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1. Experimental evidence for long-distance electrodynamic intermolecular forces

Author

Lechelon, Mathias, Meriguet, Yoann, Gori, Matteo, Ruffenach, Sandra, Nardecchia, Ilaria, Floriani, Elena, Coquillat, Dominique, Teppe, Frédéric, Mailfert, Sébastien, Marguet, Didier, Ferrier, Pierre, Varani, Luca, Sturgis, James, Torres, Jeremie, Pettini, Marco, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E7 Systèmes dynamiques : théories et applications, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut d’Electronique et des Systèmes (IES), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Howard University, Modélisation et Spectroscopie THz (MOST), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Excellence Initiative of Aix-Marseille University, European Commission, ANR, CNRS, Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 765426,TeraApps, European Project: 964203,FET-Open LINkS, Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 964203 (FET-Open LINkS project)., Pettini, Marco, Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID, and Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID

Subjects
Horizon 2020, Multidisciplinary, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Electrodynamical-Interactions, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, Biophysics (molecular), Quantum Biology, TeraHertz THz, Condensed Matter - Soft Condensed Matter, Biological Physics (physics.bio-ph), collective molecular oscillations, Terahertz spectroscopy, biophysics, Fluorescence Correlation Spectroscopy, Soft Condensed Matter (cond-mat.soft), Physical sciences — Condensed Matter Physics, European Union, Physics - Biological Physics, Physics - Atomic and Molecular Clusters, Electrodynamic intermolecular interactions, Atomic and Molecular Clusters (physics.atm-clus), Spectroscopy
Abstract

Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent experiments, on the basis of different physical effects detected by fluorescence correlation spectroscopy and terahertz spectroscopy, respectively, we demonstrate experimentally the activation of resonant electrodynamic intermolecular forces. This is an unprecedented experimental proof of principle of a physical phenomenon that, having been observed for biomacromolecules and with long-range action (up to 1000 Angstroms), could be of importance for biology. In addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space., 40 pages, 8 figures, Supplementary material for this article (additional data, theory and 4 movies) is available at https://www.science.org/doi/10.1126/sciadv.abl5855#con1

Published
2022

2. Second-order cone optimization of the gradostat

Author

Alain Rapaport, Josh A. Taylor, Department of Electrical and Computer Engineering [University of Toronto] (ECE), University of Toronto, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Labex NUMEV incorporated into the I-Site MUSE, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Natural Sciences and Engineering Research Council of Canada, French LabEx NUMEV (Project ANR-10 LABX-20), incorporated into the I-Site MUSE, and ANR-10-LABX-0020,NUMEV,ANR-10 LABX-20(2010)

Subjects
020209 energy, General Chemical Engineering, 02 engineering and technology, Gradostat, 020401 chemical engineering, Simple (abstract algebra), second-order cone programming, FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, biogas, Applied mathematics, Growth rate, 0204 chemical engineering, Diffusion (business), Mathematics - Optimization and Control, Mathematics, Steady state, convex relaxation, 6. Clean water, Computer Science Applications, Constraint (information theory), wastewater treatment, Cone (topology), Optimization and Control (math.OC), Outflow, Relaxation (approximation), [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract

International audience; The gradostat consists of multiple chemostats interconnected by mass flows and diffusion. It has been used to model biochemical systems such as wastewater treatment networks and microbial activity in soil. In this paper we maximize the production of biogas in a gradostat at steady state. The physical decision variables are the water, substrate, and biomass entering each tank and the flows through the interconnecting pipes. Our main technical focus is the nonconvex constraint describing microbial growth. We formulate a relaxation and prove that it is exact when the gradostat is outflow connected, its system matrix is irreducible, and the growth rate satisfies a simple condition. The relaxation has second-order cone representations for the Monod and Contois growth rates. We extend the steady state models to the case of multiple time periods by replacing the derivatives with numerical approximations instead of setting them to zero. The resulting optimizations are second-order cone programs, which can be solved at large scales using standard industrial software.

Published
2021

3. About frame estimation of growth functions and robust prediction in bioprocess modeling

Author

Emna Krichen, Alain Rapaport, Eric Fouilland, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), ADEME, Labex Numev, ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), LabeX NUMEV & ADEME, 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), ANR: 10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Rapaport, Alain, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro

Subjects
0209 industrial biotechnology, Mathematical optimization, Computer science, frame, [SDV]Life Sciences [q-bio], [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], growth functions, Biotechnologies, Functional estimation, Least square, 02 engineering and technology, Systèmes dynamiques, functional estimation, Industrial and Manufacturing Engineering, 020901 industrial engineering & automation, 020401 chemical engineering, intervals, Statistiques (Mathématiques), 0204 chemical engineering, Bioprocess, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, modélisation, biomathématique, robust prediction, estimation, Experimental data, Continuous mode, Interval observers, Growth functions, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Dynamical Systems, contrôle de bioprocédé, Computer Science Applications, [STAT]Statistics [stat], mathématiques appliquées, least square, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, Control and Systems Engineering, Modeling and Simulation, interval observers, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation
Abstract

International audience; We address the problem of determining functional framing from experimental data points in view of robust time-varying predictions, which is of crucial importance in bioprocess monitoring. We propose a method that provides guaranteed functional bounds, instead of sets of parameters values for growth functions such as the classical Monod or Haldane functions commonly used in bioprocess modeling. We illustrate the applicability of the method with bioreactor simulations in batch and continuous mode, as well as on real data. We also present two extensions of the method adding flexibility in its application, and discuss its efficiency in providing guaranteed state estimations.

Published
2020

4. Controlling recirculation rate for minimal-time bioremediation of natural water resources

Author

Alain Rapaport, P Víctor Riquelme, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Universidad Tecnica Federico Santa Maria [Valparaiso] (UTFSM), LabEx NUMEV, France incorporated into the I-Site MUSE, CONICYT, Chile : REDES 150011, FONDECYT, Chile : 1160204 3180367, BASAL program from CONICYT, Chile : CMM-AFB 170001, Labex NUMEV & I-Site MUSE, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)

Subjects
minimum-time control, feedback controller, bioreactor, environmental engineering, recirculation, 0209 industrial biotechnology, recirculation control, Mixing (process engineering), Environmental engineering, bioréacteur, 02 engineering and technology, 020901 industrial engineering & automation, Bioremediation, Optimization and Control, 0202 electrical engineering, electronic engineering, information engineering, Bioreactor, contrôle automatique, Optimisation et contrôle, Electrical and Electronic Engineering, Process engineering, business.industry, Natural water, 020208 electrical & electronic engineering, Optimal control, 6. Clean water, Volumetric flow rate, Water resources, mathématiques appliquées, Control and Systems Engineering, Environmental science, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], business
Abstract

International audience; We revisit the minimal time problem of in-situ decontamination of large water resources with a bioreactor, considering a recirculation flow rate in the resource as an additional control. This new problem has two manipulated inputs : the flow rate of the treatment in the bioreactor and the recirculation flow rate of the water resource between the pumping and reinjection locations. Although the velocity set of the dynamics is non convex, we show that the optimal control is reached among non-relaxed controls. The optimal strategy consists in three sequential steps: 1. do not mix and take the flow rate of treatment that maximizes the concentration decay in the resource. 2. mix as much as possible and carry on with the flow rate that maximizes the concentration decay. 3. carry on mixing but do not treat the water. Finally, we show on numerical simulations that a significant gain in processing time can be achieved time when controlling in addition the recirculation flow rate.

Published
2019

5. Optimal periodic control for scalar dynamics under integral constraint on the input

Author

Fatima Zahra Tani, Alain Rapaport, Térence Bayen, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), LabEx NUMEV incorporated into the I-Site MUSE (AAP2017- 2-08), French-Algerian AVERROES program of PhD 'bourses d'excellence', ANR: 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Labex NUMEV and I-Site MUSE (AAP2017- 2-08), Institut Montpelliérain Alexander Grothendieck ( IMAG ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie ( MISTEA ), Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), ANR : 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, 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), EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), 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), AVERROES program between Algeria and France, LabEx NUMEV incorporated into the I-Site MUSE : AAP2017-2-08, and ANR-16-CE04-0003,Thermomic,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes(2016)

Subjects
Discrete mathematics, [ MATH ] Mathematics [math], [ MATH.MATH-OC ] Mathematics [math]/Optimization and Control [math.OC], 0209 industrial biotechnology, 021103 operations research, Control and Optimization, Periodic solutions, Optimal Control, Applied Mathematics, Scalar (mathematics), 0211 other engineering and technologies, 02 engineering and technology, Optimal control, Pontryagin's minimum principle, Chemostat Model, 020901 industrial engineering & automation, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Over-yielding, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], [MATH]Mathematics [math], Pontryagin Maximum Principle, Mathematics
Abstract

This paper studies a periodic optimal control problem governed by a one-dimensional system, linear with respect to the control \begin{document}$ u $\end{document} , under an integral constraint on \begin{document}$ u $\end{document} . We give conditions for which the value of the cost function at steady state with a constant control \begin{document}$ \bar u $\end{document} can be improved by considering periodic control \begin{document}$ u $\end{document} with average value equal to \begin{document}$ \bar u $\end{document} . This leads to the so-called "over-yielding" met in several applications. With the use of the Pontryagin Maximum Principle, we provide the optimal synthesis of periodic strategies under the integral constraint. The results are illustrated on a single population model in order to study the effect of periodic inputs on the utility of the stock of resource.

Published
2018

6. Emplacements optimaux de rejets pour la recharge de réservoirs hydriques à l’aide d’eaux usées traitées - application au cas d’étude du lac de Jaunay

Author

Crespo Moya, Maria, Orsoni, Julien, Bortoli, Jérôme, Rapaport, Alain, Rousseau, Antoine, Jauzein, Vincent, Université de Montpellier (UM), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Vendée Eau, Littoral, Environment: MOdels and Numerics (LEMON), 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)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), SAUR - Direction de la Recherche et Développement, SAUR, Labex Numev, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie ( MISTEA ), Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Université de Montpellier ( UM ), Littoral, Environnement : Méthodes et Outils Numériques ( LEMON ), 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 ), Labex NUMEV, 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), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR: 10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)

Subjects
lac, [ MATH.MATH-OC ] Mathematics [math]/Optimization and Control [math.OC], modélisation informatique, water resources management, optimisation multiobjective, [SDE.IE]Environmental Sciences/Environmental Engineering, Mécanique des fluides, stratégie optimale, computational modelling, pollutant propagation, wastewater reuse, réutilisation des eaux usées traitées, gestion des ressources en eau, [ SDE.IE ] Environmental Sciences/Environmental Engineering, mathématiques appliquées, multi-objective optimization, [ SPI.FLUID ] Engineering Sciences [physics]/Reactive fluid environment, Optimization and Control, réutilisation des eaux usées, propagation de polluant, modélisation computationnelle, optimisation multi-objectif, Fluids mechanics, Optimisation et contrôle, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], eaux usées, modélisation
Abstract

In this work, we study optimal strategies of wastewater reuse for refilling a large hydric reservoir (such as lake, pond, lagoon…) which shows an alarming volume reduction due to the human water intake. To grasp the multiple issues to ascertain the appropriate location for the reused water discharge, computational modelling is particularly adapted for testing different conditions (physical, meteorological) and optimizing the system to achieve targets (maximum allowable concentration of pollutant for drinking water and recreational uses). We focus on modelling the distribution of a generic pollutant in the reservoir, which is expected to vary with time and space. The model assumes that the reservoir volume stays constant (because the flow rates at the refilling and removal points are considered to be quasi-identical), the density of the pollutant is smaller than that of the reservoir water (so that the pollutant remains at the top level of the water column) and its dynamics is influenced by two main effects: wind and water currents. The model accounts for the reservoir geometry, the operating conditions of the transfer pipes (input and output) and real data regarding chronicles of wind velocity and river flow. Then, we tackle a multi-optimization problem which aims to find optimal refilling locations which reduce the pollutant concentration at two strategic regions of the reservoir. A Pareto front is presented as a decision-tool to choose the optimal strategy according to different water quality criteria. The methodology has been applied in the case of Jaunay Lake, a water reservoir located on the French western coast., Dans ce travail, nous étudions des stratégies optimales de réutilisation d’eaux usées pour le remplissage d’un grand réservoir d’eau (lac, étang, lagune…), qui montre une réduction de volume alarmante due à la consommation humaine. Afin d’appréhender les multiples difficultés pour déterminer l'emplacement approprié du point de rejet, la modélisation computationnelle est particulièrement adaptée pour tester différentes conditions (physiques, météorologiques) et optimiser le système pour atteindre des cibles (concentration maximale du polluant pour de l'eau potable et des activités récréatives). Nous nous concentrons sur la modélisation de la distribution d'un polluant générique dans le réservoir qui varie en temps et en espace. Le modèle suppose que le volume du réservoir reste constant (en considérant que les débits aux points du rejet et de la prise d’eau sont quasiment identiques). La densité du polluant est supposée inférieure à celle de l'eau (donc le polluant reste à la surface de la colonne d’eau) et sa dynamique est influencée par deux effets principaux: les courants d’eau et le vent. Le modèle tient compte de la géométrie du réservoir, des conditions du pompage (en entrée et en sortie) et des données réelles concernant les chroniques du vent et du débit de la rivière. Ensuite, nous abordons un problème d’optimisation multi-objectifs qui vise à trouver des emplacements optimaux de recharge qui réduisent la concentration du polluant dans deux régions stratégiques du réservoir. Un front de Pareto est présenté comme un outil de décision qui permet de choisir la stratégie optimale en fonction des différents critères sur la qualité de l'eau. La méthodologie a été appliquée dans le cas du Lac de Jaunay, un réservoir d'eau situé sur la côte ouest française.

