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1. Spectral bandits

Author

Kocák, Tomáš, Munos, Rémi, Kveton, Branislav, Agrawal, Shipra, Valko, Michal, École normale supérieure de Lyon (ENS de Lyon), Scool (Scool), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), DeepMind [Paris], Google Research, Columbia University [New York], The research presented in this paper was supported by French Ministry of Higher Education and Research, by European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no270327 (project CompLACS), European CHIST-ERA project DELTA, French Ministry of Higher Education and Research, Inria and Otto-von-GuerickeUniversit¨at Magdeburg associated-team North-European project Allocate, Nord-Pas-deCalais Regional Council, CPER Nord-Pas de Calais/FEDER DATA Advanced data science and technologies 2015-2020, French National Research Agency projects ExTra-Learn (n°ANR-14-CE24-0010-01) and BoB (n°ANR-16-CE23-0003), Intel Corporation, FMJH Program PGMO with the support to this program from CRITEO., ANR-14-CE24-0010,ExTra-Learn,Extraction et transfert de connaissances dans l'apprentissage par renforcement(2014), ANR-16-CE23-0003,BoB,Inférence bayésienne à ressources limitées - données massives et modèles coûteux(2016), and École normale supérieure - Lyon (ENS Lyon)

Subjects
[STAT.ML]Statistics [stat]/Machine Learning [stat.ML]
Abstract

International audience; Smooth functions on graphs have wide applications in manifold and semi-supervised learning. In this work, we study a bandit problem where the payoffs of arms are smooth on a graph. This framework is suitable for solving online learning problems that involve graphs, such as content-based recommendation. In this problem, each item we can recommend is a node of an undirected graph and its expected rating is similar to the one of its neighbors. The goal is to recommend items that have high expected ratings. We aim for the algorithms where the cumulative regret with respect to the optimal policy would not scale poorly with the number of nodes. In particular, we introduce the notion of an effective dimension, which is small in real-world graphs, and propose three algorithms for solving our problem that scale linearly and sublinearly in this dimension. Our experiments on contentrecommendation problem show that a good estimator of user preferences for thousands of items can be learned from just tens of node evaluations.

Published
2020

2. Odorant-binding proteins mutants having novel binding properties

Author

Barou, Emilie, Belloir, Christine, Poirier, Nicolas, Neiers, Fabrice, Briand, Loïc, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), The French Ministry for Higher Education and Research, the Regional Council of Burgundy France (PARI Agral 1) and the FEDER (European Funding for Regional Economical Development)., Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), French Ministry for Higher Education and Research Regiona Council of Burgundy France (PARI Agral 1) FEDER (European Funding for Regional Economical Development), European Chemorecept Res Org, Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC)

Subjects
Physiology, [ SDV.NEU ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Food Science & Technology, Neurosciences, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Behavioral Sciences, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS
Abstract

Odorant-binding proteins (OBP) are small soluble proteins present in the nasal mucus covering the olfactory epithelium. Vertebrate OBPs belong to the lipocalin superfamily, whose members share a common scaffold made of 8-stranded β-barrel. This folding pattern defines a central apolar cavity, named calyx, whose role is to bind hydrophobic molecules such as odorants. Although the physiological role of OBPs is not clearly established, they are supposed to carry odorants from the air to olfactory receptors through the aqueous nasal mucus. OBPs have been described in numerous species including pig, rat and human beings. OBPs are broadly tuned and bind a large spectrum of volatile molecules. Interestingly, it has been shown that the three rat OBP subtypes (rOBP1, rOBP2, rOBP3) have different and complementary ligand properties [1], suggesting that OBPs are involved in odorant discrimination. Protein sequence alignment of the three rat OBPs reveals the presence of an amino acid residue located in the binding pocket, which may be important for guiding binding specificity. Using site-directed mutagenesis, we generated variants of rOBP3, in which this amino acid residue has been substituted. Using isothermal titration calorimetry, we found that some substitutions decreased the affinity of rOBP3 towards some odorant molecules while others generated OBPs possessing novel binding properties. Our work gives new elements to understand the binding mechanisms of OBPs and opens the way towards technological applications based on OBP, as odorant biosensors. [1] D. Löbel, M. Jacob, M. Volkner, H. Breer, Odorants of different chemical classes interact with distinct odorant binding protein subtypes, Chem. Senses, 27 (2002) 39-44.

Published
2016
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3. The performance of approximate equation of motion coupled cluster for valence and core states of heavy element systems

Author

Halbert, Loïc, Gomes, Andre Severo Pereira, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF), Project CPER WAVETECH, French national supercomputing facilities (grants DARI A0090801859, A0110801859), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-16-IDEX-0004,ULNE,ULNE(2016), and ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019)

Subjects
Chemical Physics (physics.chem-ph), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Physics - Chemical Physics, FOS: Physical sciences
Abstract

The equation of motion coupled cluster singles and doubles model (EOM-CCSD) is an accurate, black-box correlated electronic structure approach to investigate electronically excited states and electron attachment or detachment processes. It has also served as a basis for developing less computationally expensive approximate models such as partitioned EOM-CCSD (P-EOM-CCSD), the second-order many-body perturbation theory EOM (EOM-MBPT(2)), and their combination (P-EOM-MBPT(2)) [S. Gwaltney et al., Chem. Phys. Lett. 248, 189-198 (1996)]. In this work we outline an implementation of these approximations for four-component based Hamiltonians and investigate their accuracy relative to EOM-CCSD for valence excitations, valence and core ionizations and electron attachment, and this for a number of systems of atmospheric or astrophysical interest containing elements across the periodic table. We have found that across the different systems and electronic states of different nature considered, partition EOM-CCSD yields results with the largest deviations from the reference, whereas second-order based approaches tend show a generally better agreement with EOM-CCSD. We trace this behavior to the imbalance brought about by the removal of excited state relaxation in the partition approaches, with respect to degree of electron correlation recovered., Comment: 5 figures, 4 tables

Published
2023

4. Protein - ligand interactions from a quantum fragmentation perspective : the case of the SARS-CoV-2 main protease interacting with α−ketoamide inhibitors

Author

Genovese, Luigi, Dawson, William, Nakajima, Takahito, Cristiglio, Viviana, Vallet, Valérie, Masella, Michel, Laboratory of Atomistic Simulation (LSIM), Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), RIKEN Center for Computational Science [Kobe] (RIKEN CCS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut Laue-Langevin (ILL), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), TGCC HPC resources under the allocation 2019-2020[A0070307078] and the Grand Challenge allocation [GC0429] made by GENCI, MAX EU Center of Excellence, CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), and ANR-16-IDEX-0004,ULNE,ULNE(2016)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

International audience; We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable Molecular Modeling, MM, approach to perform MD simulations and on an efficient DFT Linear Scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme in particular by checking the ability of MM and DFT to reproduce results from high-end ab initio computations regarding such inhibitors. The DFT approach enables an a posterior fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs.

Published
2023
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5. How does bending the uranyl unit influence its spectroscopy and luminescence

Author

Hanna Oher, André Severo Pereira Gomes, Richard E. Wilson, David D. Schnaars, Valérie Vallet, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Chemical Sciences and Engineering Division [Argonne], Argonne National Laboratory [Lemont] (ANL), Deutsche Forschung Gemeinschaft JA 2329/6, I-SITE ULNE projects OVERSEE, I-SITE ULNE MESONM International Associated Laboratory (LAI), French Ministry of Higher Education and Research, Région Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, WaveTech, French national supercomputing facilities (grants DARI A0130801859, A0110801859, U.S. DOE Office of Science, Office of Basic Energy Sciences, Chemical Sciences Geological and Biosciences Division,Heavy Element Chemistry program under Contract DE-AC02-06CH11357, ANR-21-CE29-0027,CHESS,Chimie, spectroscopie et spéciation du protactinium(2021), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-16-IDEX-0004,ULNE,ULNE(2016), and ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.INOR]Chemical Sciences/Inorganic chemistry
Abstract

International audience; Bent uranyl complexes can be formed with chloride ligands and 1,10-phenanthroline (phen) ligands bound to the equatorial and axial planes of the uranyl(VI) moiety, as revealed by the crystal structures, IR and Raman spectroscopy and quantum chemical calculations. With the goal of probing the influence of chloride and phenanthroline coordination enforcing the bending on the absorption and emission spectra of this complex, spin-orbit time-dependent density functional theory calculations for the bare uranyl complexes as well as for the free UO2Cl2 subunit and the UO2Cl2(phen)2 ligand were performed. The emission spectra has been fully simulated by ab initio methods and compared to experimental photoluminescence spectra, recorded for the first time for UO2Cl2(phen)2. Notably, the bending of uranyl in UO2Cl2 and UO2Cl2(phen)2 triggers excitations of the uranyl bending mode, yielding a denser luminescence spectrum.

Published
2023
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6. Complex 4q35 and 10q26 Rearrangements

Author

Delourme, Megane, Charlene, Chaix, Gerard, Laurene, Ganne, Benjamin, Perrin, Pierre, Vovan, Catherine, Bertaux, Karine, Nguyen, Karine, Bernard, Rafaelle, Magdinier, Frederique, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de ressources biologiques Tissus ADN Cellules [Hôpital de la Timone - APHM] (CRB TAC), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Association Française contre les Myopathies (AFM-Telethon, TRIM-RD and MoThARD poles)French Ministry of Higher education and Research

Subjects
[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, [SDV]Life Sciences [q-bio], [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Background and Objectives After clinical evaluation, the molecular diagnosis of type 1 facioscapulohumeral dystrophy (FSHD1) relies in most laboratories on the detection of a shortened D4Z4 array at the 4q35 locus by Southern blotting. In many instances, this molecular diagnosis remains inconclusive and requires additional experiments to determine the number of D4Z4 units or identify somatic mosaicism, 4q-10q translocations, and proximal p13E-11 deletions. These limitations highlight the need for alternative methodologies, illustrated by the recent emergence of novel technologies such as molecular combing (MC), single molecule optical mapping (SMOM), or Oxford Nanopore-based long-read sequencing providing a more comprehensive analysis of 4q and 10q loci. Over the last decade, MC revealed a further increasing complexity in the organization of the 4q and 10q distal regions in patients with FSHD with cis -duplication of D4Z4 arrays in approximately 1%–2% of cases. Methods By using MC, we investigated in our center 2,363 cases for molecular diagnosis of FSHD. We also evaluated whether previously reported cis -duplications might be identified by SMOM using the Bionano EnFocus FSHD 1.0 algorithm. Results In our cohort of 2,363 samples, we identified 147 individuals carrying an atypical organization of the 4q35 or 10q26 loci. Mosaicism is the most frequent category followed by cis -duplications of the D4Z4 array. We report here chromosomal abnormalities of the 4q35 or 10q26 loci in 54 patients clinically described as FSHD, which are not present in the healthy population. In one-third of the 54 patients, these rearrangements are the only genetic defect suggesting that they might be causative of the disease. By analyzing DNA samples from 3 patients carrying a complex rearrangement of the 4q35 region, we further showed that the SMOM direct assembly of the 4q and 10q alleles failed to reveal these abnormalities and lead to negative results for FSHD molecular diagnosis. Discussion This work further highlights the complexity of the 4q and 10q subtelomeric regions and the need of in-depth analyses in a significant number of cases. This work also highlights the complexity of the 4q35 region and interpretation issues with consequences on the molecular diagnosis of patients or genetic counseling.

Published
2023
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7. Modeling environment effect on heavy-element compounds

Author

Olejniczak, Małgorzata, Vallet, Valérie, Severo Pereira Gomes, André, Centre of New Technologies, Medical University of Warsaw - Poland, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), he French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF) projects CPER CLIMIBIO and WAVETECH, Deutsche Forschungsgemeinschaft JA 2329/6-1, Polish National Science Centre (NCN) (grantnumber 2020/38/E/ST4/00614, ANR-16-IDEX-0004,ULNE,ULNE(2016), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-21-CE29-0027,CHESS,Chimie, spectroscopie et spéciation du protactinium(2021), and ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry
Abstract

Modeling the behavior of molecular complexes containing one or more heavy elements by means of electronic structure calculations, in particular when attempting to understand their molecular properties, is a very challenging task since one has to account not only for electron correlation and relativistic effects but in many cases consider the effect of other species in their vicinity as well. In this chapter, we address how such environment effects can be taken into account in a computationally efficient manner through different flavors of so-called embedding theories, underscoring the applicability, strengths, and weaknesses of the most commonly used approaches.

