHave, Belgium [M-VT-G, CH], 'Conseil Regional de la Region Centre', France, Ministere de l'Enseignement Superieur et de la Recherche, and ANRT, France [0379/2008]

Subjects
0106 biological sciences, Time Factors, bolting, Physiology, HYPOMETHYLATION, [SDV]Life Sciences [q-bio], DNMT, LINES, Plant Science, 01 natural sciences, Gene Expression Regulation, Plant, DNA (Cytosine-5-)-Methyltransferases, Plant Proteins, Genetics, 0303 health sciences, Bolting, DNA methylation, VERNALIZATION INSENSITIVE 3 (VIN3), food and beverages, Methylation, Vernalization, Adaptation, Physiological, Cold Temperature, VERNALIZATION, Sugar beet, Beta vulgaris, DNA (Cytosine-5-)-Methyltransferase 1, EXPRESSION, FLOWERING TIME, GENES, Genotype, Meristem, Molecular Sequence Data, Beta vulgaris altissima (sugar beet), FLOWERING LOCUS C (FLC), LOCUS-C FLC, Flowers, Biology, McrBC, DEMETHYLATION, Cytosine, 03 medical and health sciences, Botany, bisulfite, RNA, Messenger, Epigenetics, devernalization, PLANT, 030304 developmental biology, Base Sequence, fungi, biology.organism_classification, ARABIDOPSIS-THALIANA, Biennial plant, 010606 plant biology & botany
Abstract

International audience; An epigenetic control of vernalization has been demonstrated in annual plants such as Arabidopsis and cereals, but the situation remains unclear in biennial plants such as sugar beet that has an absolute requirement for vernalization. The role of DNA methylation in flowering induction and the identification of corresponding target loci also need to be clarified. In this context, sugar beet (Beta vulgaris altissima) genotypes differing in bolting tolerance were submitted to various bolting conditions such as different temperatures and/or methylating drugs. DNA hypomethylating treatment was not sufficient to induce bolting while DNA hypermethylation treatment inhibits and delays bolting. Vernalizing and devernalizing temperatures were shown to affect bolting as well as DNA methylation levels in the shoot apical meristem. In addition, a negative correlation was established between bolting and DNA methylation. Genotypes considered as resistant or sensitive to bolting could also be distinguished by their DNA methylation levels. Finally, sugar beet homologues of the Arabidopsis vernalization genes FLC and VIN3 exhibited distinct DNA methylation marks during vernalization independently to the variations of global DNA methylation. These vernalization genes also displayed differences in mRNA accumulation and methylation profiles between genotypes resistant or sensitive to bolting. Taken together, the data suggest that the time course and amplitude of DNA methylation variations are critical points for the induction of sugar beet bolting and represent an epigenetic component of the genotypic bolting tolerance, opening up new perspectives for sugar beet breeding.

Published
2011

15. Availability of essential amino acids, nutrient utilisation and growth in juvenile black tiger shrimp, Penaeus monodon, following fishmeal replacement by plant protein

Author

Sadasivam Kaushik, Vincent Rigolet, Anne Surget, Inge Geurden, Lenaïg Richard, Nutrition, Métabolisme, Aquaculture (NUMEA), Institut National de la Recherche Agronomique (INRA), Aqualma, UNIMA, and The authors acknowledge Frederic Terrier and Peyo Aguirre for their help during diet manufacturing and to Marie Jo Borthaire and Vincent Michel for assistance with the laboratory analyses. Special thanks are due to Christian Ramamonjisoa (Aqualma facility) for his technical assistance. L. R., S. K. and I. G designed the study. L. R. did the data analysis. L. R., S. K. and I. G contributed to the drafting of the paper. A. S. did the AA analyses. L. R. and V. R. contributed to the organisation of the experiment in Madagascar. There are no contractual agreements for the presented data which might cause conflicts of interest. The authors acknowledge UNIMA and institutional funds from INRA for funding this study and ANRT (France) for the scholarship to L.R. (CIFRE PhD Research Grant).

Subjects
Aquatic Science, Penaeus monodon, 03 medical and health sciences, Nutrient, Fish meal, Animal science, plant protein, farine de poisson, Dry matter, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Meal, biology, fishmeal, fungi, 04 agricultural and veterinary sciences, biology.organism_classification, Shrimp, Biochemistry, Plant protein, digestibility, fisheries, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Corn gluten meal, shrimp, marine and freshwater biology, amino acid, penaeus monodon
Abstract

International audience; Two trials with juvenile black tiger shrimp (Penaeus monodon) were undertaken to study the effects of replacing fishmeal by different levels of plant proteins on growth performances and nutrient utilisation of shrimp in semi-intensive conditions (Expt. 1) and on the availability of dietary nitrogen (N) and amino acids (Expt. 2). Five isoproteic diets (on crude protein basis) were formulated to contain 34, 24, 16, 8, or 0% fishmeal, with fishmeal being replaced by a mixture of plant protein (corn gluten meal, wheat gluten, and rapeseed meal). In Expt. 1, the shrimp (initial body weight, IBW 1.5 ± 0.1 g) were reared in earthen ponds for 144 days and fed one of the experimental diets. Apparent digestibility of nutrients and AA were assessed in Expt. 2, using 150 L tanks and shrimp of 12.8 ± 0.4 g IBW. After 144 days in grow-out ponds, shrimp fed the diet with 24% of fishmeal had similar growth as those fed the control diet containing 34% fishmeal (0% replacement). When 50% or more of the fishmeal were replaced, weight gain as well as N and energy gains significantly decreased. Digestibility of dry matter, protein and energy was also significantly lower in all fishmeal-replaced diets. In particular, leucine digestibility decreased by 26% at 100% replacement, which was significantly correlated to an increased incorporation of corn gluten meal. Our data confirm the need to improve our knowledge on AA availability and raw material quality in order to improve fishmeal replacement in P. monodon diets.

Published
2011

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