Published
2018

7. Dynamic Modeling and Identification of an Heterogeneously Actuated Underwater Manipulator Arm

Author

Francois Leborne, Ahmed Chemori, Vincent Creuze, Lorenzo Brignone, Département Systèmes Sous-Marins - IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Conception et commande de robots pour la manipulation (DEXTER), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ifremer (demi-bourse de thèse)Labex NUMEV (demi-bourse de thèse), and Collaboration Ifremer / LIRMM (co-financement Labex NUMEV)

Subjects
0209 industrial biotechnology, Computer science, Manipulator arm, Marine robotics, 02 engineering and technology, Kinematics, Linear actuator, Revolute joint, Remotely operated vehicle, System dynamics, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Vehicle dynamics, Computer Science::Robotics, Identification (information), 020901 industrial engineering & automation, Underwater vehicle, Control theory, Manipulator, Actuator, Underwater manipulation
Abstract

International audience; This paper deals with the dynamic modeling and identification of an electrically driven underwater robot ma-nipulator. The proposed study includes the dynamic modeling of the actuators of the arm as well as the identification of the parameters of the model. The proposed method deals with the specific case of heterogeneously actuated arms, namely arms with actuators behaving differently for each joint, being considered at the kinematic level. Indeed, we show how to estimate the arms parameters when some of their revolute joints are directly actuated by geared motors, while the others are actuated by linear actuators. A minimum set of identifiable parameters is determined, and adequate excitation trajectories are generated and used in the identification procedure. Real-time experimental validation on the manipulator arms of Ifremer's HROV (Hybrid Remotely Operated Vehicle) Ariane underwater vehicle demonstrates that the proposed method improves the estimation of the dynamic model.

Published
2018

8. The orientation of the stimulating bipolar probe modulates axono-cortical evoked potentials

Author

Schlosser-Perrin, Félix, Rossel, Olivier, Duffau, Hugues, Matsumoto, Riki, Mandonnet, Emmanuel, Bonnetblanc, François, CAMIN Team, INRIA, Montpellier, France (INRIA), Département de Neurochirurgie, Centre Hospitalier Universitaire de Montpellier Gui de Chauliac, Montpellier, France (CHU GC), Division of Neurology, Kobe University Graduate School of Medicine, Japan (KU), Service de neurochirurgie [AP-HP Hôpital Lariboisière], AP-HP Groupe Hospitalier Lariboisière, Research supported by French 'Association pour la Recherche sur le Cancer' (ARC-France, project n° ARCPGA12019110000940_1572), the LabEx NUMEV project (n°ANR- 10-LABX-0020) within the I-Site MUSE (ANR-16-IDEX-0006), and and INRIA through an associate team between France (FB) and Japan (RM). RM was supported by a Kobe University Strategic International Collaborative Research Grant (Type B Fostering Joint Research).

Subjects
[PHYS]Physics [physics], [SCCO]Cognitive science
Abstract

International audience

Published
2023

9. Solution landscapes in nematic microfluidics

Author

Angel M. Ramos, M. Crespo, Apala Majumdar, Ian M. Griffiths, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM), Department of Mathematical Sciences, Department of Mathematical Sciences, NMSU, Departamento de Matemática Aplicada & Instituto de Matemática Interisciplinar, Universidad Complutense de Madrid [Madrid] (UCM), Mathematical Institute, Radcliffe Observatory Quarter, University of Oxford, Spanish Ministry of Economy and Competitiveness : MTM2011-22658, MTM2015-64865-P, French Labex Numev at UMR MISTEA : APP2016-1-023, ANR-10-LABX-20, EPSRC : EP/J001686/1, EP/J001686/2 OCIAM, Advanced Studies Centre at Keble College, Royal Society, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), 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), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), University of Oxford [Oxford], French Labex Numev at UMR MISTEA : APP2016-1-023, and ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)

Subjects
Asymptotic analysis, 35B30, 35B35, 35B40, 35C20, 35Q35, 76A05, Inverse, FOS: Physical sciences, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, 01 natural sciences, Anchoring strength, 010305 fluids & plasmas, modèle mathématique, Mathematics - Analysis of PDEs, Liquid crystal, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0103 physical sciences, Calculus, FOS: Mathematics, applied mathematics, Sensitivity (control systems), QA, QC, Pressure gradient, Mathematics, Steady state, Leslie–Ericksen model, Mathematical analysis, Statistical and Nonlinear Physics, Function (mathematics), 021001 nanoscience & nanotechnology, Condensed Matter Physics, mathématiques appliquées, Flow (mathematics), Nematic microfluidics, Soft Condensed Matter (cond-mat.soft), 0210 nano-technology, mathematical model, Analysis of PDEs (math.AP)
Abstract

We study the static equilibria of a simplified Leslie--Ericksen model for a unidirectional uniaxial nematic flow in a prototype microfluidic channel, as a function of the pressure gradient $\mathcal{G}$ and inverse anchoring strength, $\mathcal{B}$. We numerically find multiple static equilibria for admissible pairs $(\mathcal{G}, \mathcal{B})$ and classify them according to their winding numbers and stability. The case $\mathcal{G}=0$ is analytically tractable and we numerically study how the solution landscape is transformed as $\mathcal{G}$ increases. We study the one-dimensional dynamical model, the sensitivity of the dynamic solutions to initial conditions and the rate of change of $\mathcal{G}$ and $\mathcal{B}$. We provide a physically interesting example of how the time delay between the applications of $\mathcal{G}$ and $\mathcal{B}$ can determine the selection of the final steady state.

Published
2016

10. Proposal for a protocol using an infrared microbolometer camera and wavelet analysis to study foot thermoregulation

Author

Hervé Louche, Vincent Serantoni, Franck Jourdan, Ariane Sultan, Gibier, François, Biomécanique des Interactions et de l'Organisation des Tissus et des Cellules (BIOTIC), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ThermoMécanique des Matériaux (ThM2), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and This work was supported by the LabEx NUMEV (2011-LABX-076) incorporated into the I-SITE MUSE

Subjects
[SPI.OPTI] Engineering Sciences [physics]/Optics / Photonic, Computer science, Measure (physics), Wavelet analysis, 030204 cardiovascular system & hematology, 01 natural sciences, 010309 optics, 03 medical and health sciences, 0302 clinical medicine, Wavelet, [SPI.MECA.BIOM] Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], 0103 physical sciences, Electrical and Electronic Engineering, motion correction, Instrumentation, [SPI.MECA.THER] Engineering Sciences [physics]/Mechanics [physics.med-ph]/Thermics [physics.class-ph], [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, Protocol (science), thermoregulation, skin temperature, Healthy subjects, [SPI.MECA.BIOM]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], Skin temperature, Microbolometer, Thermoregulation, thermal drift correction, microbolometer infrared camera, [SPI.MECA.THER]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Thermics [physics.class-ph], [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Foot (unit), Biomedical engineering
Abstract

International audience; Here we propose a protocol to: (i) generate skin temperature (SkT) oscillations on glabrous tissues (plantar foot) in healthy subjects under controlled clinical environment conditions; (ii) measure quantitative temperature fields with an inexpensive microbolometer 2 (MB) infrared camera in a clinical environment; and (iii) quantify the characteristics of skin temperature (SkT) oscillations through spectral analysis. We paid particular attention to the metrology of thermal measurements, with a special bench, including four homemade black body reference areas. We propose a live calibration procedure using this setup while correcting the thermal drift. After all of these correction steps, the experimental thermal resolution () for the temporal variation in each pixel was about 25. Finally, a movement removal procedure was also applied to the thermal images to avoid foot spatial movement over the 10 min observation period. Thermoregulation was stimulated by a 6-min walking exercise test on six volunteers and was then studied using three kinds of scalar indicators evaluated before and after exercise per thermal image pixel. We demonstrated that the 6-min walk exercise increased the thermoregulation activity beneath the plantar foot sole. Moreover, unlike manually placed local thermal probes, the indicator fields proposed in this paper allow the operator to select the exact thermoregulation activation locations and analyse the spatial distribution patterns at these locations.

Published
2019

11. Experimental evidence for long-distance electrodynamic intermolecular forces

Author

Lechelon, Mathias, Meriguet, Yoann, Gori, Matteo, Ruffenach, Sandra, Nardecchia, Ilaria, Floriani, Elena, Kudashova, Anastasiia, Coquillat, Dominique, Teppe, Frédéric, Mailfert, Sébastien, Marguet, Didier, Ferrier, Pierre, Varani, Luca, Sturgis, James, Torres, Jeremie, Pettini, Marco, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E7 Systèmes dynamiques : théories et applications, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut d’Electronique et des Systèmes (IES), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Howard University, Modélisation et Spectroscopie THz (MOST), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Excellence Initiative of Aix-Marseille University, European Commission, ANR, CNRS, Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS]Physics [physics], collective molecular oscillations, Terahertz spectroscopy, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], biophysics, Fluorescence Correlation Spectroscopy, Electrodynamic intermolecular interactions
Abstract

International audience; Both Classical and Quantum Electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces, however these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent approaches, we demonstrate experimentally for the first time the activation of resonant electrodynamic intermolecular forces. We characterize clustering transitions induced by these forces by fluorescence correlation spectroscopy when out-of-equilibrium conditions induce collective molecular oscillation observed by Terahertz (THz) spectroscopy. This is an unprecedented experimental \textit{proof of principle} of a physical phenomenon that, having been observed for bio-macromolecules and with a long-range of action (up to 1000 ${\mathring{A}}$), could be of importance for biology. Therefore, in addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space. We anticipate our findings will provide a basis for future systematic deepening of physical aspects of the reported phenomena and for future systematic assessment of the relevance of electrodynamic forces in shaping the dynamics of biomolecular encounters and recognition in biology.

Published
2021

12. A new kinetics model to predict the growth of micro-algae subjected to fluctuating availability of light

Author

Alain Rapaport, Emna Krichen, Eric Fouilland, Emilie Le Floc'h, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Labex NUMEV, ADEME, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), ADEME French Agency, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and 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)

Subjects
020209 energy, media_common.quotation_subject, Population, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Interactions, 02 engineering and technology, Competition (biology), 03 medical and health sciences, 0202 electrical engineering, electronic engineering, information engineering, Range (statistics), Poly-culture, Growth rate, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, education, 030304 developmental biology, media_common, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, education.field_of_study, Attenuation, Modeling, Ray, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Micro-algae, Expression (mathematics), Light availability, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biological system, Reduction (mathematics), Density dependency, Agronomy and Crop Science
Abstract

International audience; Light is a key environmental factor for the growth of micro-algae, and optimizing the capture of light is critical for high efficiency production systems. As the density of the population of micro-algae increases, the availability of light decreases, leading to a reduction in the growth rate because of mutual shading, while other effects, such as photo-inhibition, might be especially frequent when the population density is low. Several models in the literature have been developed to take into account light phenomena and predict micro-algal growth, particularly in a mono-culture. With the help of a simple expression for the attenuation of the light, we propose and justify a new growth function that incorporates both photo-inhibition and photolimitation. In agreement with the experimental data, this new formulation describes the micro-algal response to a wide range of situations of excessive or insufficient light intensities through an explicit dependence on both the incident light and the biomass concentration. While simple, the proposed expression can be satisfactorily applied to practical cases under nutrient replete conditions in photo-bioreactors with different sizes and geometries. It extends naturally to the growth of different species, providing a dynamic model which can simulate experiments in a mono-culture as well as in polycultures. The investigation of the competition for light-limited growth shows that the model predicts competitive exclusion, which has also been experimentally demonstrated. This leads to new perspectives for the control and optimization of mixed micro-algal cultures.