Published
2023

8. Transition Moments Beyond the Electric-Dipole Approximation: Visualization and Basis Set Requirements

Author

Martin van Horn, Nanna Holmgaard List, Trond Saue, Laboratoire de Chimie et Physique Quantiques Laboratoire (LCPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Royal Institute of Technology [Stockholm] (KTH ), French Ministry of Higher Education and Research, CALMIP (Calcul en Midi-Pyrenées, project P13154), SNIC (Swedish National Infrastructure for Computing, and SNIC 2022/5-220)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, General Physics and Astronomy, Physical and Theoretical Chemistry
Abstract

In the simulation of X-ray absorption spectroscopy, the validity of the electric dipole approximation comes into question. Three different schemes exist to go beyond thisapproximation: the first scheme is based on the full semi-classical light-matter inter-action, whereas the latter two schemes, referred to as the generalized length and velocity representation, are based on truncated multipole expansions. Even though these schemes have been successfully implemented in several quantum chemistry codes,their basis set requirements remained largely unknown. Here, we assess the basis set requirements of the full interaction operator and the generalized length and velocity representations. These three schemes were applied in the calculation of radial distributions of transition moment densities corresponding to the 1s1/2 and 7s1/2 7p1/2transition in the radium atom, representative of core and valence excitations, respectively. We have performed calculations with the dyall.aeXz (X=2,3,4) basis sets at the four-component relativistic TD-HF level of theory and compared them withequivalent finite-difference calculations. We find that the full interaction is extremelystable with respect to the choice of basis set, already being converged with dyall.ae2z.With respect to truncated interaction, we find that the length representation electric multipoles is the easiest to converge, requiring the dyall.ae2z basis for low-order multipoles and the dyall.ae4z basis at higher orders. The magnetic multipole moments follow a similar trend, although they are more diffcult to converge. The velocity representation electric multipoles are the most difficult to converge: at high orders, thedyall.ae3z and dyall.ae4z basis sets introduce artificial peaks and oscillations, which increase the overall error. These artifacts are associated with linear dependence issues in the small component space of the larger basis sets. The full interaction operator,however, does not suffer from these problems, and we therefore recommend its use in the simulation of x-ray spectroscopy.

Published
2023
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9. Behavioural syndrome between boldness and aggressiveness and link with reproductive success in a wild bird population

Author

Thibault Tamin, Jennifer Morinay, Marion Germain, Charlotte Récapet, Blandine Doligez, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne = University of Lausanne (UNIL), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French Ministry of Higher Education and Research, CNRS, Region Rhone-Alpes, and Zoological Institute of Uppsala University

Subjects
behavioural test, fledging success, neophobia, recruitment, Ficedula albicollis, personality trait, Animal Science and Zoology, among- and within-individual correlation, collared flycatcher, heritability, repeatability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Boldness, defined as the behavioural response of individuals when facing a risky situation, is a majorpersonality trait and often phenotypically correlates with other behavioural traits, in particular aggressiveness,exploration behaviour and neophobia. Yet, whether such links result from among-individualcorrelations, i.e. form behavioural syndromes sensu stricto, is often ignored and whether such syndromesmay yield individual fitness benefits, and thus be selected for, remains poorly explored. Wemeasured boldness as the nest defence behaviour against a dummy nest predator in a natural populationof a small passerine bird, the collared flycatcher, Ficedula albicollis, and investigated the existence of abehavioural syndrome between boldness and two other behavioural traits, aggressiveness (measured asthe agonistic response to competitors) and neophobia (measured as the behavioural response to a novelobject in a known environment). Then we assessed the links between this potential syndrome andreproductive success, measured as fledging and recruitment success. Boldness score differed between thesexes and depended on whether the partner was present during the test. Nevertheless, it was repeatable,showing that boldness can be considered as a personality trait in our population. We found a positiveamong-individual correlation between boldness and aggressiveness, showing the existence of a behaviouralsyndrome between both personality traits. This syndrome was related to reproductive success: thenumber of fledged young (but not recruitment probability) increased with one integrative value of theboldnesseaggressiveness syndrome. Conversely, boldness score was not correlated with neophobia. Ourresults thus clearly reveal a behavioural syndrome between boldness and aggressiveness with possibleconsequences for reproductive success in the study population, and therefore raise the question of theevolutionary implications of such a behavioural syndrome

Published
2023
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10. CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection

Author

Andrew E. Prendergast, Kin Ki Jim, Hugo Marnas, Laura Desban, Feng B. Quan, Lydia Djenoune, Valerio Laghi, Agnès Hocquemiller, Elias T. Lunsford, Julian Roussel, Ludovic Keiser, Francois-Xavier Lejeune, Mahalakshmi Dhanasekar, Pierre-Luc Bardet, Jean-Pierre Levraud, Diederik van de Beek, Christina M.J.E. Vandenbroucke-Grauls, Claire Wyart, Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of Amsterdam [Amsterdam] (UvA), Vrije Universiteit Amsterdam [Amsterdam] (VU), Amsterdam institute for Infection and Immunity [Amsterdam, The Netherlands] (A3I), Macrophages et Développement de l’Immunité, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by the Fondation Schlumberger pour l’Education et la Recherche (FSER/2017), the Fondation pour la Recherche Médicale (FRM no. Equation 202003010612), the ERC Starting Grant 'Optoloco' no. 311673, ERC PoC 'ZebraZoom' no. 825273, and ERC Consolidator Grant 'Exploratome' no. 101002870 (to C.W.). We acknowledge support from 'MeninGene' no. 281156 and the HFSP Program grant nos. RGP0063/2014 and RGP0063/2017 and grants from the Agence Nationale de la Recherche (ANR) ASCENTS no. ANR-21-CE13-0008, MOTOMYO no. ANR-21-CE14-0042, and ANR LOCOCONNECT no. ANR-22-CE37-0023 et la Fondation Bettencourt-Schueller don 0031. D.v.d.B. was supported by a ZonMw VICI grant no. 391819627. A.E.P. was supported by an EMBO long-term fellowship (ALTF-549-2013) and a Research in Paris grant from the Marie de Paris. L. Desban was supported by the French Ministry of Higher Education and Research doctoral fellowship. M.D. was supported by a PhD fellowship from the Sorbonne Université Ecole Doctorale ED3C., ANR-21-CE13-0008,ASCENTS,Étude d'une asymétrie structurelle nouvellement identifiée du centriole des vertébrés et de son impact sur le développement et la santé(2021), ANR-21-CE14-0042,MOTOMYO,Appariement entre sous types de motoneurones et sous types de myofibres: du développement à la pathologie(2021), ANR-22-CE37-0023,LOCONNECT,Transmission d'information causale lors de la locomotion(2022), European Project: 311673,EC:FP7:ERC,ERC-2012-StG_20111109,OPTOLOCO(2013), Medical Microbiology and Infection Prevention, AII - Infectious diseases, AII - Inflammatory diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, ANS - Neuroinfection & -inflammation, and Neurology

Subjects
[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, in-situ hybridization, interoception, substance inducing transformation, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, General Biochemistry, Genetics and Molecular Biology, cerebrospinal fluid, volatile metabolites, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, central nervous system infection, innate immunity, cytolysins, solitary chemosensory cells, pneumococcal types, chemical nature, zebrafish, gene-expression, pathogen detection, cerebrospinal-fluid, cytokines, sensory neurons, host defense, peptides, taste receptors, neurosecretion, General Agricultural and Biological Sciences, bacterial meningitis, bitter compounds
Abstract

International audience; The pathogenic bacterium Streptococcus pneumoniae (S. pneumoniae) can invade the cerebrospinal fluid (CSF) and cause meningitis with devastating consequences. Whether and how sensory cells in the central nervous system (CNS) become activated during bacterial infection, as recently reported for the peripheral nervous system, is not known. We find that CSF infection by S. pneumoniae in larval zebrafish leads to changes in posture and behavior that are reminiscent of pneumococcal meningitis, including dorsal arching and epileptic-like seizures. We show that during infection, invasion of the CSF by S. pneumoniae massively activates in vivo sensory neurons contacting the CSF, referred to as “CSF-cNs” and previously shown to detect spinal curvature and to control posture, locomotion, and spine morphogenesis. We find that CSF-cNs express orphan bitter taste receptors and respond in vitro to bacterial supernatant and metabolites via massive calcium transients, similar to the ones observed in vivo during infection. Upon infection, CSF-cNs also upregulate the expression of numerous cytokines and complement components involved in innate immunity. Accordingly, we demonstrate, using cell-specific ablation and blockade of neurotransmission, that CSF-cN neurosecretion enhances survival of the host during S. pneumoniae infection. Finally, we show that CSF-cNs respond to various pathogenic bacteria causing meningitis in humans, as well as to the supernatant of cells infected by a neurotropic virus. Altogether, our work uncovers that central sensory neurons in the spinal cord, previously involved in postural control and morphogenesis, contribute as well to host survival by responding to the invasion of the CSF by pathogenic bacteria during meningitis.

Published
2023
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11. Broadly neutralizing anti-HIV-1 antibodies tether viral particles at the surface of infected cells

Author

Jérémy Dufloo, Cyril Planchais, Stéphane Frémont, Valérie Lorin, Florence Guivel-Benhassine, Karl Stefic, Nicoletta Casartelli, Arnaud Echard, Philippe Roingeard, Hugo Mouquet, Olivier Schwartz, Timothée Bruel, Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École Doctorale Bio Sorbonne Paris Cité [Paris] (ED562 - BioSPC), Université Sorbonne Paris Cité (USPC)-Université Paris Cité (UPCité), Immunologie humorale - Humoral Immunology, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Trafic membranaire et Division cellulaire - Membrane Traffic and Cell Division, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Plateforme IBISA de Microscopie Electronique [CHRU de Tours] (UNIV Tours), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Université de Tours (UT), Vaccine Research Institute [Créteil, France] (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), O.S. is funded by Institut Pasteur, Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), Sidaction, the Vaccine Research Institute (ANR-10-LABX-77), Labex IBEID (ANR-10-LABX-62-IBEID), 'TIMTAMDEN' ANR-14-CE14-0029, 'CHIKV-Viro-Immuno' ANR-14-CE14-0015-01, and the Gilead HIV cure program. J.D. is funded by a Ph.D grant from the French Ministry of Higher Education and Research. H.M. is funded by the Institut Pasteur, the Milieu Intérieur Program (ANR-10-LABX-69-01), INSERM, ANRS, and Gilead HIV cure program. C.P. was supported by an ANRS fellowship. A.E. and S.F. are funded by Institut Pasteur, CNRS, and ANRS (ANRS-21020 AP2020-2). P.R. is funded by INSERM, Université de Tours and ANRS., ANR-10-LABX-0077,VRI,Initiative for the creation of a Vaccine Research Institute(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-14-CE14-0029,TIMTAMDEN,Rôle des récepteurs TIM et TAM dans l'infection des cellules cibles par le virus de la dengue(2014), ANR-14-CE14-0015,CHIKV-Viro-Immuno,Multiplication et Relation avec l'hôte du virus Chikungunya(2014), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Vaccine Research Institute (VRI), Institut Pasteur, Agence Nationale de la Recherche (France), Ministére de l'Education Nationale de la Recherche et de la Technologie (France), and Université de Tours

Subjects
MESH: Epitopes, T-Lymphocytes, Science, viruses, General Physics and Astronomy, HIV Infections, MESH: Host Microbial Interactions, HIV Antibodies, General Biochemistry, Genetics and Molecular Biology, Cell Line, MESH: Antibodies, Neutralizing, MESH: HIV-1, Epitopes, MESH: Antibody-Dependent Cell Cytotoxicity, Humans, MESH: Broadly Neutralizing Antibodies, Multidisciplinary, MESH: Humans, Host Microbial Interactions, MESH: HIV Antibodies, Antibody-Dependent Cell Cytotoxicity, Virion, env Gene Products, Human Immunodeficiency Virus, virus diseases, General Chemistry, MESH: HIV Infections, Antibodies, Neutralizing, MESH: Cell Line, MESH: T-Lymphocytes, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, MESH: Virion, MESH: env Gene Products, Human Immunodeficiency Virus, Broadly Neutralizing Antibodies
Abstract

Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) are promising molecules for therapeutic or prophylactic interventions. Beyond neutralization, bNAbs exert Fc-dependent functions including antibody-dependent cellular cytotoxicity and activation of the complement. Here, we show that a subset of bNAbs targeting the CD4 binding site and the V1/V2 or V3 loops inhibit viral release from infected cells. We combined immunofluorescence, scanning electron microscopy, transmission electron microscopy and immunogold staining to reveal that some bNAbs form large aggregates of virions at the surface of infected cells. This activity correlates with the capacity of bNAbs to bind to Env at the cell surface and to neutralize cell-free viral particles. We further show that antibody bivalency is required for viral retention, and that aggregated virions are neutralized. We have thus identified an additional antiviral activity of bNAbs, which block HIV-1 release by tethering viral particles at the surface of infected cells., O.S. is funded by Institut Pasteur, Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS), Sidaction, the Vaccine Research Institute (ANR-10-LABX-77), Labex IBEID (ANR-10-LABX-62-IBEID), “TIMTAMDEN” ANR-14-CE14-0029, “CHIKV-Viro-Immuno” ANR-14-CE14-0015-01, and the Gilead HIV cure program. J.D. is funded by a Ph.D grant from the French Ministry of Higher Education and Research. H.M. is funded by the Institut Pasteur, the Milieu Intérieur Program (ANR-10-LABX-69-01), INSERM, ANRS, and Gilead HIV cure program. C.P. was supported by an ANRS fellowship. A.E. and S.F. are funded by Institut Pasteur, CNRS, and ANRS (ANRS-21020 AP2020-2). P.R. is funded by INSERM, Université de Tours and ANRS.