Published
2021

13. Necessary optimality condition for the minimal time crisis relaxing transverse condition via regularization

Author

Kenza Boumaza, Térence Bayen, Alain Rapaport, EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), Bourse de doctorat d'excellence algérienne, LabEx ’NUMEV’ incorporated into the I-Site ’MUSE’ (Montpellier), and Rapaport, Alain

Subjects
0209 industrial biotechnology, Control and Optimization, Hybrid Maximum Principle, Boundary (topology), 02 engineering and technology, 01 natural sciences, Regularization (mathematics), Hamiltonian system, 020901 industrial engineering & automation, Maximum principle, Transverse crossing time, Convergence (routing), Regularization, Applied mathematics, Limit (mathematics), 0101 mathematics, Necessary optimality conditions, Mathematics, Sequence, Time crisis, Computer Science::Information Retrieval, 010102 general mathematics, [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], Optimal control, Computational Mathematics, Control and Systems Engineering, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract

We derive necessary optimality conditions for the time of crisis problem under a more general hypothesis than the usual one encountered in the hybrid setting, which requires that any optimal solution should cross the boundary of the constraint set transversely. Doing so, we apply the Pontryagin Maximum Principle to a sequence of regular optimal control problems whose integral cost approximates the time of crisis. Optimality conditions are derived by passing to the limit in the Hamiltonian system (without the use of the hybrid maximum principle). This convergence result essentially relies on the boundedness of the sequence of adjoint vectors in L∞. Our main contribution is to relate this property to the boundedness in L1 of a suitable sequence which allows to avoid the use of the transverse hypothesis on optimal paths. An example with non-transverse trajectories for which necessary conditions are derived highlights the use of this new condition.

Published
2021

14. La protéine NF-Y contrôle la fidelité de l'initiation de la transcription aux promoteurs de gènes à travers la maintenance de région déplétée en nucléosome

Author

Raja Jothi, Telmo Henriques, Christopher A. Lavender, Dhirendra Kumar, Senthilkumar Cinghu, Karen Adelman, Andrew J. Oldfield, Brian D. Bennett, Adam B. Burkholder, Pengyi Yang, Damien Paulet, Benjamin S. Scruggs, Eric Rivals, Epigenetics and Stem Cell Biology Laboratory [Durham] (ESCBL-NIEHS-NIH), National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), Maharishi Valmiki Hospital, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Marquette University, National Institutes of Health [Bethesda] (NIH), ATGC bioinformatics platform Montpellier. the Institut de Biologie Computationnelle (ANR-11-BINF-0002) Institut Français de Bioinformatique (ANR-11-INBS-0013)GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)France Génomique., ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013/11-INBS-0013,ReNaBi-IFB,Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Marquette University [Milwaukee], ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)

Subjects
0301 basic medicine, General Physics and Astronomy, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], 02 engineering and technology, Mice, 0302 clinical medicine, Transcription (biology), Gene expression, Gene Knockdown Techniques, RNA, Small Interfering, Promoter Regions, Genetic, lcsh:Science, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 021001 nanoscience & nanotechnology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, Nucleosomes, 3. Good health, Cell biology, Transcription Initiation Site, 0210 nano-technology, Transcription, Science, Protein domain, Site Transcription Initiation, Genomics, Biology, Small Interfering, Article, General Biochemistry, Genetics and Molecular Biology, Cell Line, Promoter Regions, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Nucleosome, Transcription factor, Embryonic Stem Cells, 030304 developmental biology, Promoter, General Chemistry, Metabolism, 030104 developmental biology, CCAAT-Binding Factor, RNA, lcsh:Q, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract

Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation., The mechanisms underlying specific TSS selection in mammals remain unclear. Here the authors show that the ubiquitously expressed transcription factor NF-Y regulate fidelity of transcription initiation at gene promoters, maintaining the region upstream of TSSs in a nucleosome-depleted state, while protecting this region from ectopic transcription initiation.

Published
2019

15. Towards a better understanding of grass bed dynamics using remote sensing at high spatial and temporal resolutions

Author

Estelle Pitard, Xavier Fortuny, Guillaume Papuga, Samuel Alleaume, Frédéric Andrieu, Marion Menu, Guilhem Debarros, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Conservatoire Botanique National Méditerranéen de Porquerolles, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ADENA - Réserve Naturelle Nationale du Bagnas, University of California [Berkeley] (UC Berkeley), University of California (UC), Agence de l'Eau ('appel a projet Biodiversite 2016'), University of Montpellier - AAP 2017-1-08, LabeX NUMEV - AAP 2017-1-08, UC Berkeley's Geospatial Innovation Facility (GIF), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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), University of California [Berkeley], and University of California

Subjects
0106 biological sciences, National natural reserve of the bagnas (France), 010504 meteorology & atmospheric sciences, Occupancy, Stochastic modelling, Pondweed grass beds, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Aquatic Science, Oceanography, Ecological indicator, 01 natural sciences, Resilience (network), Image resolution, Mesohaline lagoon, Ecosystem management, Wetlands conservation, 0105 earth and related environmental sciences, Remote sensing, Stuckenia pectinata, biology, 010604 marine biology & hydrobiology, Temporal survey, Sentinel-2 satellites, 15. Life on land, biology.organism_classification, Field (geography), [SDE]Environmental Sciences, Environmental science
Abstract

International audience; Wetlands conservation and resilience capacities are key issues in many places over the globe. Understanding these issues will benefit from a precise knowledge of seagrass species occupancy and coverage over time and over space. Such information can be obtained from remote sensing images and their classification thanks to a vegetation index, to be used in a complementary manner to field work inventories. Sentinel-2 data, which are available with a frequent revisit time (

Published
2021

16. Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest

Author

Renaud Vitalis, Eric Lombaert, Arnaud Estoup, Louis Raynal, Mathieu Gautier, Jean-Michel Marin, François-David Collin, Ghislain Durif, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported by funds from the French Agence Nationale pour la Recherche (projects SWING ANR-16-CE02-0015, GANDHI ANR-20-CE02-0018), ABSint ANR-18-CE40-0034, the INRAE scientific division SPE (AAP-SPE 2016), and the LabEx NUMEV ANR-10-LABX-0020., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-20-CE02-0018,GANDHI,Génomique de l'invasion de la coccinelle Harmonia axyridis(2020), ANR-18-CE40-0034,ABSint,Solutions bayésiennes approchées pour l'inférence dans de grands jeux de données et dans des modèles complexes(2018), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Feature vector, Population, SNP, Context (language use), Biology, Machine learning, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Set (abstract data type), 03 medical and health sciences, approximate Bayesian computation, Genetics, Computer Simulation, supervised machine learning, education, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Demography, education.field_of_study, Estimation theory, business.industry, Special Issue, RESOURCE ARTICLES, pool‐sequencing, 0402 animal and dairy science, population genetics, Bayes Theorem, 04 agricultural and veterinary sciences, demographic history, 040201 dairy & animal science, Molecular and Statistical Advances, Random forest, 030104 developmental biology, Genetics, Population, model or scenario selection, Artificial intelligence, Approximate Bayesian computation, business, parameter estimation, computer, Algorithms, random forest, Biotechnology
Abstract

International audience; Simulation-based methods such as Approximate Bayesian Computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. RF allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated datasets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user-friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo-observed and real datasets corresponding to pool-sequencing and individual-sequencing SNP datasets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP datasets to make inferences about complex population genetic histories.

Published
2021

17. Parametric recurrence quantification analysis of autoregressive processes for pattern recognition in multichannel electroencephalographic data

Author

Stéphane Caron, Anthony Boyer, Frédéric Bouchara, François Bonnetblanc, Hugues Duffau, Annick Lesne, Sofiane Ramdani, Interactive Digital Humans (IDH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Contrôle Artificiel de Mouvements et de Neuroprothèses Intuitives (CAMIN), 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), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] (CAPS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Informatique et Systèmes (LIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the LabEx NUMEV project (ANR-10-LABX-20) funded by the French government’s 'Investisse- ments d’Avenir' program managed by the French National Re- search Agency (ANR), grants from the Institut Universitaire de France, and INSERM laboratory (U1093)., ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
[INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Computer science, Recurrence quantification analysis, Physics::Medical Physics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], 02 engineering and technology, 01 natural sciences, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Artificial Intelligence, 0103 physical sciences, Recurrence plots, 0202 electrical engineering, electronic engineering, information engineering, EEG Data, Asymptotic recurrence measures, [NLIN]Nonlinear Sciences [physics], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, Recurrence plot, Autoregressive stochastic processes, Parametric statistics, Series (mathematics), business.industry, Stochastic process, [SCCO.NEUR]Cognitive science/Neuroscience, Pattern recognition, Function (mathematics), Autoregressive model, Signal Processing, Pattern recognition (psychology), 020201 artificial intelligence & image processing, Computer Vision and Pattern Recognition, Artificial intelligence, business, Multichannel data, Software
Abstract

accepted 2020-08-04; International audience; Recurrence quantification analysis (RQA) is an acknowledged method for the characterization of experimental time series. We propose a parametric version of RQA, pRQA, allowing a fast processing of spatial arrays of time series, once each is modeled by an autoregressive stochastic process. This method relies on the analytical derivation of asymptotic expressions for five current RQA measures as a function of the model parameters. By avoiding the construction of the recurrence plot of the time series, pRQA is computationally efficient. As a proof of principle, we apply pRQA to pattern recognition in multichannel electroencephalographic (EEG) data from a patient with a brain tumor.

Published
2021

18. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Author

Park, Sangsoo, Park, Sung Gwan, Cazaux, Bastien, Park, Kunsoo, Rivals, Eric, Samsung Electronics [Korea], Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Seoul National University [Seoul] (SNU), Institute of Computer Science of University of Wrocław, Poland., Gawrychowski, Pawel, Starikovskaya, Tatiana, Samsung Electronics, Seoul, Korea, GEM Flagship project from LABEX NUMEV, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), and Gawrychowski, Paweł

Subjects
FOS: Computer and information sciences, hierarchical overlap graph, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], overlap graph, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], 16. Peace & justice, Computer Science::Computer Vision and Pattern Recognition, Computer Science - Data Structures and Algorithms, [INFO]Computer Science [cs], Data Structures and Algorithms (cs.DS), Theory of computation → Pattern matching, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], shortest superstring problem, border array
Abstract

The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P|| + n^2)., Comment: 8 pages, 2 figures, submitted to CPM 2021

Published
2021
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19. Optimisation et prédiction de la production algale en polycultures, approches expérimentales et modélisation mathématique

Author

Krichen, Emna, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV et ADEME, Université Montpellier, Alain Rapaport, Eric Fouilland, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Rapaport, Alain, and Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID

Subjects
fluctuations des ressources, modélisation dynamique, microalgues, nitrogen, bactéries, interval estimation, biomasse, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, bacteria, polycultures, azote, lumière, biomass, dynamical modeling, microalgae, estimation par intervalles, [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], interactions, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, resource fluctuations, light
Abstract