Published
2022
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12. Bandwidth Enhancement by Interconnecting Double Hexagonal Loops FSS

Author

Nur Biha Mohamed Nafis, Mohamad Kamal A. Rahim, Mohamed Himdi, Universiti Teknologi Malaysia (UTM), Institut d'Électronique et des Technologies du numéRique (IETR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Mobility Grant from Rennes Metropole, European Union through the European Regional Development Fund, French Ministry of Higher Education and Research, Region Bretagne, CPER Project 2015-2020 SOPHIE/STIC, Ministry of Higher Education (MOHE) [FRGS/1/2021/TK0/UTM/01/7], Universite de Rennes 1, Ondes, School of Postgraduate Studies (SPS), Research Management Centre, School of Electrical Engineering [09G19], and Universiti Teknologi Malaysia (UTM), Johor Bahru [09G19]

Subjects
[SPI]Engineering Sciences [physics], low cross-polarisation, interconnect, fractal, mosaic frequency selective surface, wideband
Abstract

International audience; The paper proposed a mosaic frequency selective surface (MFSS) which comprises of the integration between Koch fractal and a basic double hexagonal loop FSS. Through this integration, the bandwidth (BW) within the first bandstop and bandpass frequency responses achieved a wideband frequency response (fractional bandwidth (FBW) > 50%), while the BW of the second bandstop frequency response improved (FBW similar to 20%). The simulation process is conducted by using the CST software, and the FR4 substrate is used as the dielectric substrate for all of the proposed unit cells. With narrow trace width of the MFSS, the structural element can be further applied for optical transparency application with wideband filtering characteristics.

Published
2022
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13. Geometries, interaction energies and bonding in [Po(H2O)n]4+ and [PoCln]4-n complexes

Author

Nadiya Zhutova, Florent Réal, Valérie Vallet, Rémi Maurice, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique subatomique et des technologies associées (SUBATECH), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), MITI of CNRS (80|Prime project MSM4Po), HPC resources from the CCIPL (‘‘Centre de calcul intensif des Pays de la Loire’’), French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO., ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), and ANR-16-IDEX-0004,ULNE,ULNE(2016)

Subjects
Chemical Physics (physics.chem-ph), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Physics - Chemical Physics, General Physics and Astronomy, FOS: Physical sciences, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry
Abstract

International audience; Polonium (Z = 84) is one of the rarest elements on Earth. More than a century after its discovery, its chemistry remains poorly known and even basic questions have not yet been satisfactorily addressed. In this work, we perform a systematic study of the geometries, interactions energies and bonding in basic polonium(IV) species, namely the hydrated [Po(H2O)n]4+ and chlorinated [PoCl2]4-n complexes by means of gas-phase electronic structure calculations. We show that while up to nine water molecules can fit in the first coordination sphere of the polonium(IV) ion, its coordination sphere can already be filled with eight chloride ligands. Capitalising on previous theoretical studies, a focused methodological study based on interaction energies and bond distances allows us to validate the MP2/def2-TZVP level of theory for future ground-state studies. After discussing the similarities and differences between complexes with the same number of ligands, we perform topological analyses of the MP2 electron densities in the quantum theory of atoms in molecules (QTAIM) fashion. While the water complexes display typical signatures of closed-shell interactions, we reveal large Po–Cl delocalisation indices, especially in the hypothetical [PoCl]3+ complex. This “enhanced” covalency opens the way for a significant spin–orbit coupling (SOC) effect on the corresponding bond distance, which has been studied using two independent approaches (i.e. one a priori and one a posteriori). We finally conclude by stressing that while the SOC may not affect much the geometries of high-coordinated polonium(IV) complexes, it should definitely not be neglected in the case of low-coordinated ones.

Published
2022
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14. Risk-aware linear bandits with convex loss

Author

Saux, Patrick, Maillard, Odalric-Ambrym, Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Scool (Scool), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and French National Research Agency, the French Ministry of Higher Education and Research, Inria, the MEL and the I-Site ULNE regarding project R-PILOTE-19-004-APPRENF and Bandits For Health (B4H).

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, risk-awareness, online gradient descent, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Statistics - Machine Learning, Machine Learning (stat.ML), Contextual bandit, elicitable risk measures, Machine Learning (cs.LG), UCB
Abstract

International audience; In decision-making problems such as the multi-armed bandit, an agent learns sequentially by optimizing a certain feedback. While the mean reward criterion has been extensively studied, other measures that reflect an aversion to adverse outcomes, such as mean-variance or conditional value-at-risk (CVaR), can be of interest for critical applications (healthcare, agriculture). Algorithms have been proposed for such risk-aware measures under bandit feedback without contextual information. In this work, we study contextual bandits where such risk measures can be elicited as linear functions of the contexts through the minimization of a convex loss. A typical example that fits within this framework is the expectile measure, which is obtained as the solution of an asymmetric least-square problem. Using the method of mixtures for supermartingales, we derive confidence sequences for the estimation of such risk measures. We then propose an optimistic UCB algorithm to learn optimal risk-aware actions, with regret guarantees similar to those of generalized linear bandits. This approach requires solving a convex problem at each round of the algorithm, which we can relax by allowing only approximated solution obtained by online gradient descent, at the cost of slightly higher regret. We conclude by evaluating the resulting algorithms on numerical experiments.

Published
2022

15. Small RNA-sequencing reveals the involvement of microRNA-132 in benzo[a]pyrene-induced toxicity in primary human blood cells

Author

Rima Souki, Jérémy Amosse, Valentine Genêt, Morgane Le Gall, Benjamin Saintpierre, Franck Letourneur, Anne Maître, Christine Demeilliers, Eric Le Ferrec, Dominique Lagadic-Gossmann, Normand Podechard, Lydie Sparfel, Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Environnement et Prévention en Santé des Populations (TIMC-EPSP ), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), and The funding of this work was supported by The French National Research Program for Environmental and Occupational Health of Anses (2019/1/010) Rima Souki had a doctoral fellowship from the French Ministry for Higher Education and Research. Jeremy Amosse was a post-doctoral recipient from Anses. We are also thankful to the faculty of Pharmacy of Rennes, for funding the extended contract of Rima Souki.

Subjects
Benzo[a]pyrene, Cytochromes P-450 1A1 and 1B1, Peripheral blood mononuclear cells, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, miR-132–3p, [SDE]Environmental Sciences, General Medicine, Toxicology, Pollution, Aryl hydrocarbon receptor, Polycyclic aromatic hydrocarbons, microRNAs
Abstract

International audience; Polycyclic aromatic hydrocarbons (PAHs) are widely distributed environmental contaminants, triggering deleterious effects such as carcinogenicity and immunosuppression, and peripheral blood mononuclear cells (PBMCs) are among the main cell types targeted by these pollutants. In the present study, we sought to identify the expression profiles and function of miRNAs, gene regulators involved in major cellular processes recently linked to environmental pollutants, in PBMC-exposed to the prototypical PAH, benzo[a]pyrene (B[a]P). Using small RNA deep sequencing, we identified several B[a]P-responsive miRNAs. Bioinformatics analyses showed that their predicted targets could modulate biological processes relevant to cell death and survival. Further studies of the most highly induced miRNA, miR-132, showed that its up-regulation by B[a]P was time- and dose-dependent and required aryl hydrocarbon receptor (AhR) activation. By evaluating the role of miR-132 in B[a]P-induced cell death, we propose a mechanism linking B[a]P-induced miR-132 expression and cytochromes P-450 (CYPs) 1A1 and 1B1 mRNA levels, which could contribute to the apoptotic response of PBMCs. Altogether, this study increases our understanding of the roles of miRNAs induced by B[a]P and provides the basis for further investigations into the mechanisms of gene expression regulation by PAHs.

Published
2023
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16. Spatial dependence between training and test sets: another pitfall of classification accuracy assessment in remote sensing

Author

N. Karasiak, Claude Monteil, Jean-François Dejoux, David Sheeren, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-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), Centre d'études spatiales de la biosphère (CESBIO), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), and French Ministry of Higher Education and Research (University of Toulouse)

Subjects
Contextual image classification, Pixel, Property (programming), Computer science, Overfitting, Cross-validation, 02 engineering and technology, Remote sensing, Python (programming language), Accuracy assessment, Artificial Intelligence, Sample size determination, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], 020201 artificial intelligence & image processing, Spatial dependence, computer, Spatial analysis, Spatial autocorrelation, Software, Independence (probability theory), computer.programming_language
Abstract

International audience; Spatial autocorrelation is inherent to remotely sensed data. Nearby pixels are more similar than distant ones. This property can help to improve the classification performance, by adding spatial or contextual features into the model. However, it can also lead to overestimation of generalisation capabilities, if the spatial dependence between training and test sets is ignored. In this paper, we review existing approaches that deal with spatial autocorrelation for image classification in remote sensing and demonstrate the importance of bias in accuracy metrics when spatial independence between the training and test sets is not respected. We compare three spatial and non-spatial cross-validation strategies at pixel and object levels and study how performances vary at different sample sizes. Experiments based on Sentinel-2 data for mapping two simple forest classes show that spatial leave-one-out cross-validation is the better strategy to provide unbiased estimates of predictive error. Its performance metrics are consistent with the real quality of the resulting map contrary to traditional non-spatial cross-validation that overestimates accuracy. This highlight the need to change practices in classification accuracy assessment. To encourage it we developped Museo ToolBox, an open-source python library that makes spatial cross-validation possible.

Published
2021
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17. Paternalistic Countryside : the Hard Way towards Local Development in the Rural Municipalities of Central Hungary

Author

Samuel Depraz, Environnement Ville Société (EVS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), French Ministry for Higher Education and Research / Laboratory MTE / UMR 5045 CNRS, Montpellier. Material support was kindly given by the Alföld Institute of the Centre for Regional Studies of the Hungarian Academy of Sciences directed by Pr. Bálint CSATÁRI., Program of the French Ministry for Higher Education and Research, ACI 'Espace et territoires', lead in by Pr. Marie-Claude MAUREL (EHESS, Paris), Environnement Ville Société ( EVS ), École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Moulin - Lyon III-Université Jean Monnet [Saint-Étienne] ( UJM ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Ecole Nationale Supérieure des Mines de Saint-Etienne-École nationale supérieure d'architecture de Lyon ( ENSAL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Hungary, Local Development, Rural Élite, [SHS.GEO]Humanities and Social Sciences/Geography, Municipal Policies, [ SHS.GEO ] Humanities and Social Sciences/Geography
Abstract

This paper is an improved and enlarged version of DEPRAZ S. (2005), « Développement local et politiques de gestion des communes rurales en Hongrie post-socialiste », in Bulletin de l’Association de géographes français, vol. 82 n°2 : « Les territoires ruraux centre-européens face aux enjeux de l’intégration », p. 168-181 : halshs-01547048v1 / DOI : ; International audience; The new political and budgetary standards for Hungarian local governments, introduced as early as 1990 in accordance with the criteria of the European integration, aimed at promoting local democracy and reinforced the autonomy of local governments. Furthermore, they were supposed to stimulate development on the short term, so that local societies would show initiative through co-operation and a fair territorial competition.The results of this policy seem nevertheless to remain beyond expectations, at least in rural areas of the Hungarian Great Plain. Rural poverty, together with an unfavourable settlement structure, are often seen as the main causes of this miscarriage. But a somewhat grudging local budgetary policy and, which is more, a strong stability of local representatives inherited from a conservative social hierarchy make Hungarian local societies quite unable to run efficiently endogenous development policies. Thus the legacy of the socialist era does not seem to be the perpetuation of the values of the former system, but rather the reinforcement of a long-lasting paternalistic social structure of the countryside.