The stability and the performances of microalgae production systems are challenging issues, particularly in the context of the use of microalgae for the bioremediation of effluents and the production of biomass ofindustrial interest. One of the challenging axes of research is to take advantage of the diversity of microalgae through the use of assemblages (polycultures) for improving the overall production performances. However, theexploitation of these complex assemblages in an open system is subject to various stresses : biotic (undesirable microalgae or competing bacteria) and abiotic (limitation of resources, especially nitrogen and light). Thesestressing factors could influence interactions within assemblages, making thereby difficult the prediction and the optimization of the overall production. The objective of this thesis is to propose methods and tools forunderstanding, predicting, and optimizing the biomass production of an algal assemblage (natural or artificially designed microbial consortium) under the fluctuation of resources and culture conditions. More specifically,we have developed mathematical models based on dynamical systems that can be compared to laboratory and pilot-scale experiments. Firstly, an experimental method was defined for characterizing the specific growth rate of photosynthetic microorganisms, according to the limiting resource. Furthermore, a new functional estimation method is proposed. This method provides two growth curves that envelop scattering growth rate data and thus allow dynamic estimates of the state variables with guaranteed intervals. Secondly, the type of the interactions between two microalgae Chlorella sorokiniana and Scenedesmus pectinatus, which typically have successional trends in the outdoor ponds used for the treatment of urban wastewater, has been characterized ; first according to the fluctuation of the different forms of nitrogen (NH+4/NH3), and secondly to the light availability. The mathematical models associated with the experiments carried out during this thesis demonstrate that the initial development of an opportunistic microalgal species, which is more resistant to high levels of NH+4/NH3 was required for the subsequent development of a more efficient microalgal species under low light availability in these turbid processes. Third, we explored the paradoxical interactions occurring between microalgae and heterotrophic bacteria. Through the exudation of carbon, microalgae stimulate its competitors for common resources : nitrogen or phosphorus. We have thus studied the influence of this phenomenon by proposing a four-dimensional model. The mathematical analysis revealed that the equilibrium of coexistence is unique, and the installation of bacteria is robust, as it has been shown that the equilibrium without bacteria is unstable. We show that when the concentration of the mineral resource that continuously feeds the bioreactor is large enough, there are renewal rate values for which there is coexistence, while bacteria could not grow in the absence of microalgae under these same operating conditions. Finally, it has been shown, using simulations, that during coexistence their biomasses can oscillate. These results demonstrate the complexity of biotic interactions, provide methods applicable to other model organisms, and raise promising application possibilities for the optimization and the control of bioprocess dynamical systems for future work., Dans le contexte de l’utilisation des microalgues pour la bioremédiation d’effluents et la production de biomasse d’intérêt industriel, la stabilité et les performances des systèmes de production sont des enjeux majeurs. Unedes voies de recherche privilégiées est la mise à profit de la diversité des microalgues en assemblages (polycultures) pour l’amélioration des performances de la production. Néanmoins, l’exploitation de ces assemblages complexes en système ouvert extérieur est sujette à divers stress biotiques (microalgues indésirables ou bactéries compétitrices) et abiotiques (limitation des ressources, notamment l’azote et la lumière) qui influencent les interactions au sein des assemblages, rendant difficiles la prédiction et l’optimisation de la production. L’objectif de la présente thèse est de proposer des méthodes et des outils permettant de comprendre, prédire et optimiser la production de biomasse d’un assemblage algal (consortium microbien naturel ou artificiellement composé) sous la fluctuation des ressources et des conditions de culture. Plus particulièrement, nous avons développé des modèles mathématiques basés sur des systèmes dynamiques, qui peuvent être confrontés à des expériences en laboratoire et à l’échelle-pilote. Les premiers travaux de cette thèse ont consisté à choisir une méthode expérimentale pour la caractérisation de la vitesse de croissance spécifique des microorganismes photosynthétiques en fonction de la ressource limitante. Par ailleurs, une nouvelle méthode d’estimation fonctionnelle est proposée produisant deux courbes de croissance qui encadrent les données de vitesse de croissance et permettant ainsi des estimations dynamiques des variables d’état par intervalles garantis. Dans un deuxième temps, la nature des interactions entre deux microalgues Chlorella sorokiniana et Scenedesmus pectinatus, qui se succèdent classiquement dans les bassins extérieurs utilisés pour le traitement des eaux usées urbaines, a été caractérisée en fonction de la fluctuation des différentes formes de l’azote (NH+4/NH3) et ensuite de la lumière disponible. Les modèles mathématiques associés aux expérimentations menées au cours de cette thèse ont permis de démontrer que le développement initial d’une espèce microalgale de type opportuniste, plus résistante aux fortes teneurs en NH+4/NH3 était nécessaire pour que puisse s’établir ensuite une espèce microalgale plus efficace vis-à-vis de la faible lumière disponible dans ces procédés très turbides. Dans un troisième temps, nous avons exploré les interactions paradoxales qui existent entre les microalgues et les bactéries hétérotrophes. En effet, les microalgues stimulent, à travers l’exsudation du carbone, leurs compétiteurs pour une ressource commune : l’azote ou le phosphore. Nous avons étudié l’influence de ce phénomène en proposant un modèle dynamique en dimension quatre. L’analyse mathématique a révélé l’unicité de l’équilibre de coexistence et la robustesse de l’installation des bactéries, car il a été démontré que l’équilibre en absence de bactéries est répulsif. Nous montrons que lorsque la concentration de la ressource minérale alimentant en continu le bioréacteur est suffisamment grande, il existe des valeurs du taux de renouvellement du réacteur pour lesquelles il y a coexistence, alors que les bactéries ne pourraient pas se développer en l’absence de microalgues dans ces mêmes conditions opératoires. Enfin, il a été montré à l’aide de simulations que lors de la coexistence, leur biomasse respectives peut osciller. Ces résultats témoignent de la complexité des interactions biotiques, fournissent des méthodes applicables à d’autres organismes modèles permettant de les étudier, et soulèvent des possibilités d’application prometteuses pour l’optimisation et le contrôle des systèmes dynamiques de procédés pour les travaux futurs.

Published
2020

20. Additive rheology of complex granular flows

Author

Thanh-Trung Vo, Farhang Radjai, Jean-Yves Delenne, Saeid Nezamabadi, Patrick Mutabaruka, Danang Architecture University (DAU), Physique et Mécanique des Milieux Divisés (PMMD), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-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), Multiscale Material Science for Energy and Environment (MSE 2), Massachusetts Institute of Technology (MIT), Ministry of Education and Training in Vietnam, Campus France, and Labex NUMEV (University of Montpellier).

Subjects
Inertial frame of reference, Materials science, Science, General Physics and Astronomy, Atomic packing factor, 01 natural sciences, Texture (geology), General Biochemistry, Genetics and Molecular Biology, Article, 010305 fluids & plasmas, Stress (mechanics), Physics::Fluid Dynamics, Rheology, 0103 physical sciences, [SPI.MECA.MEMA]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanics of materials [physics.class-ph], Civil engineering, Colloids, lcsh:Science, 010306 general physics, Anisotropy, Multidisciplinary, Process chemistry, Physics, [SPI.MECA.BIOM]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], General Chemistry, Mechanics, Condensed Matter::Soft Condensed Matter, lcsh:Q, Quasistatic process, Dimensionless quantity
Abstract

Granular flows are omnipresent in nature and industrial processes, but their rheological properties such as apparent friction and packing fraction are still elusive when inertial, cohesive and viscous interactions occur between particles in addition to frictional and elastic forces. Here we report on extensive particle dynamics simulations of such complex flows for a model granular system composed of perfectly rigid particles. We show that, when the apparent friction and packing fraction are normalized by their cohesion-dependent quasistatic values, they are governed by a single dimensionless number that, by virtue of stress additivity, accounts for all interactions. We also find that this dimensionless parameter, as a generalized inertial number, describes the texture variables such as the bond network connectivity and anisotropy. Encompassing various stress sources, this unified framework considerably simplifies and extends the modeling scope for granular dynamics, with potential applications to powder technology and natural flows., Granular materials are abundant in nature, but we haven’t fully understood their rheological properties as complex interactions between particles are involved. Here, Vo et al. show that granular flows can be described by a generalized dimensionless number based on stress additivity.

Published
2020

21. Comprendre les spécificités physiques et vibro-mécaniques des Palissandres, bois du genre pantropical menacé Dalbergia

Author

Suarez Diaz, Sebastian, Guibal, Daniel, Cabrolier, Pierre, Thevenon, Marie-France, Langbour , Patrick, Brémaud, Iris, Bois (BOIS), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BioWooEB (UPR BioWooEB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Chercheur indépendant, Centre National de la Recherche Scientifique (CNRS), and Labex NUMEV

Subjects
bois, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Palissandres, Dalbergia, propriétés vibro-mécaniques, artisanat, [SDE.ES]Environmental Sciences/Environmental and Society, colorimétrie, [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], CITES, chémo-taxonomie, bois précieux, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], usages, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

22. Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals

Author

Sérgio Ferreira-Cardoso, Frédéric Delsuc, Lionel Hautier, Pierre-Henri Fabre, Benoit de Thoisy, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The Natural History Museum [London] (NHM), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Association Kwata - Etude et protection de la nature [Guyane], Sérgio Ferreira-Cardoso, Lionel Hautier and Frédéric Delsuc were supported by a European Research Council (ERC) consolidator grant (ConvergeAnt project #683257). Lionel Hautier and Frédéric Delsuc were supported by Centre National de la Recherche Scientifique (CNRS). This work was supported by 'Investissements d’Avenir' grants managed by Agence Nationale de la Recherche Labex CEBA (ANR-10-LABX-25-01), Labex CEMEB (ANR-10-LABX-0004), and Labex NUMEV (ANR-10-LABX-0020). The MRI platform member of the national infrastructure France-BioImaging is supported by the French National Research Agency (ANR-10-INBS-04, ‘Investments for the future’). The JAGUARS collection is supported through a FEDER/ERDF grant attributed to Kwata NGO, funded by the European Union, the Collectivité Territoriale de Guyane, and the DEAL Guyane., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, Tamandua, Anatomy and Physiology, Masticatory apparatus, [SDV]Life Sciences [q-bio], lcsh:Medicine, Context (language use), 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, biology.animal, Cyclopedidae, 030304 developmental biology, 0303 health sciences, Anteater, Anteaters, biology, Comparative anatomy, General Neuroscience, lcsh:R, Tamandua tetradactyla, General Medicine, Anatomy, biology.organism_classification, Evolutionary Studies, Myrmecophagy, Myology, Jugal bone, Myrmecophagidae, General Agricultural and Biological Sciences, Convergence, Zoology
Abstract

BackgroundEcological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (µ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability.MethodsWe used an iodine staining solution (I2KI) to perform contrast-enhanced µ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals.ResultsWe found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences.

Published
2020

23. Phase separation of polymer-bound particles induced by loop-mediated one dimensional effective long-range interactions

Author

Jean-Charles Walter, John Palmeri, Frédéric Geniet, Nils-Ole Walliser, Gabriel David, Jérôme Dorignac, Andrea Parmeggiani, Chase P. Broedersz, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Arnold Sommerfeld Center for Theoretical Physics, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München (LMU), Vrije Universiteit Amsterdam [Amsterdam] (VU), LPHI - Laboratory of Pathogen Host Interactions (LPHI), This project received partial financial support from theFrench Agence Nationale de la Recherche [Imaging andModeling Bacterial Mitosis (IBM) Project No. ANR-14-CE09-0025-01], the CNRS Défi Inphyniti (Projet StructurantNo. 2015–2016), and the LabEx NUMEV (ANR-10-LABX-0020) within the I-SITE MUSE of the Université deMontpellier [No. AAP 2013-2-005, No. 2015-2-055, No.2016-1-024, and Flagship Project Gene Expression Modeling(2017–2020)] (G.D., J.C.W., J.D., F.G., A.P., N.O.W., J.P.).G.D. acknowledges doctoral thesis and A.T.E.R postdoctoralsupport from the French Ministère de l’Enseignementsupérieur, de la Recherche et de l’Innovation. This work wassupported in part by a Modélisation pour le Vivant FrenchCNRS Grant (CoilChrom project). This project was alsosupported by the Deutsche Forschungsgemeinschaft (DFG)Grant No. TRR174 (C.P.B.)., and ANR-14-CE09-0025,IBM,Visualisation et Modélisation de la Mitose Bactérienne(2014)

Subjects
chemistry.chemical_classification, Physics, 0303 health sciences, Phase transition, Quantitative Biology::Biomolecules, Gaussian, Polymer, 01 natural sciences, 03 medical and health sciences, symbols.namesake, Variational method, chemistry, Chemical physics, Lattice (order), 0103 physical sciences, symbols, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, 030304 developmental biology, Phase diagram, Bacterial dna
Abstract

International audience; The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membraneless compartments in order to confine and localize particles like proteins. In many cases, these particles are bound to fluctuating polymers like DNA or RNA. We propose a general theoretical framework for such polymer-bound particles and derive an effective 1D lattice gas model with both nearest-neighbor and emergent long-range interactions arising from looped configurations of the fluctuating polymer. We argue that 1D phase transitions exist in such systems for both Gaussian and self-avoiding polymers and, using a variational method that goes beyond mean-field theory, we obtain the complete mean occupation-temperature phase diagram. To illustrate this model, we apply it to the biologically relevant case of ParABS, a prevalent bacterial DNA segregation system.

Published
2020

24. Insight into gluten structure in a mild chaotropic solvent by asymmetrical flow field-flow fractionation (AsFlFFF) and evidence of non-covalent assemblies between glutenin and ω-gliadin

Author

Marie-Hélène Morel, Ameur Louhichi, Frédéric Violleau, Paul Menut, Laurence Ramos, Amélie Banc, Justine Pincemaille, Edouard Chauveau, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Paris-Saclay Food and Bioproduct Engineering (SayFood), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-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), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Chimie Agro-Industrielle (CAI), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Doctoral School GAIA and the Labex Numev (ANR-10-LAB-20) for the funding of the PhD Grant, scientific council of Montpellier SupAgro, and ANR-18-CE06-0012,ELASTOBIO,Gels élastomériques de biopolymères soumis à des déformations extrêmes(2018)

Subjects
chemistry.chemical_classification, Molar mass, 010304 chemical physics, biology, General Chemical Engineering, Size-exclusion chromatography, food and beverages, 04 agricultural and veterinary sciences, General Chemistry, Polymer, 040401 food science, 01 natural sciences, Gluten, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chaotropic agent, 0404 agricultural biotechnology, Glutenin, chemistry, Dynamic light scattering, Chemical engineering, 0103 physical sciences, biology.protein, Gliadin, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract

International audience; Wheat gluten, one of the most complex viscoelastic protein networks in nature, is unique to get the specific texture of bread. Due to its complex protein composition, its insolubility in most solvents and the very high molar mass of half of the proteins (glutenin, the other half being gliadin), the architecture of the network is still not well understood. In this work, we have investigated model gluten protein extracts with contrasted compositions in glutenin and gliadin solubilized in a mild chaotropic solvent: ethanol/water (50/50 v/v). The samples display a liquid-liquid phase separation with an upper critical solution temperature that depends on the protein composition. The phase diagrams are consistent with the presence of supramolecular assemblies of proteins. To confirm the presence of these assemblies and fully characterize the objects dispersed in ethanol/water, we have used an asymmetrical flow field-flow fractionation (AsFlFFF) setup coupled with differential refractive index, multi-angle light scattering and dynamic light scattering detections to probe very dilute protein suspensions. We have identified three classes of objects, with distinctive molar mass, characteristic size and conformation: protein monomers, polymeric structures, and very loose protein assemblies with molar mass larger than 2.10 6 g/mol. A molecular characterization of the species by size exclusion chromatography in a denaturing solvent shows that polymers and assemblies are mainly composed of glutenin and ω-gliadin. The high content of ω-gliadin, devoid of cysteines, indicates the importance of non-covalent interactions involved in protein assemblies and might play a major role in gluten rheology

Published
2020

25. Penalty function method for the minimal time crisis problem

Author

Kenza Boumaza, Alain Rapaport, Térence Bayen, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), Bourse de doctorat d'excellence algérienne, LabEx ’NUMEV’ incorporated into the I-Site ’MUSE’ (Montpellier), and Bayen, Térence

Subjects
T57-57.97, 0209 industrial biotechnology, Mathematical optimization, Applied mathematics. Quantitative methods, Computer science, 010102 general mathematics, Control (management), [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], 02 engineering and technology, 01 natural sciences, Set (abstract data type), 020901 industrial engineering & automation, Convergence (routing), QA1-939, Penalty method, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, Mathematics
Abstract

International audience; In this note, we propose a new method to approximate the minimal time crisis problem using an auxiliary control and a penalty function, and show its convergence to a solution to the original problem. The interest of this approach is illustrated on numerical examples for which optimal trajectories can leave and enter the crisis set tangentially.; Dans cette note, nous proposons une nouvelle méthode pour approcher le problème du temps de crise en introduisant un contrôle additionnel et une fonction de pénalisation. Nous montronsla convergence des solutions approchées vers une solution du problème original. L’intérêt de cette approche est illustrée sur un exemple numérique pour lequel les trajectoires optimales peuvent entrerou sortir tangentiellement de l’ensemble de crise.

Published
2020

26. A Note on Optimal and Sub-Optimal Feedback Controls for Biogas Production

Author

Antoine Haddon, Alain Rapaport, Héctor Ramírez, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Departamento de Ingeniería Matemática [Santiago] (DIM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) 1160567, CONICYT FONDECYT 1160567, Basal Program from CONICYT-Chile : CMM-AFB 170001, Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) : PFCHA/Doctorado Nacional/2017-21170249, and LabEx NUMEV incorporated into the I-Site MUSE

Subjects
Mathematical optimization, 021103 operations research, Control and Optimization, Singular Arc, Applied Mathematics, 0211 other engineering and technologies, 010103 numerical & computational mathematics, 02 engineering and technology, Management Science and Operations Research, 7. Clean energy, 01 natural sciences, Optimal control, Infinite horizon, Sub-optimality, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, Biogas production, Mathematics, Chemostat model
Abstract

Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 1160567 1160204 Basal Program from CONICYT-Chile CMM-AFB 170001 Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) PFCHA/Doctorado Nacional/2017-21170249 LabEx NUMEV incorporated into the I-Site MUSE

Published
2020

27. A multi observers approach when observability index is higher than the state dimension - a case study

Author

Alain Rapaport, Ihab Haidar, Jean-Pierre Barbot, Laboratoire QUARTZ (QUARTZ ), Université Paris 8 Vincennes-Saint-Denis (UP8)-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-SUPMECA - Institut supérieur de mécanique de Paris-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Université Paris 8 Vincennes-Saint-Denis (UP8)-SUPMECA - Institut supérieur de mécanique de Paris-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Université Paris 8 Vincennes-Saint-Denis (UP8)-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-SUPMECA - Institut supérieur de mécanique de Paris (SUPMECA)-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), ENSEA, LabEx NUMEV incorporated into the I-Site MUSE, and IEEE

Subjects
Estimation theory, optimisation, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Scalar (physics), Estimator, Systèmes dynamiques, Dynamical Systems, estimation d'erreur, Optimization and Control, Embedding, Applied mathematics, Gravitational singularity, Observability, Optimisation et contrôle, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics
Abstract

International audience; We address a family of observation problems that would classically require the construction of an embedding, by a different approach which consists in the design of several estimators in parallel. In principle, for a dynamics in dimension n with a scalar output y, each estimator uses the knowledge of only n − 1 derivatives of the output, and the further derivatives are used to discriminate at any time among the estimators. Estimators are built here by roots tracking technique. We illustrate our approach on the parameter estimation of a polynomial dynamics. The simulations show that the final estimation jumps from one estimator to another when passing through observability singularities, or when the parameter suddenly changes, preserving a good estimation error.

Published
2019

28. Demonstration of facilitation between microalgae to face environmental stress

Author

Eric Fouilland, Emna Krichen, Emilie Le Floc'h, Alain Rapaport, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Labex NUMEV, ADEME, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and ANR-16-IDEX-0006,MUSE,MUSE(2016)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Range (biology), Biodiversité et Ecologie, colonisation, [SDE.MCG]Environmental Sciences/Global Changes, lcsh:Medicine, Chlorella, Biotechnologies, Wastewater, Biology, Generalist and specialist species, Microbiology, 01 natural sciences, Environmental stress, Article, Water Purification, Biodiversity and Ecology, 03 medical and health sciences, Nutrient, Stress, Physiological, Microalgae, Colonization, microbiologie, lcsh:Science, Author Correction, modélisation, micro-algue, Chlorella sorokiniana, Multidisciplinary, Pioneer species, Ecology, 010604 marine biology & hydrobiology, lcsh:R, 15. Life on land, Modélisation et simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, Modeling and Simulation, stress environnemental, Facilitation, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology, Scenedesmus, Biotechnology
Abstract

Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001 Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001The original version of this Article omitted an affiliation for Emna Krichen and the Acknowledgements section contained typographical errors and was incomplete. This erratum is available as an annex file.; International audience; Positive interactions such as facilitation play an important role during the biological colonization and species succession in harsh or changing environments. However, the direct evidence of such ecological interaction in microbial communities remains rare. Using common freshwater microalgae isolated from a High Rate Algal Pond HRAP treating wastewaters, we investigated with both experimental and modeling approaches the direct facilitation between two algal strains during the colonization phase. Our results demonstrate that the first colonization by microalgae under a severe chemical condition arose from the rapid growth of pioneer species such as Chlorella sorokiniana, which facilitated the subsequent colonization of low growth specialists such as Scenedesmus pectinatus. The pioneer species rapidly depleted the total available ammonia nitrogen favoring the specialist species initially inhibited by free ammonia toxicity. This latter species ultimately dominated the algal community through competitive exclusion under low nutrient conditions. We show that microbial successions are not only regulated by climatic conditions but also by interactions between species based on the ability to modify their growth conditions. We suggest that facilitation within the aquatic microbial communities is a widespread ecological interaction under a vast range of environmental stress.

Published
2019

29. AgroPortal: A vocabulary and ontology repository for agronomy

Author

Vincent Emonet, Pierre Larmande, Sophie Aubin, Esther Dzale Yeumo, Clement Jonquet, Valeria Pesce, Marie-Angélique Laporte, John Graybeal, Elizabeth Arnaud, Anne Toulet, Mark A. Musen, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), DIST Délégation Information Scientifique et Technique (DV-IST), Institut National de la Recherche Agronomique (INRA), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), French National Research Agency [ANR-12-JS02-01001], NUMEV Labex [ANR-10-LABX-20], Computational Biology Institute of Montpellier [ANR-11-BINF-0002], University of Montpellier, CNRS, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), European Project: 701771,H2020,H2020-MSCA-IF-2015,SIFRm(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Stanford University [Stanford], Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Food and Agricultural Organization of the United Nations (FAO), United Nations Organization, ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)

Subjects
0301 basic medicine, Computer science, 02 engineering and technology, Horticulture, Knowledge organization system, Ontology (information science), Domain (software engineering), Ontology repository, Open Biomedical Ontologies, 03 medical and health sciences, A50 - Recherche agronomique, Controlled vocabulary, Ontologies, 0202 electrical engineering, electronic engineering, information engineering, Semantic Web, ontologie, vocabulaire, Metadata, Semantic annotation, U10 - Informatique, mathématiques et statistiques, [INFO.INFO-WB]Computer Science [cs]/Web, Forestry, Biodiversity, computer.file_format, Recommendation, Knowledge organization systems or artifacts, Agronomy, Computer Science Applications, 030104 developmental biology, C30 - Documentation et information, Mapping, Food, Simple Knowledge Organization System, 020201 artificial intelligence & image processing, Controlled vocabularies, Banque de données, Plant sciences, Agronomy and Crop Science, computer, Modèle mathématique
Abstract

International audience; Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences. We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). In this paper, we present our platform's content and features, including the additions to the original technology, as well as preliminary outputs of five driving agronomic use cases that participated in the design and orientation of the project to anchor it in the community. By building on the experience and existing technology acquired from the biomedical domain, we can present in AgroPortal a robust and feature-rich repository of great value for the agronomic domain.

Published
2018

30. Stress transmission in cemented bidisperse granular materials

Author

Valerie Lullien-Pellerin, Matthieu George, Jean-Yves Delenne, Farhang Radjai, Xavier Frank, Karsta Heinze, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-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), Physique et Mécanique des Milieux Divisés (PMMD), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), INRAE (division for Science for Food and Bioproduct Engineering, Grant No. 140948), and Labex Numev (Grant No. 2014-1-012) for the Ph.D. grant

Subjects
Materials science, Granular material, 01 natural sciences, 010305 fluids & plasmas, [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], Surface-area-to-volume ratio, [SDV.IDA]Life Sciences [q-bio]/Food engineering, 0103 physical sciences, Homogeneity (physics), Volume fraction, Ultimate tensile strength, Composite material, 010306 general physics, Porosity, Porous medium, Stress concentration
Abstract

International audience; We analyze stress distributions in a two-dimensional bidisperse cemented granular packing for a broad range of the values of particle-size ratio, the volumes of large and small particles, and the amount of cementing matrix. In such textured porous materials, the stress concentration, which controls the fracture and fragmentation of the material under tensile loading or in grinding processes, reflects not only the porosity but also the contact network of the particle phase and the resulting stress chains. By means of peridynamic simulations under tensile loading, we show how both the texture and stress distribution depend on size ratio, volume ratio, and the amount of the cementing matrix. In particular, the volume fraction of the class of small particles plays a key role in homogenizing stresses across the system by reducing porosity. Interestingly, the texture controls not only the porosity but also the distribution of pores inside the system with its statistical variability, found to be strongly correlated with the homogeneity of stresses inside the large particles. The most homogeneous stress distribution occurs for the largest size ratio and largest volume fraction of small particles, corresponding to the lowest pore size dispersion and the cushioning effect of small particles and its similar role to the binding matrix for stress redistribution across the packing. At higher porosity, the tensile stresses above the mean stress fall off exponentially in all phases with an exponent that strongly depends on the texture. The exponential part broadens with decreasing matrix volume fraction and particle-size ratio. These correlations reveal the strong interplay between size polydispersity and the cohesive action of the binding matrix for stress distribution, which is significant for the behavior of textured materials in grinding operations.