Published
2006

18. Topological Analysis of Hydroxyquinoline Derivatives Interacting with Aluminum Cations or with an Al(111) Surface

Author

Corinne Lacaze-Dufaure, Christine Lepetit, Yann Bulteau, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and French Ministry of Higher Education and Research

Subjects
Anions, Matériaux, Substituent, Reaction products, Ionic bonding, 02 engineering and technology, 010402 general chemistry, Topology, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, Inorganic Chemistry, Aluminum Cation, chemistry.chemical_compound, Deprotonation, Adsorption, Molecule, Moiety, Physical and Theoretical Chemistry, Molecules, 021001 nanoscience & nanotechnology, 0104 chemical sciences, chemistry, Density functional theory, 0210 nano-technology, Aluminum
Abstract

International audience; The reactivity of hydroxyquinoline derivatives (native molecules (Hq) and modified species (HqX, X = Br, SO3H, or SO3–)) is investigated either (i) with aluminum cations for the formation of chelates or (ii) with aluminum surfaces for their adsorption properties, in the framework of the dispersion-corrected Density Functional Theory (DFT-D). It is shown that the substituent X has no influence on the complexation to the aluminum cation of the deprotonated active form, i.e., the one exhibiting a phenolate moiety and referred to as q– for the native Hq and qXn– (n = 1 or 2) for its derivatives. The formation energies of the Alq3 and Al(qX)3 complexes, taking values of −60.87 ± 3.10 eV in vacuum and −24.30 ± 0.29 eV in water, are indicative of a strong chelating affinity of the q– and qXn– (n = 1 or 2) anions for the aluminum cations. ELF and QTAIM topological analyses on these complexes evidence that the bonding of the deprotonated species with the Al3+ ion is ionic with a very weak covalence degree. The para or ortho substituent X of the phenolate moiety of the qXn– (n = 1 or 2) derivatives modifies the electronic structure only locally and thus does not influence their O- or N-coordinating properties. The adsorption properties of the latter on an Al(111) surface have also been studied within periodic DFT-D calculations. The adsorbed species are strongly interacting with the Al(111) surface, as shown by the value of the adsorption energy of −3.69 ± 0.21 eV for the most stable geometries. Various adsorption modes of the q– and qXn– (n = 1 or 2) derivatives are characterized on the Al surface, depending on stabilizing or destabilizing interactions with the substituents X. On the basis of QTAIM descriptors, the bonding of the hydroxyquinoline species on the aluminum surface is characterized as ionic with a weak covalent character.

Published
2020
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19. CD5 signalosome coordinates antagonist TCR signals to control the generation of Treg cells induced by foreign antigens

Author

Ki-Duk Song, Hélène Daniels-Treffandier, Gaëtan Blaize, Meryem Aloulou, Anne Gonzalez de Peredo, Renaud Lesourne, Mylène Gador, Mariette F. Ducatez, Mehdi Benamar, Marlène Marcellin, Cui Yang, Nicolas Fazilleau, Abdelhadi Saoudi, Paul E. Love, Odile Burlet-Schiltz, Nelly Rouquié, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), This work was supported by INSERM and Sanofi (Avenir grant to R.L.), the Association pour la Recherche sur le Cancer, the Intramural Research Program of the Eunice Kennedy Shriver, National Institute of Child Healthand Human Development, a Marie Curie International Reintegration Grant (to R.L.), the French Ministry of Higher Education and Research (PhD fellow-ship to G.B.), the Région Midi-Pyrénées, European funds (Fonds Européensde Développement Régional), Toulouse Métropole, and the French Ministry of Research with the ‘Investissement d’Avenir Infrastructures Nationales en Biologie et Santé' program (ProFI, Proteomics French Infrastructure project ANR-10-INBS-08) (to O.B.-S.)., and ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010)

Subjects
0301 basic medicine, T cell, Primary Cell Culture, T cells, Receptors, Antigen, T-Cell, Mice, Transgenic, chemical and pharmacologic phenomena, CD5 Antigens, Lymphocyte Activation, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, T-Lymphocytes, Regulatory, Mass Spectrometry, Mice, 03 medical and health sciences, Transactivation, 0302 clinical medicine, Immune system, Antigen, hemic and lymphatic diseases, medicine, Animals, Antigens, Multidisciplinary, Chemistry, T-cell receptor, FOXP3, Cell Differentiation, hemic and immune systems, Biological Sciences, Cell biology, coreceptors, CRKL, 030104 developmental biology, medicine.anatomical_structure, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Gene Expression Regulation, 030220 oncology & carcinogenesis, Phosphorylation, signaling, Signal Transduction
Abstract

CD5 is characterized as an inhibitory coreceptor with an important regulatory role during T cell development. The molecular mechanism by which CD5 operates has been puzzling and its function in mature T cells suggests promoting rather than repressing effects on immune responses. Here, we combined quantitative mass spectrometry and genetic studies to analyze the components and the activity of the CD5 signaling machinery in primary T cells. We found that T cell receptor (TCR) engagement induces the selective phosphorylation of CD5 tyrosine 429, which serves as a docking site for proteins with adaptor functions (c-Cbl, CIN85, CRKL), connecting CD5 to positive (PI3K) and negative (UBASH3A, SHIP1) regulators of TCR signaling. c-CBL acts as a coordinator in this complex enabling CD5 to synchronize positive and negative feedbacks on TCR signaling through the other components. Disruption of CD5 signalosome in mutant mice reveals that it modulates TCR signal outputs to selectively repress the transactivation of Foxp3 and limit the inopportune induction of peripherally induced regulatory T cells during immune responses against foreign antigen. Our findings bring insights into the paradigm of coreceptor signaling, suggesting that, in addition to providing dualistic enhancing or dampening inputs, coreceptors can engage concomitant stimulatory and inhibitory signaling events, which act together to promote specific functional outcomes.

Published
2020
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20. A non-human primate model of stroke reproducing endovascular thrombectomy and allowing long-term imaging and neurological read-outs

Author

F. Taborik, Karine Portier, Norbert Nighoghossian, Adrien Oudotte, Michaël Verset, Thomas Troalen, Omer Eker, Denis Vivien, Inés Mérida, Christelle Leon, Christian Tourvieille, Didier Le Bars, Emmanuelle Canet-Soulas, Michel Ovize, Hugues Contamin, Nicolas Costes, Nikolaos Makris, Véronique Agin, Joachim Confais, Tae-Hee Cho, Mohamed Aggour, Sophie Lancelot, Justine Debatisse, Jean-Baptiste Langlois, Océane Wateau, Marjorie Villien, Imagerie Tomographique et Radiothérapie, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche et d'Application en Traitement de l'Image et du Signal (CREATIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Supérieure Chimie Physique Électronique de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire en imagerie du vivant (CERMEP - imagerie du vivant), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Cynbiose, CYNBIOSE, Institut Claude Bourgelat (ICLB), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Siemens Healthcare [France], Siemens AG [Munich], Institute of Electronic Structure and Laser (FORTH-IESL), Foundation for Research and Technology - Hellas (FORTH), Radiopharmaceutical and Neurochemical Biomarkers Team (BioRaN), Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Cardiology, Hospices Civils de Lyon (HCL), Laboratoire de Chimie de la Matière Condensée de Paris (site ENSCP) (LCMCP (site ENSCP)), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC), French Ministry of Higher Education and Research (ANRT), ANR-15-CE17-0020,CYCLOPS,CYCLOsporine A : effet neuroprotecteur dans un modèle Primate de Stroke en imagerie(2015), ANR-16-RHUS-0009,MARVELOUS,MARVELOUS(2016), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, [SDV]Life Sciences [q-bio], Executive Function, 0302 clinical medicine, Occlusion, Stroke, Thrombectomy, 0303 health sciences, Behavior, Animal, Endovascular Procedures, Infarction, Middle Cerebral Artery, Magnetic Resonance Imaging, 3. Good health, Treatment Outcome, Neurology, Blood-Brain Barrier, Motor Skills, Reperfusion Injury, Middle cerebral artery, Cardiology, medicine.symptom, Cardiology and Cardiovascular Medicine, medicine.medical_specialty, Ischemia, Context (language use), ischemia–reperfusion, Asymptomatic, Lesion, 03 medical and health sciences, medicine.artery, Internal medicine, medicine, Animals, cardiovascular diseases, Thrombus, Ischemic Stroke, 030304 developmental biology, business.industry, Original Articles, medicine.disease, Disease Models, Animal, Macaca fascicularis, Endovascular non-human primate stroke model, PET-MRI imaging, Positron-Emission Tomography, neurofunctional tests, Neurology (clinical), Tomography, X-Ray Computed, business, 030217 neurology & neurosurgery
Abstract

International audience; Stroke is a devastating disease. Endovascular mechanical thrombectomy is dramatically changing the management of acute ischemic stroke, raising new challenges regarding brain outcome and opening up new avenues for brain protection. In this context, relevant experiment models are required for testing new therapies and addressing important questions about infarct progression despite successful recanalization, reversibility of ischemic lesions, blood-brain barrier disruption and reperfusion damage. Here, we developed a minimally invasive non-human primate model of cerebral ischemia (Macaca fascicularis) based on an endovascular transient occlusion and recanalization of the middle cerebral artery (MCA). We evaluated per-occlusion and post-recanalization impairment on PET-MRI, in addition to acute and chronic neuro-functional assessment. Voxel-based analyses between per-occlusion PET-MRI and day-7 MRI showed two different patterns of lesion evolution: "symptomatic salvaged tissue" (SST) and "asymptomatic infarcted tissue" (AIT). Extended SST was present in all cases. AIT, remote from the area at risk, represented 45% of the final lesion. This model also expresses both worsening of fine motor skills and dysexecutive behavior over the chronic post-stroke period, a result in agreement with cortical-subcortical lesions. We thus fully characterized an original translational model of ischemia-reperfusion damage after stroke, with consistent ischemia time, and thrombus retrieval for effective recanalization.

Published
2020
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21. Laser Direct Writing of Silver Clusters‐Based Subwavelength Periodic Structures Embedded in Mid‐Infrared Gallo‐Germanate Glass

Author

Théo Guérineau, Alexandre Fargues, Jerome Lapointe, Réal Vallée, Younès Messaddeq, Lionel Canioni, Yannick Petit, Thierry Cardinal, Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Département de physique, de génie physique et d'optique, Université Laval, Québec, Université Laval [Québec] (ULaval), Centre d'Etudes Lasers Intenses et Applications (CELIA), Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), This work has received funding from the French Government, managed bythe French National Research Agency (ANR-17-CE08-0042-01 and ANR-19-CE08-0021) and the Nouvelle Aquitaine Region (APPR2020-2019-8193110), and from the Canadian Government, managed by SentinelNorth program of University Laval and the Canadian Research Chair pro-gram (CERC). This project has also received funding from the innovationprogram under the Marie-Skłodowska-Curie grant agreement N°823941(FUNGLASS). The corresponding author, T.G., holds a Sentinel NorthExcellence Postdoctoral Fellowship and held an Excellence doctoral schol-arship from the French Ministry of Higher Education and Research duringthe preparation of this work., ANR-17-CE08-0042,PROTEus,ImPRession laser de fibres exOtiques Multi-MaTEriaux(2017), and ANR-19-CE08-0021,ArchiFLUO,Architectures photoniques intégrées inscrites par laser femtoseconde pour étalonnage en microscopie de fluorescence dans l'infrarouge(2019)

Subjects
Physics::Optics, General Medicine, [CHIM.MATE]Chemical Sciences/Material chemistry
Abstract

International audience; The direct laser writing (DLW) using femtosecond lasers allows for the inscription of 3D microstructures embedded inside optical materials. Based solely on the silver ions photochemistry, the DLW in silver-containing glasses enables to locally induce inside glasses a unique combination of optical properties. The physical modifications of the material encompass not only a refractive index change, but also new physical properties like fluorescence, second- and third-harmonic generations, and surface plasmon resonance. Numerous efforts are deployed to develop the DLW-assisted silver photochemistry in phosphate glasses. However, this glass family is suffering from its near-infrared optical cutoff as opposed to the silver-doped gallo-germanate glasses. With an extended mid-infrared (mid-IR) transmission, these glasses are synthesized via the melt-quenching technique. Depending on the glass composition, either a glass matrix-based single track (Type I) or a silver cluster-based double track (Type A) of refractive index change is produced. By enabling an order of magnitude smaller structures than with Type I, Type A modification is further expanded to embed, for the first time, periodic structures below the inter-track spacing. Demonstrated with a pitch down to 400 nm, these Type A–based periodic structures bring new insights through the fabrication of 3D diffractive gratings in mid-IR glasses.

Published
2022
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22. Mosaic Frequency Selective Surface with Wideband Response for the Optically Transparent and Absorber Applications

Author

Nafis, Nur Biha Mohamed, Himdi, Mohamed, Rahim, Mohamad Kamal A, Merzaki, Faissal, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Universiti Putra Malaysia, Universiti Teknologi Malaysia (UTM), Institut d'Électronique et des Technologies du numéRique (IETR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Mobility Grant from Rennes Metropole, European Union through the European Regional Development Fund, French Ministry of Higher Education and Research, Region Bretagne, CPER Project 2015-2020 SOPHIE/STIC, Ondes, Ministry of Higher Education (MOHE) [FRGS/1/2021/TK0/UTM/01/7], School of Postgraduate Studies (SPS), Research Management Centre, School of Electrical Engineering, and Universiti Teknologi Malaysia (UTM), Johor Bahru [06G15, 4B588, 09G19]

Subjects
[SPI]Engineering Sciences [physics], fractal, low cross-polarization, absorber, mosaic frequency selective surface, wideband, optical transparency
Abstract

International audience; This study investigated the performance of a Mosaic Frequency Selective Surface (MFSS) structure for two different applications: optical transparency and absorber. The MFSS for optical transparency application is comprised of a polycarbonate substrate with permittivity, epsilon(r) of 2.9, and the MFSS for absorber application utilized a Polyethylene Terephthalate (PET) substrate with epsilon(r) of 2.7. The MFSS unit cell is composed of a conductive metallic element design that integrates the Koch fractal and the double hexagonal loop for the optical transparency application. Meanwhile, the resistive MFSS unit cell with sheet resistivity of 100 Omega/sq is utilized for the absorber application. A Computer Simulation Technology (CST) Microwave Studio software is employed to carry out the calculation and frequency response analysis for both applications. Based on the results, it was concluded that the transparent MFSS yielded a wideband stopband and passband responses (fractional bandwidth (FBW) > 50%) with a low cross-polarization (-37 dB), and a wideband absorptivity response was achieved with thin MFSS absorber. In addition, the simulated and measured responses of the transparent MFSS achieved well-fitted correlations. The findings indicated that the proposed MFSS unit cell able to provide wideband response for both applications.