Published
2019

31. About overyielding with mixed cultures in batch processes

Author

Tibault Nidelet, Alain Rapaport, Jérôme Harmand, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 la Recherche Agronomique (INRA), 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), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), LabEx NUMEV incorporated into the I-Site MUSE, and Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0209 industrial biotechnology, bioprocédé, Resource (biology), media_common.quotation_subject, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], bioréacteur, 02 engineering and technology, Systèmes dynamiques, Competition (biology), 020901 industrial engineering & automation, 0202 electrical engineering, electronic engineering, information engineering, Economics, variable yield, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, overyielding, competition, mortality, batch processes, Génie des procédés, media_common, 020208 electrical & electronic engineering, Modélisation et simulation, simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Dynamical Systems, Process Engineering, Control and Systems Engineering, Modeling and Simulation, Biochemical engineering
Abstract

International audience; This paper investigates-via modeling-several possible explanations of overyielding observed in mixed cultures cultivated in batch reactors. It is first shown that the classical model of competition of N species for a single resource cannot explain such overyielding. Then, three hypotheses are introduced and discussed at the light of numerical simulations.

Published
2019

32. About modeling and control strategies for scheduling crop irrigation

Author

Kenza Boumaza, Carole Sinfort, Alain Rapaport, Sébastien Roux, Nesrine Kalboussi, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Euro-Mediterranean network TREASURE, LabEx NUMEV incorporated into the I-Site MUSE, ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), and ANR-16-CONV-0004,DigitAg,Digital Agriculture Convergence Lab(2016)

Subjects
0209 industrial biotechnology, Irrigation, Mathematical optimization, Computer science, media_common.quotation_subject, State constraint, Scheduling (production processes), [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Crop irrigation, 02 engineering and technology, irrigation, Scarcity, state constraint, optimal control, 020901 industrial engineering & automation, contrôle optimal, Optimization and Control, water management, 0202 electrical engineering, electronic engineering, information engineering, biomasse, Optimisation et contrôle, media_common, 020208 electrical & electronic engineering, Irrigation scheduling, simulation numérique, Optimal control, Agricultural sciences, Control and Systems Engineering, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Sciences agricoles
Abstract

International audience; We propose a new simplified crop irrigation model and study the optimal control which consists in maximizing the biomass production at harvesting time, under a constraint on the total amount of water used. Under water scarcity, we show that a strategy with a singular arc can be better than a simple bang-bang control as commonly used. The gain is illustrated on numerical simulations. This result is a promising first step towards the application of control theory to the problem of optimal irrigation scheduling.

Published
2019

33. Experimental and theoretical study of the erosion of semi-crystalline polymers and the subsequent generation of microparticles

Author

Pascale Fabre, Thibaut Gaillard, Emmanuelle Gastaldi, Frédéric Nallet, Matthieu George, Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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), Centre de recherches Paul Pascal (CRPP), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), LabEx NUMEV (2011-LABX-076), I-Site MUSE, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)

Subjects
chemistry.chemical_classification, Microplastics, Materials science, Degradation kinetics, Kinetics, Pattern formation, 02 engineering and technology, General Chemistry, Polymer, 010402 general chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Microstructure, 01 natural sciences, 0104 chemical sciences, chemistry, Erosion, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Composite material, 0210 nano-technology, Joint (geology), [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The increase of plastics and microplastics in the environment is a major environmental challenge. Still, little is known about the degradation kinetics of macroplastics into smaller particles, under the joint actions of micro-organisms and physico-chemical factors, like UV or mechanical constraints. In order to gain insight into (bio)-degradation in various media, we perform accelerated erosion experiments by using a well-known enzymatic system. We show that the microstructure of semi-crystalline polymers plays a crucial role in the pattern formation at their surface. For the first time, the release of fragments of micrometric size is evidenced, through a mechanism that does not involve fracture propagation. A geometric erosion model allows a quantitative understanding of erosion rates and surface patterns, and provides a critical heterogeneity size, parting two types of behavior: spherulites either released, or eroded in situ. This new geometric approach could constitute a useful tool to predict the erosion kinetics and micro-particle generation in various media.

Published
2019

34. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

Author

Oldfield, Andrew, Henriques, Telmo, Kumar, Dhirendra, Burkholder, Adam, Cinghu, Senthilkumar, Paulet, Damien, Bennett, Brian, Yang, Pengyi, Scruggs, Benjamin, Lavender, Christopher, Rivals, Eric, Adelman, Karen, Jothi, Raja, Epigenetics and Stem Cell Biology Laboratory [Durham] (ESCBL-NIEHS-NIH), National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), Maharishi Valmiki Hospital, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Marquette University, National Institutes of Health [Bethesda] (NIH), ATGC bioinformatics platform Montpellier. the Institut de Biologie Computationnelle (ANR-11-BINF-0002) Institut Français de Bioinformatique (ANR-11-INBS-0013)GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)France Génomique., ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013/11-INBS-0013,ReNaBi-IFB,Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Marquette University [Milwaukee], ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)

Subjects
Site Transcription Initiation, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Small Interfering, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, Nucleosomes, Promoter Regions, Mice, Metabolism, CCAAT-Binding Factor, Gene Knockdown Techniques, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA, Transcription Initiation Site, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Embryonic Stem Cells
Abstract

International audience; Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation.

Published
2019

35. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Author

Cazaux, Bastien, Rivals, Eric, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Support from the Institut de Biologie Computationnelle (ANR-11-BINF-0002).Eric Rivals: thanks the GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)., University of Pisa, Nadia Pisanti, Solon P. Pissis, ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)

Subjects
Run Length Encoding (RLE), Aho-Corasick automaton, Aho-Corasick Tree, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Burrows Wheeler Transform, Compression, XBWT, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Data Structures, Algorithm, 2012 ACM Subject Classification Mathematics of computing → Discrete mathematics, Theory of computation → Randomness, geometry and discrete structures, Theory of computation → Data structures and algorithms for data management, Indexing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Stringology
Abstract

URN: urn:nbn:de:0030-drops-104955URL: http://drops.dagstuhl.de/opus/volltexte/2019/10495/ISBN ={978-3-95977-103-0},ISSN ={1868-8969},; International audience; The boom of genomic sequencing makes compression of sets of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the Burrows-Wheeler Transform (BWT), a reversible permutation of a text that improves its compressibility. A similar data structure, the eXtended Burrows-Wheeler Transform (XBW), is able to index a tree labelled with alphabet symbols. A link between a multi-string BWT and the Aho-Corasick automaton has already been found and led to a way to build a XBW from a multi-string BWT. We exhibit a stronger link between a multi-string BWT and a XBW by using the order of the concatenation in the multi-string. This bijective link has several applications: first, it allows one to build one data structure from the other; second, it enables one to compute an ordering of the input strings that optimises a Run-Length measure (i.e., the compressibility) of the BWT or of the XBW.

Published
2019

36. A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random Forest

Author

Louis Raynal, Christophe Plantamp, Christine N. Meynard, Marie Pierre Chapuis, Jean-Michel Marin, Arnaud Estoup, Laurence Blondin, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), This work was supported by research funds from the French Agricultural Research Centre for International Development (CIRAD), the project ANR-16-CE02-0015 (SWING), the INRA scientific department SPE (AAP-SPE 2016), and the Labex NUMEV (NUMEV, ANR10-LABX-0020). The data used in this work were partly produced through the technical facilities of the Centre Méditerranéen Environnement Biodiversité (CeMEB, ANR-10-LABX-0004), Montpellier, France., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CAractérisation et Suivi des Phénomènes d'Evolution de Résistance aux pesticides (CASPER), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Population, divergence time, 010603 evolutionary biology, 01 natural sciences, paleo-vegetation, 03 medical and health sciences, Glacial period, Desert locust, education, 030304 developmental biology, Local adaptation, 0303 health sciences, education.field_of_study, Random Forest, biology, Holocene, Ecology, 15. Life on land, biology.organism_classification, colonization, Geography, Habitat, Orthoptera, Schistocerca, Approximate Bayesian computation, Locust
Abstract

This article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology.; International audience; Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario among a set of possible scenarios, and estimation of the parameter(s) of interest under the chosen scenario. Such inferences greatly benefit from new statistical approaches including approximate Bayesian computation - Random Forest (ABC-RF), the latter providing reliable inference at a low computational cost, with the possibility to take into account prior knowledge on both biogeographical history and genetic markers. Here, we used ABC-RF, including independent information on evolutionary rate and pattern at microsatellite markers, to decipher the evolutionary history of the African arid-adapted pest locust, Schistocerca gregaria . We found that the evolutionary processes that have shaped the present geographical distribution of the species in two disjoint northern and southern regions of Africa were recent, dating back 2.6 Ky (90% CI: 0.9 – 6.6 Ky). ABC-RF inferences also supported a southern colonization of Africa from a low number of founders of northern origin. The inferred divergence history is better explained by the peculiar biology of S. gregaria , which involves a density-dependent swarming phase with some exceptional spectacular migrations, rather than a continuous colonization resulting from the continental expansion of open vegetation habitats during more ancient Quaternary glacial climatic episodes.

Published
2019
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37. Hierarchical Space-Time Modeling of Asymptotically Independent Exceedances With an Application to Precipitation Data

Author

Gwladys Toulemonde, Carlo Gaetan, Jean-Noël Bacro, Thomas Opitz, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Ambientali, Informatica e Statistica [Venezia] (DAIS), University of Ca’ Foscari [Venice, Italy], Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), 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), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Biostatistique et Processus Spatiaux (BioSP), Littoral, Environment: MOdels and Numerics (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), French National Programme LEFE/INSU, LabEx NUMEV, financial support from Ca’ Foscari University, Italy, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
Statistics and Probability, Quasi-maximum likelihood, Computer science, 01 natural sciences, Composite likelihood, 010104 statistics & probability, Asymptotic independence, Gamma random fields, Hourly precipitation, Space-time convolution, Space-time extremes, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0502 economics and business, Precipitation, Statistical physics, 0101 mathematics, 050205 econometrics, [STAT.AP]Statistics [stat]/Applications [stat.AP], Symptotic independence, Space time, 05 social sciences, Statistical model, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [STAT]Statistics [stat], Event data, Key (cryptography), Statistics, Probability and Uncertainty, Settore SECS-S/01 - Statistica
Abstract

International audience; The statistical modeling of space-time extremes in environmental applications is key to understanding complex dependence structures in original event data and to generating realistic scenarios for impact models. In this context of high-dimensional data, we propose a novel hierarchical model for high threshold exceedances defined over continuous space and time by embedding a space-time Gamma process convolution for the rate of an exponential variable, leading to asymptotic independence inspace and time. Its physically motivated anisotropic dependence structure is based on geometric objects moving through space-time according to a velocity vector. We demonstrate that inference based on weighted pairwise likelihood is fast and accurate. The usefulness of our model is illustrated by an application to hourly precipitation data from a study region in Southern France, where it clearly improves on an alternative censored Gaussian space-time random field model. While classical limit models based on threshold-stability fail to appropriately capture relatively fast joint tail decay rates between asymptotic dependence and classical independence, strong empirical evidence from our application and other recent case studies motivates the use of more realistic asymptotic independence models such as ours.

Published
2019

38. 4D compressive sensing holographic microscopy imaging of small moving objects

Author

Nitin Rawat, Michel Gross, Daniel Alexandre, Alexey Brodoline, Nicolas Cubedo, Brodoline, Alexey, Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Electrical & Computer Engineering Department [Storrs, CT, USA], University of Connecticut (UCONN), Mécanismes moléculaires dans les démences neurodégénératives (MMDN), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), We acknowledge Corinne Fournier and Laurent Daudet for fruitful discussions, and LabEx NUMEV (ANR-10-LABX-20 , French National Research Agency: Micro Holo 4D) and CNRS ( Dé: Instrumentation aux limites 2018 ) for funding., ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)

Subjects
Physics, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Laser scattering, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Scattering, Holography, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Atomic and Molecular Physics, and Optics, law.invention, 010309 optics, Optics, Compressed sensing, Three dimensional imaging, law, 0103 physical sciences, Microscopy, Digital holographic microscopy, 0210 nano-technology, business
Abstract

International audience; We show that compressive sensing (CS) calculations are very ecient to reconstruct in 3D sparse objects whose 2D hologram has been recorded by digital holographic microscopy. The method is well adapted to image small scattering objects moving within a larger motionless object. This situation corresponds to red blood cells (RBCs) circulating in the vascular system of a zebrash (Danio rerio) larva. RBCs positions are imaged in 3D from a single hologram, while the RBCs trajectories, i.e. the perfused blood vessels, are imaged from a sequence of holograms. With respect to previous work (Donnarumma et al., Opt. express, 24, 26887, 2016), we get a gain of ∼ 500 in calculation speed.

Published
2019

39. Timber grading of Pinus uncinata , a lesser known pine species from the pyrenean mountain range

Author

Eduard Correal Modol, Jordi Gené Sera, Marcel Vilches Casals, Patrick Langbour, Bernard Thibaut, Cédric Montero, Agnès Burgers, Bois (BOIS), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Català de la Fusta (INCAFUST), BioWooEB (UPR BioWooEB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This work has been supported thanks to the support of the LabEx NUMEV project on Digital and Hardware Solutions and Modeling for the Environement and Life Sciences (N° ANR-10-LABX-20) funded by the «Investissements d’Avenir» French 537 Government program, managed by the French National Research Agency (ANR)

Subjects
Clear-wood properties, K50 - Technologie des produits forestiers, clear-wood properties, Materials Science (miscellaneous), variability, Young's modulus, Industrial and Manufacturing Engineering, Bois, symbols.namesake, Pinus uncinata, Current regulation, lcsh:Manufactures, [SPI.MECA.MEMA]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanics of materials [physics.class-ph], Chemical Engineering (miscellaneous), lcsh:Forestry, Grading (education), Propriété physicochimique, geography, modulus of rupture, geography.geographical_feature_category, modulus of elasticity, mountain pine, Forestry, 15. Life on land, timber grading, Propriété technologique, symbols, lcsh:SD1-669.5, Environmental science, Physical geography, Mountain pine, lcsh:TS1-2301, Mountain range
Abstract

International audience; Timber grading is an essential step into the value process to determine wood usability for structural uses. It requires well-described characteristics obtained easily by taking non-destructive measurements to quantify reliable indicators of mechanical properties. In this paper we present an approach based on both timber scale and clear-wood scale measurements using the case of Mountain Pine (Pinus uncinata). An important experimental plan have been performed from collected trees of French and Spain Pyrenean regions allowing significantly the use of inter-correlations between measurements. The physical properties of clear wood present an important adaptation of tree growth condition with a lower modulus of elasticity (MOE) as a consequence of microstructure at cell-wall level but a conventional modulus or rupture (MOR) in bending for pines. However, the results on timber presents an important the difference between visual and machine grading for this species in view of mechanical properties considered. The results obtained also show possible improvement and limitations of current regulation in the grading mountain pine timber for structural use.

Published
2019

40. Cyprinid herpesvirus 3 Evolves In Vitro through an Assemblage of Haplotypes that Alternatively Become Dominant or Under-Represented

Author

Klafack, Sandro, Fiston-Lavier, Anna-Sophie, Bergmann, Sven M., Hammoumi, Saliha, Schröder, Lars, Fuchs, Walter, Lusiastuti, Angela, Lee, Pei-Yu, Heredia, Sarahi Vega, consortium, Master student consortium Master student, Gosselin-Grenet, Anne-Sophie, Avarre, Jean-Christophe, Institute of Infectology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institute of Molecular Virology and Cell Biology, Research Institute for Freshwater Aquaculture and Fisheries Extension, GenReach Biotechnology, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Friedrich-Loeffler-Institut, ANR-11-EMID-0006,MOLTRAQ(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Bergmann, Sven, Avarre, Jean-Christophe, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), ERA-NET EMIDA [ANR-11-EMIDA-006], and LabEx NUMEV [ANR 10 LABX-00-76]

Subjects
0301 basic medicine, Biodiversité et Ecologie, Cyprinid herpesvirus 3, 030106 microbiology, ved/biology.organism_classification_rank.species, lcsh:QR1-502, Virulence, virus, Biology, Article, lcsh:Microbiology, Virus, Biodiversity and Ecology, 03 medical and health sciences, Common carp, cell culture passages, haplotype sequence, Virology, Digital polymerase chain reaction, analyse génomique, virus evolution, Genetics, ved/biology, Haplotype, herpes, DNA virus, herpes simplex, 3. Good health, virulence, 030104 developmental biology, Infectious Diseases, Viral evolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Viruses are able to evolve in vitro by mutations after serial passages in cell cultures, which can lead to either a loss, or an increase, of virulence. Cyprinid herpesvirus 3 (CyHV-3), a 295-kb double-stranded DNA virus, is the etiological agent of the koi herpesvirus disease (KHVD). To assess the influence of serial passages, an isolate of CyHV-3 (KHV-T) was passaged 99 times onto common carp brain (CCB) cells, and virus virulence was evaluated during passages through the experimental infections of common carp. After 78 CCB passages, the isolate was much less virulent than the original form. A comparative genomic analysis of these three forms of KHV-T (P0, P78 and P99) revealed a limited number of variations. The largest one was a deletion of 1363 bp in the predicted ORF150, which was detected in P78, but not in P99. This unexpected finding was confirmed by conventional PCR and digital PCR. The results presented here primarily suggest that, CyHV-3 evolves, at least in vitro, through an assemblage of haplotypes that alternatively become dominant or under-represented.

Published
2019

41. Lien entre Transformée de Burrows-Wheeler (BWT) et BWT étendue (XBW) via l'automate d'Aho-Corasick : applications en compression par encodage des longueurs

Author

Cazaux, Bastien, Rivals, Eric, Pisanti, Nadia, Pissis, Solon P., Department of Computer Science, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Support from the Institut de Biologie Computationnelle (ANR-11-BINF-0002).Eric Rivals: thanks the GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)., University of Pisa, Nadia Pisanti, Solon P. Pissis, ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Run Length Encoding (RLE), 000 Computer science, knowledge, general works, Aho-Corasick automaton, Aho-Corasick Tree, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], education, Burrows Wheeler Transform, Compression, Data_CODINGANDINFORMATIONTHEORY, 0102 computer and information sciences, 02 engineering and technology, XBWT, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Data Structures, 113 Computer and information sciences, 01 natural sciences, Algorithm, 2012 ACM Subject Classification Mathematics of computing → Discrete mathematics, Theory of computation → Randomness, geometry and discrete structures, Theory of computation → Data structures and algorithms for data management, 010201 computation theory & mathematics, Computer Science, 0202 electrical engineering, electronic engineering, information engineering, Indexing, 020201 artificial intelligence & image processing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Stringology
Abstract

URN: urn:nbn:de:0030-drops-104955URL: http://drops.dagstuhl.de/opus/volltexte/2019/10495/ISBN ={978-3-95977-103-0},ISSN ={1868-8969},; International audience; The boom of genomic sequencing makes compression of sets of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the Burrows-Wheeler Transform (BWT), a reversible permutation of a text that improves its compressibility. A similar data structure, the eXtended Burrows-Wheeler Transform (XBW), is able to index a tree labelled with alphabet symbols. A link between a multi-string BWT and the Aho-Corasick automaton has already been found and led to a way to build a XBW from a multi-string BWT. We exhibit a stronger link between a multi-string BWT and a XBW by using the order of the concatenation in the multi-string. This bijective link has several applications: first, it allows one to build one data structure from the other; second, it enables one to compute an ordering of the input strings that optimises a Run-Length measure (i.e., the compressibility) of the BWT or of the XBW.

Published
2019

42. Phase separation dynamics of gluten protein mixtures

Author

Amélie Banc, Paul Menut, Marie Helene Morel, Marie-Sousai Appavou, Edouard Chauveau, Justine Pincemaille, Laurence Ramos, Salvatore Costanzo, Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Jülich Centre for Neutron Science (JCNS), Ingénierie, Procédés, Aliments (GENIAL), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Labex Numev (ANR-10-LAB-20), Banc, A., Pincemaille, J., Costanzo, S., Chauveau, E., Appavou, M. -S., Morel, M. -H., Menut, P., Ramos, L., Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), and 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)

Subjects
Work (thermodynamics), Materials science, Glutens, gluténine, Spinodal decomposition, Thermodynamics, FOS: Physical sciences, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, Chemical Fractionation, 010402 general chemistry, 01 natural sciences, Viscoelasticity, law.invention, Viscosity, Glutenin, law, synchrotron, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Scattering, Radiation, ddc:530, chemistry.chemical_classification, biology, Scattering, Temperature, viscoélasticité, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Gluten, Synchrotron, 0104 chemical sciences, 3. Good health, Condensed Matter::Soft Condensed Matter, chemistry, gluten, biology.protein, Soft Condensed Matter (cond-mat.soft), 0210 nano-technology, Synchrotrons, glutenin, procédé de séparation
Abstract

We investigate by time-resolved Synchrotron ultra-small X-ray scattering the dynamics of liquid-liquid phase-separation (LLPS) of gluten protein suspensions following a temperature quench. Samples at a fixed concentration (237 mg/ml) but with different protein compositions are investigated. In our experimental conditions, we show that fluid viscoelastic samples depleted in polymeric glutenin phase-separate following a spinodal decomposition process. We quantitatively probe the late stage coarsening that results from a competition between thermodynamics that speeds up the coarsening rate as the quench depth increases, and transport that slows downs the rate. For even deeper quenches, the even higher viscoelasticity of the continuous phase leads to a "quasi" arrested phase separation. Anomalous phase-separation dynamics is by contrast measured for a gel sample rich in glutenin, due to elastic constraints. This work illustrates the role of viscoelasticity in the dynamics of LLPS in protein dispersions., Comment: accepted for publication in Soft Matter

Published
2019

43. Functional Selectivity of Lumbosacral Stimulation: Methodological Approach and Pilot Study to Assess Visceral Function in Pigs

Author

David Guiraud, Claire Delleci, David Andreu, Thomas Guiho, Jean-Rodolphe Vignes, Luc Bauchet, Christine Azevedo-Coste, Control of Artificial Movement and Intuitive Neuroprosthesis (CAMIN), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-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), CHU de Bordeaux Pellegrin [Bordeaux], Neurochirurgie [Hôpital Gui de Chauliac], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [Montpellier], Labex NUMEV, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [CHU Montpellier], and Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)

Subjects
Neuroprosthetics, Neural Prostheses, Swine, medicine.medical_treatment, media_common.quotation_subject, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Population, Urinary Bladder, 030232 urology & nephrology, Biomedical Engineering, Bowel management, Stimulation, Pilot Projects, Urination, [SPI.AUTO]Engineering Sciences [physics]/Automatic, 03 medical and health sciences, 0302 clinical medicine, Internal Medicine, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, education, Spinal Cord Injuries, media_common, education.field_of_study, Spinal Cord Stimulation, Rehabilitation, business.industry, Electromyography, General Neuroscience, Lumbosacral Region, Rectum, Spinal cord, Gastrointestinal Tract, medicine.anatomical_structure, Spinal Cord, SCI, Anesthesia, Dura Mater, Nerve Net, business, Spinal Nerve Roots, 030217 neurology & neurosurgery, Lumbosacral joint
Abstract

International audience; Nearly all spinal cord injured (SCI) individuals lose bladder control and are prone to kidney complications if intermittent catheterization is not applied. Electrical stimulation (ES) of the sacral anterior roots with an implantable neuroprosthesis is one means to restore continence and control micturition. However, only a small percentage of the SCI population benefits from this solution because of its drawbacks, e.g. section of sacral posterior roots with loss of spared sensitivity. There has been renewed interest in spinal cord stimulation in recent years, but most studies have focused on locomotion and only few have reported the impact on visceral functions. Moreover, even though the lumbosacral spinal cord is the location of many pre-cabled neural networks (involved in locomotion, bladder, bowel management etc.), the functional selectivity of spinal stimulations has never been investigated in detail. Here we present: i) a methodology designed to study lumbosacral epispinal-intradural stimulation selectivity, ii) preliminary results assessing the impact of epispinal stimulation on bladder and bowel functions in two domestic pigs, and iii) a comparison of these visceral responses with abdominal and lower limb activities. Our experiments resulted in selective bladder and rectal responses, i.e. without hind paw responses, thus reaffirming the rehabilitation potential of spinal cord stimulation.

Published
2018

44. Improvement of performances of the chemostat used for continuous biological water treatment with periodic controls

Author

Térence Bayen, Alain Rapaport, Fatima Zahra Tani, EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), AVERROES program, and LabEx NUMEV incorporated

Subjects
0209 industrial biotechnology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, convexity, 020208 electrical & electronic engineering, periodic control, Duality (optimization), 02 engineering and technology, Chemostat, 6. Clean water, Constraint (information theory), optimal control, 020901 industrial engineering & automation, Control and Systems Engineering, 0202 electrical engineering, electronic engineering, information engineering, duality, Applied mathematics, Water treatment, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Electrical and Electronic Engineering, integral constraint, Chemostat model, Mathematics
Abstract

We investigate the benefit of operating the chemostat model with periodic controls for biological water decontamination. The first problem that we consider is to minimize the average output concentration of pollution under a constraint on the total quantity of water treated over the period. The second one consists in maximizing this quantity under a constraint on the average output concentration. We first give conditions on the growth characteristics of micro-organisms for which an improvement of the objective function (for the two problems) is possible, compared to the value at steady-state. We then provide the (global) optimal periodic control strategies for the first problem, and we then show a duality property both problems, which allows us to deduce the solutions of the second problem from the solutions of the first one. Results are illustrated on Monod’s, Haldane’s, Hill’s, and Contois’s kinetics.