Published
2022
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23. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity

Author

Yeh, Shih-Chia, Strilets, Tania, Tan, Wei-Lian, Castillo, David, Medkour, Hacene, Rey-Cadilhac, Félix, Serrato-Pomar, Idalba, Rachenne, Florian, Chowdhury, Avisha, Chuo, Vanessa, Azar, Sasha, Singh, Moirangthem Kiran, Hamel, Rodolphe, Missé, Dorothée, Kini, R, Kenney, Linda, Vasilakis, Nikos, Marti-Renom, Marc a, Nir, Guy, Pompon, Julien, Garcia-Blanco, Mariano, Duke-NUS Medical School [Singapore], The University of Texas Medical Branch (UTMB), Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), National University of Singapore (NUS), Department of Computer and Information Science [Pennsylvania] (CIS), University of Pennsylvania, Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra [Barcelona] (UPF), ICREA Infection Biology Laboratory (Department of Experimental and Health Sciences), University of Texas Medical Branch at Galveston, Support for this research came from a fellowship from the McLauglin Family Foundation to TS, scholarships from the Fondation pour la Recherche Médicale (FRM project SPF202110013925) to HM, from the Institut Méditerranéen Hospitalier (IHU, Marseille) to IMSP and from the graduate school French Ministry of Higher Education and Research to FRC and FR, UTMB start-up funds and Cancer Prevention & Research Institute of Texas grant RP200650 to LJK and MKS, the Ministerio de Ciencia e Innovación (PID2020-115696RB-I00) to MAM-R, Cancer Prevention & Research Institute of Texas grant ID RR210018 to GN, Ministry of Education (Singapore) Tier3 grant (MOE2015-T3-1-003) to RMK and JP, a National Medical Research Council (Singapore) ZRRF grant (ZRRF/007/2017) to JP, a French Agence Nationale de la Recherche grant (ANR-20-CE15-0006) to JP, and the Duke-NUS Signature Research Programme funded by the Agency for Science Technology and Research (A*Star Singapore) and NIH/NIAID P01 AI150585 to MAGB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., and ANR-20-CE15-0006,VirSalivaEnhancer,Amplificateur de transmission d'origine flavivirale dans la salive de moustique(2020)

Subjects
3' UTR, Immunology, MESH: Dengue, Transfection, Mosquitoes, Microbiology, Dengue virus, Guide RNA, Ribonucleases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Virology, Genetics, MESH: Flavivirus, MESH: Animals, MESH: Saliva, Saliva, Molecular Biology, MESH: Humans, MESH: Subgenomic RNA, MESH: Virus Replication, MESH: Aedes, MESH: 3' Untranslated Regions, RNA extraction, MESH: RNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Parasitology, MESH: Culicidae
Abstract

Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3'UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3'UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission. Support for this research came from a fellowship from the McLauglin Family Foundation to TS, scholarships from the Fondation pour la Recherche Médicale (FRM project SPF202110013925) to HM, from the Institut Méditerranéen Hospitalier (IHU, Marseille) to IMSP and from the graduate school French Ministry of Higher Education and Research to FRC and FR, UTMB start-up funds and Cancer Prevention & Research Institute of Texas grant RP200650 to LJK and MKS, the Ministerio de Ciencia e Innovación (PID2020-115696RB-I00) to MAM-R, Cancer Prevention & Research Institute of Texas grant ID RR210018 to GN, Ministry of Education (Singapore) Tier3 grant (MOE2015-T3-1-003) to RMK and JP, a National Medical Research Council (Singapore) ZRRF grant (ZRRF/007/2017) to JP, a French Agence Nationale de la Recherche grant (ANR-20-CE15-0006) to JP, and the Duke-NUS Signature Research Programme funded by the Agency for Science Technology and Research (A*Star Singapore) and NIH/NIAID P01 AI150585 to MAGB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Published
2023
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24. Frozen-Density Embedding for including environmental effects in the Dirac-Kohn-Sham theory: an implementation based on density fitting and prototyping techniques

Author

De Santis, Matteo, Sorbelli, Diego, Vallet, Valerie, Gomes, Andre' Severo Pereira, Storchi, Loriano, Belpassi, Leonardo, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Istituto di Scienze e Tecnologie Chimiche 'Giulio Natta' (SCITEC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Dipartimento di Farmacia, Universita G. d Annunzio, Via dei Vestini, 66100 Chieti, Italy, MESONM International Associated Laboratory (LAI) (No. ANR-16-IDEX-0004), the French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, French national supercomputing facilities (Grant Nos. DARI A0090801859, A0110801859)., ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), and ANR-16-IDEX-0004,ULNE,ULNE(2016)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chemical Physics (physics.chem-ph), Physics - Chemical Physics, FOS: Physical sciences, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

The Frozen Density Embedding scheme represents an embedding method in which environmental effects onto a given subsystem are included by representing the other subsystems making up the surroundings quantum mechanically, by means of their electron densities. In the present paper, we extend the full 4-component relativistic Dirac-Kohn-Sham method, as implemented in the BERTHA code, to include environmental and confinement effects with the FDE scheme. This implementation has been enormously facilitated by BERTHA's python API (PyBERTHA), which provides a flexible framework of development by using all Python advantages in terms of code re-usability, portability while facilitating the interoperability with other FDE implementations available through the PyADF framework. The computational performance has been evaluated on a series of gold clusters (Au$_n$, with n=2,4,8) embedded into an increasing number of water molecules (5, 10, 20, 40 and 80 water molecules). We found that the procedure scales approximately linearly both with the size of the frozen surrounding environment (in line with the underpinnings of the FDE approach) and with the size of the active system (in line with the use of density fitting). Finally, we applied the code to a series of Heavy (Rn) and Super-Heavy elements (Cn, Fl, Og) embedded in a C_60 cage to explore the confinement effect induced by C_60 on their electronic structure. We compare the results from our simulations with more approximate models employed in the atomic physics literature, in which confinement is represented by a radial potential slightly affected by the nature of the central atom. Our results indicate that the specific interactions described by FDE are able to improve upon the cruder approximations currently employed, and thus provide a basis from which to generate more realistic radial potentials for confined atoms., Comment: 53 pages, 7 Figures

Published
2022
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25. Bregman Deviations of Generic Exponential Families

Author

Chowdhury, Sayak Ray, Saux, Patrick, Maillard, Odalric-Ambrym, Gopalan, Aditya, Microsoft Research India [Bangalore], Microsoft Research, Scool (Scool), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Indian Institute of Science [Bangalore] (IISc Bangalore), and French National Research Agency, the French Ministry of Higher Education and Research, Inria, the MEL and the I-Site ULNE regarding project R-PILOTE-19-004-APPRENF and Bandits For Health (B4H).

Subjects
Bregman divergence, FOS: Computer and information sciences, Computer Science - Machine Learning, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Concentration bounds, Exponential families, Machine Learning (cs.LG)
Abstract

International audience; We revisit the method of mixture technique, also known as the Laplace method, to study the concentration phenomenon in generic exponential families. Combining the properties of Bregman divergence associated with log-partition function of the family with the method of mixtures for super-martingales, we establish a generic bound controlling the Bregman divergence between the parameter of the family and a finite sample estimate of the parameter. Our bound is time-uniform and makes appear a quantity extending the classical information gain to exponential families, which we call the Bregman information gain. For the practitioner, we instantiate this novel bound to several classical families, e.g., Gaussian, Bernoulli, Exponential, Weibull, Pareto, Poisson and Chi-square yielding explicit forms of the confidence sets and the Bregman information gain. We further numerically compare the resulting confidence bounds to state-of-the-art alternatives for time-uniform concentration and show that this novel method yields competitive results. Finally, we highlight the benefit of our concentration bounds on some illustrative applications.

Published
2022
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26. A novel toxic effect of foodborne trichothecenes: The exacerbation of genotoxicity

Author

Marion Garofalo, Delphine Payros, Marie Penary, Eric Oswald, Jean-Philippe Nougayrède, Isabelle P. Oswald, ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Santé Digestive (IRSD ), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), This work was supported by grants from the French Agence Nationale de la Recherche (Genofood ANR-19-CE34 and GenoMyc ANR-22-CE34). MG was supported by a fellowship from the French ministry for Higher Education and Research., ANR-19-CE34-0014,Genofood,Exacerbation de la génotoxicité du microbiote intestinal par un contaminant alimentaire(2019), LESUR, Hélène, and Exacerbation de la génotoxicité du microbiote intestinal par un contaminant alimentaire - - Genofood2019 - ANR-19-CE34-0014 - AAPG2019 - VALID

Subjects
[SDV] Life Sciences [q-bio], Carcinogenic potential, Microbiota, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, Colibactin, General Medicine, Mycotoxins, Pesticides, Toxicology, Pollution
Abstract

International audience; Trichothecenes (TCT) are very common mycotoxins. While the effects of DON, the most prevalent TCT, have been extensively studied, less is known about the effect of other trichothecenes. DON has ribotoxic, pro-inflammatory, and cytotoxic potential and induces multiple toxic effects in humans and animals. Although DON is not genotoxic by itself, it has recently been shown that this toxin exacerbates the genotoxicity induced by model or bacterial genotoxins. Here, we show that five TCT, namely T-2 toxin (T-2), diacetoxyscirpenol (DAS), nivalenol (NIV), fusarenon-X (FX), and the newly discovered NX toxin, also exacerbate the DNA damage inflicted by various genotoxins. The exacerbation was dose dependent and observed with phleomycin, a model genotoxin, captan, a pesticide with genotoxic potential, and colibactin, a bacterial genotoxin produced by the intestinal microbiota. For this newly described effect, the trichothecenes ranked in the following order: T-2>DAS > FX > NIV ≥ DON ≥ NX. The genotoxic exacerbating effect of TCT correlated with their ribotoxic potential, as measured by the inhibition of protein synthesis. In conclusion, our data demonstrate that TCT, which are not genotoxic by themselves, exacerbate DNA damage induced by various genotoxins. Therefore, foodborne TCT could enhance the carcinogenic potential of genotoxins present in the diet or produced by intestinal bacteria.

Published
2023
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27. Dealing With Misspecification In Fixed-Confidence Linear Top-m Identification

Author

Réda, Clémence, Tirinzoni, Andrea, Degenne, Rémy, Maladies neurodéveloppementales et neurovasculaires (NeuroDiderot (UMR_S_1141 / U1141)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Scool (Scool), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), The research presented was supported by the 'Digital health challenge' Inserm-CNRS joint program, the French Ministry of Higher Education and Research, and the French National Research Agency [ANR-19-CE23-0026-04] (BOLD project)., ANR-19-CE23-0026,BOLD,Au delà de l'apprentissage séquentiel pour de meilleures prises de décisions(2019), Réda, Clémence, Au delà de l'apprentissage séquentiel pour de meilleures prises de décisions - - BOLD2019 - ANR-19-CE23-0026 - AAPG2019 - VALID, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)

Subjects
[INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], Computer Science - Machine Learning, recommendation systems, Computer Science - Artificial Intelligence, multi-armed bandits, linear bandits, misspecification, Mathematics - Statistics Theory, [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], fixed-confidence top-m identification, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], pure exploration, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST]
Abstract

We study the problem of the identification of m arms with largest means under a fixed error rate $\delta$ (fixed-confidence Top-m identification), for misspecified linear bandit models. This problem is motivated by practical applications, especially in medicine and recommendation systems, where linear models are popular due to their simplicity and the existence of efficient algorithms, but in which data inevitably deviates from linearity. In this work, we first derive a tractable lower bound on the sample complexity of any $\delta$-correct algorithm for the general Top-m identification problem. We show that knowing the scale of the deviation from linearity is necessary to exploit the structure of the problem. We then describe the first algorithm for this setting, which is both practical and adapts to the amount of misspecification. We derive an upper bound to its sample complexity which confirms this adaptivity and that matches the lower bound when $\delta$ $\rightarrow$ 0. Finally, we evaluate our algorithm on both synthetic and real-world data, showing competitive performance with respect to existing baselines., Comment: Virtual conference

Published
2021

28. Electronic spectra of ytterbium fluoride from relativistic electronic structure calculations

Author

Johann Valentin Pototschnig, Kenneth G. Dyall, Lucas Visscher, André Severo Pereira Gomes, Theoretical Chemistry, AIMMS, Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Dirac Solutions, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), French Ministry of Higher Education and Research, Austrian Science Fund(FWF):J 4177- N36, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, French national supercomputing facilities (grants DARI A0070801859 and A0090801859), MESONM International Associated Laboratory (LAI) (ANR-16-IDEX-0004)., ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-16-IDEX-0004,ULNE,ULNE(2016), Vrije Universiteit Amsterdam [Amsterdam] (VU), and VU University Amsterdam

Subjects
General Physics and Astronomy, FOS: Physical sciences, Electron, Electronic structure, 01 natural sciences, Fock space, symbols.namesake, Physics - Chemical Physics, 0103 physical sciences, SDG 7 - Affordable and Clean Energy, Physical and Theoretical Chemistry, 010306 general physics, Physics, Chemical Physics (physics.chem-ph), 010304 chemical physics, Configuration interaction, 3. Good health, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Dipole, Chemistry, Coupled cluster, Excited state, symbols, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Atomic physics, Hamiltonian (quantum mechanics)
Abstract

We report an investigation of the low-lying excited states of the YbF molecule--a candidate molecule for experimental measurements of the electron electric dipole moment--with 2-component based multi-reference configuration interaction (MRCI), equation of motion coupled cluster (EOM-CCSD) and the extrapolated intermediate Hamiltonian Fock-space coupled cluster (XIHFS-CCSD). Specifically, we address the question of the nature of these low-lying states in terms of configurations containing filled or partially-filled Yb $4f$ shells. We show that while it does not appear possible to carry out calculations with both kinds of configurations contained in the same active space, reliable information can be extracted from different sectors of Fock space--that is, by performing electron attachment and detachment IHFS-CCSD and EOM-CCSD calculation on the closed-shell YbF$^+$ and YbF$^-$ species, respectively. From these we observe $\Omega = 1/2, 3/2$ states that arise from the $4f^{13}\sigma_{6s}^2$, $4f^{14}5d$/$6p$, and $4f^{13}5d\sigma_{6s}$ configurations appear in the same energy range around the ground-state equilibrium geometry and they are therefore able to interact. As these states are generated from different sectors of Fock space, they are almost orthogonal and provide complementary descriptions of parts of the excited state manifold. To obtain a comprehensive picture, we introduce a simple adiabatization model to extract energies of interacting $\Omega = 1/2, 3/2$ states that can be compared to experimental observations., Comment: 28+57 pages, 8+18 tables, 5+34 figures

Published
2021
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29. Permanganate oxidation of polycyclic aromatic compounds (PAHs and polar PACs): column experiments with DNAPL at residual saturation

Author

Coralie Biache, Philippe Bataillard, Clotilde Johansson, Catherine Lorgeoux, Christian Défarge, Pierre Faure, Stéfan Colombano, Antoine Joubert, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), GeoRessources, Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre de recherches sur la géologie des matières premières minérales et énergétiques (CREGU)-Institut national des sciences de l'Univers (INSU - CNRS), Serpol (Serpol), SERPOL, Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Cellule d'Expertise et de Transfert en TRaçages Appliqués à l'Hydrogéologie et à l'Environnement (CETRAHE), Université d'Orléans (UO), Biogéosystèmes Continentaux - UMR7327, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), French Environmental Agency (ADEME), French National Association for Research and Technology (ANRT), BRGM/DEPA division, PIVOTS project by the Centre-Val de Loire region (ARD 2020 program and CPER 2015-2020), and French Ministry of Higher Education and Research (CPER 20152020 and public service subsidy to BRGM)

Subjects
Pollution, Health, Toxicology and Mutagenesis, media_common.quotation_subject, 0207 environmental engineering, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, complex mixtures, chemistry.chemical_compound, TRACER, medicine, Environmental Chemistry, Polycyclic Compounds, Coal tar, Leaching (agriculture), Polycyclic Aromatic Hydrocarbons, 020701 environmental engineering, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, media_common, Pollutant, Permanganate, Oxides, General Medicine, 6. Clean water, Potassium permanganate, chemistry, Manganese Compounds, 13. Climate action, Environmental chemistry, Oxidation-Reduction, Groundwater, Water Pollutants, Chemical, medicine.drug
Abstract

International audience; Permanganate is an oxidant usually applied for in situ soil remediation due to its persistence underground. It has already shown great efficiency for dense nonaqueous phase liquid (DNAPL) degradation under batch experiment conditions. In the present study, experimental permanganate oxidation of a DNAPL — coal tar — sampled in the groundwater of a former coking plant was carried out in a glass bead column. Several glass bead columns were spiked with coal tar using the drainage-imbibition method to mimic on-site pollution spread at residual saturation as best as possible. The leaching of organic pollutants was monitored as the columns were flushed by successive sequences: successive injections of hot water, permanganate solution for oxidation, and ambient temperature water, completed by two injections of a tracer before and after oxidation. Sixteen conventional US-EPA PAHs and selected polar PACs were analyzed in the DNAPL remaining in the columns at the end of the experiment and in the particles collected at several steps of the flushing sequences. Permanganate oxidation of the pollutants was rapidly limited by interfacial aging of the DNAPL drops. Moreover, at the applied flow rate chosen to be representative of in situ injections and groundwater velocities, the reaction time was not sufficient to reach high degradation yields but induced the formation and the leaching of oxygenated PACs

Published
2021
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30. Revisiting an IgG Fc Loss-of-Function Experiment: the Role of Complement in HIV Broadly Neutralizing Antibody b12 Activity

Author

Ann J. Hessell, Benjamin S. Goldberg, David A. Spencer, Jérémy Dufloo, Timothée Bruel, Olivier Schwartz, Margaret E. Ackerman, Chengzi I. Kaku, Dartmouth College [Hanover], Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Oregon Health and Science University [Portland] (OHSU), This work was supported by the National Institutes of Health NIAID and NIGMS under grants R01AI131975 (M.E.A.) and R01AI129801 (A.J.H.). Work in the O.S. lab is funded by the Institut Pasteur, the Urgence COVID-19 Fundraising Campaign of the Institut Pasteur, the Fondation pour la Recherche Médicale (FRM), ANRS, the Vaccine Research Institute (ANR-10-LABX-77), Labex IBEID (ANR-10-LABX-62-IBEID), ANR/FRM Flash Covid PROTEO-SARS-CoV-2, and IDISCOVR. J.D. is supported by a grant from the French Ministry of Higher Education and Research., ANR-10-LABX-0077,VRI,Initiative for the creation of a Vaccine Research Institute(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and ANR-20-COVI-0059,PROTEO-SARS-CoV-2,Protéomique du SARS-CoV-2(2020)

Subjects
viral lysis, HIV Infections, Context (language use), HIV Antibodies, Microbiology, Immunity, antibody, Virology, Animals, Humans, complement, antibody-mediated prevention, C1q, Loss function, Fc, human immunodeficiency virus, biology, Mechanism (biology), Complement C1q, HIV, Complement System Proteins, Editor's Pick, Complement fixation test, Antibodies, Neutralizing, Macaca mulatta, QR1-502, Complement system, Complement (complexity), HEK293 Cells, Immunoglobulin G, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immunology, HIV-1, biology.protein, Antibody, CDC, human activities, Broadly Neutralizing Antibodies, Research Article, mechanism of action
Abstract

The role of the complement system in HIV-1 immunity and pathogenesis is multifaceted, and an improved understanding of complement activities mediated by HIV-1-specific antibodies has the potential to inform and advance clinical development efforts. A seminal nonhuman primate challenge experiment suggested that complement was dispensable for the protective effect of the early broadly neutralizing antibody (bnAb) b12, but recent experiments have raised questions about the breadth of circumstances under which this conclusion may hold. Here, we reassess the original observation using Fc variants of IgG1 b12 that enhance complement activity and report that complement fixation on recombinant antigen, virions, and cells and complement-dependent viral and cellular lysis in vitro vary among bnAbs. Specifically, while the clinically significant V3 glycan-specific bnAb 10-1074 demonstrates activity, we found that b12 does not meaningfully activate the classical complement cascade. Consistent with avid engagement by C1q and its complex system of regulatory factors, these results suggest that complement-mediated antibody activities demonstrate a high degree of context dependence and motivate revisiting the role of complement in antibody-mediated prevention of HIV-1 infection by next-generation bnAbs in new translational studies in animal models. IMPORTANCE Given the suboptimal outcome of VRC01 antibody-mediated prevention of HIV-1 infection in its first field trial, means to improve diverse antiviral activities in vivo have renewed importance. This work revisits a loss-of-function experiment that investigated the mechanism of action of b12, a similar antibody, and finds that the reason why complement-mediated antiviral activities were not observed to contribute to protection may be the inherent lack of activity of wild-type b12, raising the prospect that this mechanism may contribute in the context of other HIV-specific antibodies.

Published
2021
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31. A Novel Neurofuzzy Approach for Semantic Similarity Measurement

Author

Josef Küng, Jorge Martinez-Gil, Abdelkader Hameurlain, Riad Mokadem, Software Competence Center Hagenberg (SCCH), Johannes Kepler Universität Linz (JKU), Optimisation Dynamique de Requêtes Réparties à grande échelle (IRIT-PYRAMIDE), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Johannes Kepler University Linz [Linz] (JKU), Austrian Ministry for Transport, Innovation and Technology, the Federal Ministry of Science, Research and Economy, and the State of Upper Austria in the frame of the COMET center SCCH, Project FR06/2020 by International Cooperation & Mobility (ICM) of the Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH), French Ministry of Higher Education and Research’ which support the Amadeus program 2020 (French-Austrian Hubert Curien Partnership – PHC) Project Number 44086TD, Matteo Golfarelli, Robert Wrembel, Gabriele Kotsis, A Min Tjoa, and Ismail Khalil

Subjects
Artificial neural network, business.industry, Computer science, 02 engineering and technology, Machine learning, computer.software_genre, Fuzzy logic, Models of neural computation, Neurofuzzy, Semantic similarity, 020204 information systems, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], Similarity (psychology), Deep learning applications, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Data integration, [INFO]Computer Science [cs], Artificial intelligence, business, computer
Abstract

Also part of the Information Systems and Applications, incl. Internet/Web, and HCI book sub series (LNISA, volume 12925); International audience; The problem of identifying the degree of semantic similarity between two textual statements automatically has grown in importance in recent times. Its impact on various computer-related domains and recent breakthroughs in neural computation has increased the opportunities for better solutions to be developed. This research takes the research efforts a step further by designing and developing a novel neurofuzzy approach for semantic textual similarity that uses neural networks and fuzzy logics. The fundamental notion is to combine the remarkable capabilities of the current neural models for working with text with the possibilities that fuzzy logic provides for aggregating numerical information in a tailored manner. The results of our experiments suggest that this approach is capable of accurately determining semantic textual similarity.

Published
2021
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32. Predictive surface complexation model of the calcite-aqueous solution interface: The impact of high concentration and complex composition of brines

Author

Mohamed Azaroual, Stefan Iglauer, Jan Vinogradov, Miftah Hidayat, Mohammad Sarmadivaleh, Philippe Leroy, Damien Jougnot, Jos Derksen, David Vega-Maza, University of Aberdeen, Milieux Environnementaux, Transferts et Interactions dans les hydrosystèmes et les Sols (METIS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Milieux Poreux - UMR7327, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), and O-ZNS project which is part of PIVOTS project (financial support provided by the Région Centre-Val de Loire and the French Ministry of Higher Education and Research).

Subjects
aqueous solutions, Work (thermodynamics), Materials science, high salinity, Thermodynamics, complex composition, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Capacitance, predictive model Stern layer capacitance, Biomaterials, chemistry.chemical_compound, zeta potential, Colloid and Surface Chemistry, Zeta potential, surface complexation model, Equilibrium constant, Calcite, Aqueous solution, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, chemistry, 13. Climate action, Ionic strength, [SDU]Sciences of the Universe [physics], 0210 nano-technology, calcite, Iceland spar
Abstract

International audience; Electrochemical interactions at calcite-water interface are characterized by the zeta potential and play an important role in many subsurface applications. In this work we report a new physically meaningful surface complexation model that is proven to be efficient in predicting calcite-water zeta potentials for a wide range of experimental conditions.Our model uses a two-stage optimization for matching experimental observations. First, equilibrium constants are optimized, and the Stern layer capacitance is optimized in the second stage. The model is applied to a variety of experimental sets that correspond to intact natural limestones saturated with equilibrated solutions of low-to-high salinity, and crushed Iceland Spar sample saturated with NaCl at non-equilibrium conditions.The proposed linear correlation of the Stern layer capacitance with the ionic strength is the main novel contribution to our surface complexation model without which high salinity experiments cannot be modelled. Our model is fully predictive given accurately known conditions. Therefore, the reported parameters and modelling protocol are of significant importance for improving our understanding of the complex calcite-water interfacial interactions. The findings provide a robust tool to predict electrochemical properties of calcite-water interfaces, which are essential for many subsurface applications including hydrology, geothermal resources, CO2 sequestration and hydrocarbon recovery.