Published
2020

45. Signal modeling of an MRI ribbon solenoid coil dedicated to spinal cord injury investigations

Author

Nicolas Lonjon, Rahima Sidiboulenouar, Eric Nativel, Florence E. Perrin, Harun N. Noristani, Maida Cardoso, Michel Zanca, Marine Lecorre, Christophe Coillot, Christophe Goze-Bac, Guillaume P. Saint-Martin, Eric Alibert, Mécanismes moléculaires dans les démences neurodégénératives (MMDN), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Coillot, Christophe, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut d’Electronique et des Systèmes (IES), Térahertz, hyperfréquence et optique (TéHO), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Labex Numev, and Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM)

Subjects
Materials science, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Physics::Medical Physics, Solenoid, Coil, lcsh:Technology, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Magnetization, 0302 clinical medicine, Nuclear magnetic resonance, Region of interest, Ribbon, medicine, Electrical and Electronic Engineering, induction sensor, Instrumentation, Spinal cord injury, lcsh:T, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, medicine.disease, [SPI.TRON] Engineering Sciences [physics]/Electronics, [SPI.TRON]Engineering Sciences [physics]/Electronics, Antenna efficiency, Magnetic field, Electromagnetic coil, 030217 neurology & neurosurgery, MRI, Biomedical engineering
Abstract

Nuclear magnetic resonance imaging (NMRI) is a powerful tool for biological investigations. Nevertheless, the imaging resolution performance results in the combination of the magnetic field (B0) and the antenna efficiency. This latter one results in a compromise between the size of the sample, the location of the region of interest and the homogeneity requirement. In the context of spinal cord imaging on mice, a ribbon solenoid coil is used to enhance the efficiency of the MRI experiment. This paper details the calculation of the local magnetization contribution to the induced voltage of MRI coils. The modeling is illustrated on ribbon solenoid antennas used in emitter–receiver mode for the study. The analytical model, which takes into account the emitting mode, the receiving step and the imaging sequence, is compared to the measurement performed on a 9.4 T VARIAN MRI apparatus. The efficiency of the antenna, in terms of signal to noise ratio, is significantly enhanced with respect to a commercial quadrature volumic antenna, given a significant advantage for the study of spinal cord injuries.

Published
2018

46. OrthoInspector 3.0: open portal for comparative genomics

Author

Nevers, Yannis, Kress, Arnaud, Defosset, Audrey, Ripp, Raymond, Linard, Benjamin, Thompson, Julie, Poch, Olivier, Lecompte, Odile, linard, benjamin, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Agence Nationale de la Recherche : BIPBIP: ANR-10-BINF-03-02, ReNaBi-IFB: ANR-11-INBS-0013, Labex Agro: ANR-10-LABX-0001-01, Labex CeMEB: ANR-10-LABX-0004, Labex NUMEV: ANR-10-LABX-20, Universite de Strasbourg, Centre National de la Recherche Scientifique, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Méthodes et Algorithmes pour la Bioinformatique (MAB), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Internet, Bacteria, Proteome, Eukaryota, Genomics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Classification, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Evolution, Molecular, Gene Ontology, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Sequence Homology, Nucleic Acid, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Databases, Genetic, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Database Issue, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms, Phylogeny, Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Forecasting
Abstract

International audience; OrthoInspector is one of the leading software suites for orthology relations inference. In this paper, we describe a major redesign of the OrthoInspector online resource along with a significant increase in the number of species: 4753 organisms are now covered across the three domains of life, making OrthoInspector the most exhaustive orthology resource to date in terms of covered species (excluding viruses). The new website integrates original data exploration and visualization tools in an ergonomic interface. Distributions of protein orthologs are represented by heatmaps summarizing their evolutionary histories, and proteins with similar profiles can be directly accessed. Two novel tools have been implemented for comparative genomics: a phylogenetic profile search that can be used to find proteins with a specific presence-absence profile and investigate their functions and, inversely, a GO profiling tool aimed at deciphering evolutionary histories of molecular functions, processes or cell components. In addition to the re-designed website, the OrthoInspector resource now provides a REST interface for programmatic access. OrthoInspector 3.0 is available at http://lbgi.fr/orthoinspectorv3.

Published
2018

47. Alterations of EEG rhythms during motor preparation following awake brain surgery

Author

Bénédicte Poulin-Charronnat, Anthony Boyer, Sofiane Ramdani, David Guiraud, Hugues Duffau, François Bonnetblanc, Control of Artificial Movement and Intuitive Neuroprosthesis ( CAMIN ), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier ( LIRMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -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 ), Efficience Déficience Motrice [Montpellier] ( EDM ), Université Montpellier 1 ( UM1 ), Hôpital Gui de Chauliac, Université Montpellier 1 ( UM1 ) -Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ), Equipe Perception et cognition musicales, Sciences et Technologies de la Musique et du Son ( STMS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IRCAM-Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IRCAM-Centre National de la Recherche Scientifique ( CNRS ), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] ( CAPS ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences ( 2010 ), Control of Artificial Movement and Intuitive Neuroprosthesis (CAMIN), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), Interactive Digital Humans (IDH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Gui de Chauliac [CHU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Laboratoire d'Etude de l'Apprentissage et du Développement [Dijon] (LEAD), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] (CAPS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), LabEx NUMEV project by the French government's 'Investissements d'Avenir' program ANR-10-LABX-20 Institut Universitaire de France INSERM laboratory U1093, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)

Subjects
Adult, Male, medicine.medical_specialty, Cognitive Neuroscience, [SDV.CAN]Life Sciences [q-bio]/Cancer, Experimental and Cognitive Psychology, Spectral analysis, 050105 experimental psychology, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Lesion, 03 medical and health sciences, Cognition, 0302 clinical medicine, Arts and Humanities (miscellaneous), Awake brain surgery, Reaction Time, Developmental and Educational Psychology, medicine, Humans, 0501 psychology and cognitive sciences, Brainwaves, Wakefulness, Balance (ability), Brain Neoplasms, [SCCO.NEUR]Cognitive science/Neuroscience, 05 social sciences, Healthy subjects, Brain, Electroencephalography, Middle Aged, Surgery, Electrophysiology, Neuropsychology and Physiological Psychology, Behavioral data, Diffuse low-grade glioma, [ SCCO.NEUR ] Cognitive science/Neuroscience, Eeg rhythms, Female, medicine.symptom, Psychology, Eeg monitoring, 030217 neurology & neurosurgery
Abstract

International audience; Slow-growing, infiltrative brain tumours may modify the electrophysiological balance between the two hemispheres. To determine whether and how asymmetry of EEG rhythms during motor preparation might occur following " awake brain surgery " for this type of tumour, we recorded electroencephalograms during a simple visuo-manual reaction time paradigm performed by the patients between 3 and 12 months after surgery and compared them to a control group of 8 healthy subjects. Frequency analyses revealed imbalances between the injured and healthy hemispheres. More particularly, we observed a power increase in the δ frequency band near the lesion site and a power increase in the α and β frequency bands. Interestingly, these alterations seem to decrease for the two patients whose surgery were anterior to 9 months, independently of the size of the lesion. Reaction times did not reflect this pattern as they were clearly not inversely related to the anteriority of the surgery. Electrophysiology suggests here different processes of recovery compared to behavioral data and brings further insights for the understanding of EEG rhythms that should not be systematically confounded or assimilated with cognitive performances. EEG monitoring is rare for these patients, especially after awake brain surgery, however it is important.

Published
2018

48. Mining Frequent Subgraphs in Multigraphs

Author

Pascal Poncelet, Dino Ienco, Vijay Ingalalli, ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)

Subjects
Information Systems and Management, Theoretical computer science, Matching (graph theory), Computer science, Multigraphs, 02 engineering and technology, Frequent Subgraphs, Measure (mathematics), Theoretical Computer Science, Task (project management), [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Artificial Intelligence, Simple (abstract algebra), 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Multigraph, Graph, Computer Science Applications, Control and Systems Engineering, Graph (abstract data type), 020201 artificial intelligence & image processing, State (computer science), Software, Graph Mining, MathematicsofComputing_DISCRETEMATHEMATICS
Abstract

International audience; For more than a decade, extracting frequent patterns from single large graphs has been one of the research focuses. However, in this era of data eruption, rich and complex data is being generated at an unprecedented rate. This complex data can be represented as a multigraph structure-a generic and rich graph representation. In this paper, we propose a novel frequent subgraph mining approach MuGraM that can be applied to multigraphs. MuGraM is a generic frequent subgraph mining algorithm that discovers frequent multigraph patterns. MuGraM eciently performs the task of subgraph matching, which is crucial for support measure, and further leverages several optimization techniques for swift discovery of frequent subgraphs. Our experiments reveal two things: MuGraM discovers multigraph patterns, where other existing approaches are unable to do so; MuGraM, when applied to simple graphs, outperforms the state of the art approaches by at least one order of magnitude.

Published
2018

49. Rapid alignment-free phylogenetic identification of metagenomic sequences

Author

Krister M. Swenson, Benjamin Linard, Fabio Pardi, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), Labex CeMEB : ANR-10-LABX-0004, Labex NUMEV : ANR-10-LABX-20, Labex: Labex Agro : ANR10-LABX-0001-01, European Project: 634650,H2020,H2020-PHC-2014-two-stage,VIROGENESIS(2015), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
0106 biological sciences, Statistics and Probability, Computer science, Sequence analysis, Sequence alignment, Computational biology, computer.software_genre, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Biochemistry, DNA sequencing, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Environmental DNA, Molecular Biology, Phylogeny, 030304 developmental biology, Sequence, 0303 health sciences, Likelihood Functions, Phylogenetic tree, Biological classification, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Computational Mathematics, Tree (data structure), Computational Theory and Mathematics, chemistry, Metagenomics, Precomputation, Metagenome, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Sequence Alignment, DNA, Algorithms, Software
Abstract

Motivation Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing. Results We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics. Availability and implementation Program and sources freely available for download at https://github.com/blinard-BIOINFO/RAPPAS. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2018

50. Structure and dynamics of a polymer-nanoparticle composite: Effect of nanoparticle size and volume fraction

Author

Valerio Sorichetti, Virginie Hugouvieux, Walter Kob, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and LabEx NUMEV - Investissements d'Avenir French Government program [ANR-10-LABX-20]

Subjects
Materials science, Polymers and Plastics, FOS: Physical sciences, Nanoparticle, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, 01 natural sciences, Inorganic Chemistry, Molecular dynamics, 0103 physical sciences, Materials Chemistry, [PHYS.COND.CM-DS-NN]Physics [physics]/Condensed Matter [cond-mat]/Disordered Systems and Neural Networks [cond-mat.dis-nn], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, chemistry.chemical_classification, Condensed Matter - Materials Science, Organic Chemistry, Polymer nanoparticle, Dynamics (mechanics), Materials Science (cond-mat.mtrl-sci), Disordered Systems and Neural Networks (cond-mat.dis-nn), Polymer, Condensed Matter - Disordered Systems and Neural Networks, 021001 nanoscience & nanotechnology, chemistry, Chemical engineering, Polymer solution, Volume fraction, Soft Condensed Matter (cond-mat.soft), 0210 nano-technology, Composite effect
Abstract

We use molecular dynamics simulations to study a semidilute, unentangled polymer solution containing well dispersed, weakly attractive nanoparticles (NP) of size ($\sigma_N$) smaller than the polymer radius of gyration $R_g$. We find that if $\sigma_N$ is larger than the monomer size the polymers swell, while smaller NPs cause chain contraction. The diffusion coefficient of polymer chains ($D_p$) and NPs ($D_N$) decreases if the volume fraction $\phi_N$ is increased. The decrease of $D_p$ can be well described in terms of a confinement parameter, while $D_N$ shows a more complex dependence on $\sigma_N$, which results from an interplay between energetic and entropic effects. When $\phi_N$ exceeds a $\sigma_N$-dependent value, the NPs are no longer well dispersed and $D_N$ and $D_p$ increase if $\phi_N$ is increased.

Published
2018

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