Published
2021
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33. Biometry of the large dragonfly Anax imperator (Odonata: Aeshnidae): A study of traits from larval development to adults

Author

Mickaël Le Gall, Marceau Minot, Aurélie Husté, Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), RiverLy (UR Riverly), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Seine-Normandy Water Agency, and French Ministry of Higher Education and Research through the Normandy's Doctoral School of Integrative Biology, Health and Environment (Rouen University) : EdN BISE 497

Subjects
0106 biological sciences, media_common.quotation_subject, Zoology, Insect, sexual size dimorphism, Odonata, 010603 evolutionary biology, 01 natural sciences, anax imperator, traits, Aeshnidae, larval rearing, media_common, Larva, body length, biology, 010604 marine biology & hydrobiology, fungi, odonata, biology.organism_classification, Dragonfly, body mass, Sexual dimorphism, QL1-991, Insect Science, aeshnidae, Instar, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Insect larval development affects adult traits but the biometric relationships are usually poorly understood, including large odonates. In this study, measurements of morphological traits of larvae, exuviae and adults of Anax imperator were recorded. They were used to investigate the effects of early development on adult morphology. Results showed an increase in larval length during the final instar and the length of its exuviae significantly exceeded that of the larva. Length and body mass of teneral adults were strongly related to the length of their exuviae. Adult males were significantly longer than adult females, while both had the same body mass at emergence. Length of teneral adults was negatively related to the date of emergence in both sexes. During maturation, body mass of males only increased slightly whereas that of females increased greatly. Mature specimens were also significantly longer than teneral individuals. Body mass of mature males and length of mature females were both associated with the date of capture. Wing length did not differ between sexes or from data available from Great Britain. This study underscores the importance of taking into account larval growth in order to better understand the adult traits of odonates.

Published
2019
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34. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

Author

Jérémy Clotault, Fabrice Foucher, Jordan Marie-Magdelaine, Tom Ruttink, Valéry Malécot, Kevin Debray, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Research Institute for Agricultural, Fisheries and Food (ILVO), French Pays de la Loire region, Angers Loire Metropole, European Regional Development Fund, French Ministry of Higher Education and Research, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)

Subjects
0106 biological sciences, 0301 basic medicine, Lineage (evolution), Gene Dosage, 01 natural sciences, Coalescent theory, Phylogenomics, Species-level phylogenomics, Taxonomic rank, Plastids, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Phylogeny, UTILITY, Likelihood Functions, Vegetal Biology, Phylogenetic tree, Methodology Article, Genomics, Phylogenetic informativeness, Agricultural sciences, Botanique, GENOME, CONGRUENCE, TREES, Genome, Plant, Autre (Sciences du Vivant), Botanics, Nuclear gene, GENES, Evolution, Biology, Rosa, 010603 evolutionary biology, 03 medical and health sciences, Conflicting topologies, Nuclear single-copy orthologs, Phylogenetics, PHYLOGENETIC-RELATIONSHIPS, QH359-425, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ALGORITHM, Ecology, Evolution, Behavior and Systematics, DNA Primers, Cell Nucleus, CHLOROPLAST DNA-SEQUENCES, WILD ROSES, 030104 developmental biology, Evolutionary biology, Genetic Loci, EVOLUTIONARY, Biologie végétale, Sciences agricoles
Abstract

Background With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. Results We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. Conclusions With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1479-z) contains supplementary material, which is available to authorized users.

Published
2019
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35. Implementation of relativistic coupled cluster theory for massively parallel GPU-accelerated computing architectures

Author

Loïc Halbert, Michal Repisky, Hans Jørgen Aa. Jensen, Lucas Visscher, Anastasios Papadopoulos, Dmitry I. Lyakh, André Severo Pereira Gomes, Johann V. Pototschnig, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam [Amsterdam] (VU), National Center for Computational Sciences, Oak Ridge National Laboratory, Hylleraas Centre for Quantum Molecular Sciences (Hylleraas), Department of Chemistry [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark, Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under ContractDE-AC05-00OR22725, French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, French national supercomputing facilities (grants DARI A0070801859 and Joliot Curie grands challenges 2019 gch0417)., MESONM International Associated Laboratory (LAI) (ANR-16-IDEX-0004), Austrian Science Fund(FWF):J 4177-N36, Research Council of Norway through a Center of Excellence Grant (Grant No. 262695), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-16-IDEX-0004,ULNE,ULNE(2016), University of Southern Denmark (SDU), Theoretical Chemistry, and AIMMS

Subjects
Computer science, Dirac (software), FOS: Physical sciences, 010402 general chemistry, 01 natural sciences, Article, Field (computer science), Computational science, Set (abstract data type), Software, Physics - Chemical Physics, 0103 physical sciences, Point (geometry), SDG 7 - Affordable and Clean Energy, Physical and Theoretical Chemistry, Massively parallel, Chemical Physics (physics.chem-ph), 010304 chemical physics, business.industry, 0104 chemical sciences, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Coupled cluster, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Relativistic quantum chemistry, business
Abstract

International audience; In this paper, we report a reimplementation of the core algorithms of relativistic coupled cluster theory aimed at modern heterogeneous high-performance computational infrastructures. The code is designed for efficient parallel execution on many compute nodes with optional GPU coprocessing, accomplished via the new ExaTENSOR back end. The resulting ExaCorr module is primarily intended for calculations of molecules with one or more heavy elements, as relativistic effects on electronic structure are included from the outset. In the current work, we thereby focus on exact 2-component methods and demonstrate the accuracy and performance of the software. The module can be used as a stand-alone program requiring a set of molecular orbital coefficients as starting point, but is also interfaced to the DIRAC program that can be used to generate these. We therefore also briefly discuss an improvement of the parallel computing aspects of the relativistic self-consistent field algorithm of the DIRAC program.

Published
2021
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36. Impact of Temperature on the Immune Interaction between a Parasitoid Wasp and Drosophila Host Species

Author

Fanny Cavigliasso, Jean-Luc Gatti, Dominique Colinet, Marylène Poirié, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), University of Nice Sophia Antipolis, French Ministry of Higher Education and Research, ANR-08-BLAN-0231,CLIMEVOL,Climate change and Evolution of host-parasitoid interactions: from molecules to communities(2008), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), and ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015)

Subjects
Drosophila, Science, [SDV]Life Sciences [q-bio], fungi, temperature, encapsulation, venom composition, parasitoid wasp, parasitic success, phenotypic plasticity, Article
Abstract

Simple Summary Global warming affects most species and their interaction s. Insects are ectotherms, meaning their body temperature is affected by the ambient temperature. This is particularly important for koinobiont parasitoids, insects that keep their host insect alive during development of their eggs and larvae, the host eventually being consumed before adult parasitoids emerge. Temperature changes could therefore affect parasitoids directly and/or indirectly through their impact on the host. Here, we tested the effect of temperature on the parasitic success of two parasitoid lines on two host species, and on each partner independently, to determine whether the host immune response and/or the parasitoid venom proteins, injected with the egg to counteract the host immune response, were affected. The host’s immune defense consists of forming a capsule surrounding the parasitoid egg. In half of the interactions tested, the parasitic success increased with temperature. For one, the increase appeared to result solely from an increased capacity of the parasitoid to escape from a capsule, while for the second, it also appeared to involve a decrease in host encapsulation capacity. Finally, we observed a strong change in venom composition depending on the rearing temperature which may partially explain the change in parasitic success. Abstract Temperature is particularly important for ectotherms, including endoparasitoid wasps that develop inside another ectotherm host. In this study, we tested the impact of three temperatures (20 °C, 25 °C and 30 °C) on the host–parasitoid immune interaction using two Drosophila host species (Drosophila melanogaster and D. yakuba) and two parasitoid lines of Leptopilina boulardi. Drosophila’s immune defense against parasitoids consists of the formation of a melanized capsule surrounding the parasitoid egg. To counteract this response, Leptopilina parasitoids rely on the injection of venom during oviposition. Here, we tested the effect of temperature on parasitic success and host encapsulation capacity in response to a parasitoid egg or other foreign body. Increased temperature either promoted or did not affect the parasitic success, depending on the parasitoid–host pairs considered. The mechanisms behind the higher success seemed to vary depending on whether the temperature primarily affected the host immune response or also affected the parasitoid counter-immune response. Next, we tested the effect of parasitoid rearing temperature on its success and venom composition. Venom composition varied strongly with temperature for both parasitoid lines, partially consistent with a change in their parasitic success. Overall, temperature may have a significant impact on the host–parasitoid immune interaction.

Published
2021
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37. Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge

Author

Nicolas Gayet, Xavier Philippon, Erwann Vince, Lois Maignien, Damien Courtine, Karine Alain, Zongze Shao, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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 Français de Recherche pour l'Exploitation de la Mer (IFREMER), This work was supported by the program MERLIN Abyss to K.A, the ‘Laboratoire d'Excellence’ LabexMER Axis 3 programs ENDIV and CULTIVENT (ANR-10-LABX-1) to K.A., the Sino-French IRP 1211 MicrobSea to K.A. The study was supported by a grant from the French Ministry of Higher Education and Research, to D.C.The LABGeM (CEA/Genoscope and CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
TAPS, hydrothermal, [(2-Hydroxy-1, piezophilic. Abbreviations: ANI, PIPES, Microbiology, 2-(N-morpholino)ethanesulfonic acid, 03 medical and health sciences, N'-bis(2-ethanesulfonic acid), Ribosomal protein, Botany, Yeast extract, CAPSO, 4-bis(2-ethanesulfonic acid), 1-bis(hydroxymethyl)ethyl)amino]-1-propanesulfonic acid, mid-atlantic ridge, DMSO, piezophilic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, UBOCC, University of Brest (UBO) Culture Collection, Strain (chemistry), biology, 030306 microbiology, N-cyclohexyl-3-aminopropanesulfonic acid, hyperthermophilic, average nucleotide identity, International Committee on Systematics of Prokaryotes, General Medicine, Homopiperazine-1, piperazine-N, biology.organism_classification, 16S ribosomal RNA, dimethylsulfoxide, Thermococcales, Thermococcus, Type species, MAR, HOMOPIPES, ICSP, N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid, MES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, HEPES, Hydrothermal vent
Abstract

A coccoid-shaped, strictly anaerobic, hyperthermophilic and piezophilic organoheterotrophic archaeon, strain Iri35cT, was isolated from a hydrothermal chimney rock sample collected at a depth of 2300 m at the Mid-Atlantic Ridge (Rainbow vent field). Cells of strain Iri35cT grew at NaCl concentrations ranging from 1–5 % (w/v) (optimum 2.0 %), from pH 5.0 to 9.0 (optimum 7.0–7.5), at temperatures between 50 and 90 °C (optimum 75–80 °C) and at pressures from 0.1 to at least 50 MPa (optimum: 10–30 MPa). The novel isolate grew on complex organic substrates, such as yeast extract, tryptone, peptone or beef extract, preferentially in the presence of elemental sulphur or l-cystine; however, these molecules were not necessary for growth. Its genomic DNA G+C content was 54.63 mol%. The genome has been annotated and the metabolic predictions are in accordance with the metabolic characteristics of the strain and of Thermococcales in general. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain Iri35cT belongs to the genus Thermococcus, and is closer to the species T. celericrescens and T. siculi . Average nucleotide identity scores and in silico DNA–DNA hybridization values between the genome of strain Iri35cT and the genomes of the type species of the genus Thermococcus were below the species delineation threshold. Therefore, and considering the phenotypic data presented, strain Iri35cT is suggested to represent a novel species, for which the name Thermococcus camini sp. nov. is proposed, with the type strain Iri35cT (=UBOCC M-2026T=DSM 111003T).

Published
2021
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38. Homotopy perturbation technique for improving solutions of large quadratic eigenvalue problems: Application to friction-induced vibration

Author

F. Massa, B. Lallemand, Isabelle Turpin, El-Ghazali Talbi, Thierry Tison, Jeremy Sadet, Optimisation de grande taille et calcul large échelle (BONUS), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Automatique, de Mécanique et d'Informatique industrielles et Humaines - UMR 8201 (LAMIH), Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), Laboratoire de Mathématiques pour l’Ingénieur (LMI), Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), This work was carried out within the framework of the CNRS Research Federation on Ground Transports and Mobility, in association with the ELSAT2020 project supported by the European Community, the French Ministry of Higher Education and Research and the Hauts de France Regional Council., Optimisation de grande taille et calcul large échelle [BONUS], Laboratoire d'Automatique, de Mécanique et d'Informatique industrielles et Humaines - UMR 8201 [LAMIH], Laboratoire de Mathématiques pour l’Ingénieur [LMI], Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université de Lille-Centrale Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), and Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
0209 industrial biotechnology, Quadratic eigenvalue problem, Aerospace Engineering, 02 engineering and technology, 01 natural sciences, Projection (linear algebra), 020901 industrial engineering & automation, Quadratic equation, Normal mode, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0103 physical sciences, Applied mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Nonlinear vibration, Projection, [MATH]Mathematics [math], 010301 acoustics, Quadratic Eigenvalue Problem, Homotopy, Perturbation, Friction-induced vibration, Eigenvalues and eigenvectors, ComputingMilieux_MISCELLANEOUS, Civil and Structural Engineering, Mathematics, Mechanical Engineering, [SPI.MECA.VIBR]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Vibrations [physics.class-ph], Finite element method, Computer Science Applications, Vibration, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Control and Systems Engineering, Signal Processing
Abstract

International audience; This paper puts forward a projection technique for accurately calculating solutions of large Quadratic Eigenvalue Problem. The aim here is to stabilize the complex eigensolutions whilst reducing residual errors, especially when considering significant damping contribution or asymmetric stiffness matrices. Hence, more confident results can be obtained in the frequency band of interest. To achieve this, high order modes, calculated using the homotopy perturbation technique, are introduced in the projection step of the classical method. This numerical proposal is a generalization of the classical projection, based only on normal modes of the associated undamped problem. To evaluate the efficiency of the suggested method, a finite element application dedicated to a friction-induced vibration problem is investigated.

Published
2021
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39. Investigation of the behavior of tropospheric relevant compounds at the interface gas/organic acid aerosols: An ONIOM QM/MM study

Author

Roose, Antoine, Duflot, Denis, Fotsing-Kwetche, Césaire, Toubin, Céline, Severo Pereira Gomes, André, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre for Energy and Environment (CERI EE), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research), French national supercomputing facilities (grants DARI x2016081859 and A0050801859), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-16-IDEX-0004,ULNE,ULNE(2016), Centre for Energy and Environment (CERI EE - IMT Nord Europe), and Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Nord Europe)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

International audience; The uptake of atmospheric gaseous oxidant such as O3 or the ROx (OH, HO2, RO2) family, have a strong impact on the oxidative capacity of the atmosphere. [1], [2] Last decade, few studies have been carried out on the uptake of such compounds on atmospheric aerosol. However, the large variety of organic compounds provides uptake coefficients with a wide range of order of magnitude. [3], [4] Furthermore, the uptake resulting from the combination of different processes (mass accommodation, bulk diffusion, reactivity), the detailed understanding of such a process is not always accessible through experiments. Theoretical tools such as quantum mechanics (QM) combined with Molecular Mechanics (MM) is one way to investigate separately the different processes.The ONIOM hybrid QM/MM method [5] allows to study the reactivity of few molecules in a large system. In our group, a methodology using this computational method have been developed in order to estimate the reactive uptake of gaseous compounds onto organic aerosol particles. In this presentation, reactive uptake of HO2 and O3 onto glutaric acid and oleic acid aerosols respectively will be discussed. Comparisons will be addressed with gas phase theoretical reaction rates and with experimental data.We acknowledge support by the French government through the Program “Investissement d'avenir” through the Labex CaPPA (contract ANR-11-LABX-0005-01) and I-SITE ULNE project OVERSEE (contract ANR-16-IDEX-0004), CPER CLIMIBIO (European Regional Development Fund, Hauts de France council, French Ministry of Higher Education and Research) and French national supercomputing facilities (grants DARI x2016081859 and A0050801859). References[1] H. L. Macintyre and M. J. Evans, “Parameterisation and impact of aerosol uptake of HO2 on a global tropospheric model,” Atmos. Chem. Phys., vol. 11, no. 21, pp. 10965–10974, Nov. 2011, doi: 10.5194/acp-11-10965-2011.[2] M. Zeng and K. R. Wilson, “Efficient Coupling of Reaction Pathways of Criegee Intermediates and Free Radicals in the Heterogeneous Ozonolysis of Alkenes,” The Journal of Physical Chemistry Letters, Jul. 2020, doi: 10.1021/acs.jpclett.0c01823.[3] P. S. J. Lakey, I. J. George, L. K. Whalley, M. T. Baeza-Romero, and D. E. Heard, “Measurements of the HO2 Uptake Coefficients onto Single Component Organic Aerosols,” Environ. Sci. Technol., vol. 49, no. 8, pp. 4878–4885, Apr. 2015, doi: 10.1021/acs.est.5b00948.[4] M. Mendez, N. Visez, S. Gosselin, V. Crenn, V. Riffault, and D. Petitprez, “Reactive and Nonreactive Ozone Uptake during Aging of Oleic Acid Particles,” J. Phys. Chem. A, vol. 118, no. 40, pp. 9471–9481, Oct. 2014, doi: 10.1021/jp503572c.[5] L. W. Chung et al., “The ONIOM Method and Its Applications,” Chem. Rev., vol. 115, no. 12, pp. 5678–5796, Jun. 2015, doi: 10.1021/cr5004419.

Published
2021

40. Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane promoting fitness upon envelope stress

Author

Cyril Moulin, Yiying Yang, Violette Morales, Jérôme Rech, Gladys Munoz, Cécile Albenne, David Ranava, Raffaele Ieva, David Bikard, Lun Cui, Julien Marcoux, Anne Caumont-Sarcos, Catherine Turlan, François Rousset, Luis Orenday-Tapia, Carine Froment, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris] (IP), Institut de pharmacologie et de biologie structurale (IPBS), Further financial support was provided by: the Fondation pour la Recherche Médicale to DR, the Chinese Scholarship Council as part of a joint international PhD program with Toulouse University Paul Sabatier to YY, the French Ministry of Higher Education and Research to LO-T, the Ecole Normale Supérieure to FR, the European Research Council (Europe Union’s Horizon 2020 research and innovation program, grant agreement No 677823), the French governmental Investissement d'Avenir program and the Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) to DB, the Centre National de la Recherche Scientifique and the ATIP-Avenir program to RI., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Protein Folding, Cell division, QH301-705.5, Lipoproteins, Science, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Bama, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biology (General), 030304 developmental biology, Envelope (waves), 0303 health sciences, Microbiology and Infectious Disease, BAM, General Immunology and Microbiology, Chemistry, Outer membrane biogenesis, General Neuroscience, Escherichia coli Proteins, E. coli, Envelope stress, General Medicine, DolP, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, YraP, Cell biology, Folding (chemistry), Bacterial Outer Membrane, bacteria, Medicine, Peptidoglycan, Genetic Fitness, Bacterial outer membrane, OMPs, 030217 neurology & neurosurgery, Biogenesis, Lipoprotein, Research Article, Bacterial Outer Membrane Proteins
Abstract

In Proteobacteria, integral outer membrane proteins (OMPs) are crucial for the maintenance of the envelope permeability barrier to some antibiotics and detergents. In Enterobacteria, envelope stress caused by unfolded OMPs activates the sigmaE (σE) transcriptional response. σE upregulates OMP biogenesis factors, including the β-barrel assembly machinery (BAM) that catalyses OMP folding. Here we report that DolP (formerly YraP), a σE-upregulated and poorly understood outer membrane lipoprotein, is crucial for fitness in cells that undergo envelope stress. We demonstrate that DolP interacts with the BAM complex by associating with outer membrane-assembled BamA. We provide evidence that DolP is important for proper folding of BamA that overaccumulates in the outer membrane, thus supporting OMP biogenesis and envelope integrity. Notably, mid-cell recruitment of DolP had been linked to regulation of septal peptidoglycan remodelling by an unknown mechanism. We now reveal that, during envelope stress, DolP loses its association with the mid-cell, thereby suggesting a mechanistic link between envelope stress caused by impaired OMP biogenesis and the regulation of a late step of cell division.

Published
2021
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41. A European aerosol phenomenology - 7: High-time resolution chemical characteristics of submicron particulate matter across Europe

Author

Bressi, M., Cavalli, F., Putaud, J.P., Fröhlich, R., Petit, J.-E., Aas, W., Äijälä, M., Alastuey, A., Allan, J.D., Aurela, M., Berico, M., Bougiatioti, A., Bukowiecki, N., Canonaco, F., Crenn, V., Dusanter, S., Ehn, M., Elsasser, M., Flentje, H., Graf, P., Green, D.C., Heikkinen, L., Hermann, H., Holzinger, R., Hueglin, C., Keernik, H., Kiendler-Scharr, A., Kubelová, L., Lunder, C., Maasikmets, M., Makeš, O., Malaguti, A., Mihalopoulos, N., Nicolas, J.B., O'Dowd, C., Ovadnevaite, J., Petralia, E., Poulain, L., Priestman, M., Riffault, V., Ripoll, A., Schlag, P., Schwarz, J., Sciare, J., Slowik, J., Sosedova, Y., Stavroulas, I., Teinemaa, E., Via, M., Vodička, P., Williams, P.I., Wiedensohler, A., Young, D.E., Zhang, S., Favez, O., Minguillón, M.C., Prevot, A.S.H., Sub Atmospheric physics and chemistry, Energy, Resources & Technological Change, Marine and Atmospheric Research, Norwegian Institute for Air Research (NILU), University of Helsinki, Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, School of Earth, Atmospheric and Environmental Sciences [Manchester] (SEAES), University of Manchester [Manchester], Finnish Meteorological Institute (FMI), Environmental Chemical Processes Laboratory [Heraklion] (ECPL), Department of Chemistry [Heraklion], University of Crete [Heraklion] (UOC)-University of Crete [Heraklion] (UOC), Laboratory of Atmospheric Chemistry [Paul Scherrer Institute] (LAC), Paul Scherrer Institute (PSI), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Nord Europe), Institut Mines-Télécom [Paris] (IMT), Institute for Atmospheric and Earth System Research (INAR), German Meteorological Service, EMPA Air Pollution/Environmental Technology, Swiss Federal Laboratories for Materials Science and Technology [Dübendorf] (EMPA), King‘s College London, Leibniz Institute for Tropospheric Research (TROPOS), Institute for Marine and Atmospheric Research [Utrecht] (IMAU), Utrecht University [Utrecht], EMPA, Swiss Federal Laboratories for Materials Testing and Research, Estonian Environmental Research Center, Tallinn, Estonia, Institut für Energie- und Klimaforschung - Troposphäre (IEK-8), Forschungszentrum Jülich GmbH, CESNET [Prague], Czech Academy of Sciences [Prague] (CAS), Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Landwirtschaftliches Zentrum, Tallinn University, University of Crete [Heraklion] (UOC), Centre for Climate and Air Pollution Studies [Galway] (C-CAPS), National University of Ireland [Galway] (NUI Galway), Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Université de Strasbourg (UNISTRA), Instituto Universitario de Investigacion de Nanocienca de Aragon, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Institute of Chemical Technology [Prague] (ICT), Cancer Research UK Manchester Institute, Department of Earth Sciences [Manchester], Institut National de l'Environnement Industriel et des Risques (INERIS), JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), Chimie Atmosphérique Expérimentale (CAE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Centre for Energy and Environment (CERI EE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Norwegian Ministry of Climate and Environment Strategic Institute Program, Spanish Ministry of Economy and Competitiveness, Météo-France, EMME-CARE, UK National Research Council, UK Department of Environment, Food and Rural Affairs (DEFRA), Greek Operational Programme' Competitiveness, Entrepreneurship and Innovation' (NSRF 2014–2020), European Regional Development Fund, French Ministry of Higher Education and Research, French CNRS, French Regional Council 'Hauts-de-France', Czech ACTRIS-CZ RI (CZ.02.1.01/0.0/0.0/16_013/0001315), EPA Ireland, Irish Department of Communications, Climate Action and Environment (DCCAE), German Federal Environmental Agency, French ADEME, COST COLOSSAL CA16109, PRISMA project (CGL2012-39623-C02-1), ClearfLo project (NE/H008136/1), 'Panhellenic infrastructure for atmospheric composition and climate change, PANACEA' (MIS 5021516), CPER CLIMIBIO, CPER IRENI, Czech MEYS’s project (LTC18068), German Ultrafine Aerosol Network GUAN (F&E 370343200, F&E 371143232), ChArMEx project, ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), European Project: 262254,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,ACTRIS(2011), European Project: 654109,H2020,H2020-INFRAIA-2014-2015,ACTRIS-2(2015), European Project: 603445,EC:FP7:ENV,FP7-ENV-2013-two-stage,BACCHUS(2013), Sub Atmospheric physics and chemistry, Energy, Resources & Technological Change, Marine and Atmospheric Research, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre for Energy and Environment (CERI EE - IMT Nord Europe), Department of Physics, European Commission, Alastuey, Andrés [0000-0002-5453-5495], Minguillón, María Cruz [0000-0002-5464-0391], Alastuey, Andrés, and Minguillón, María Cruz

Subjects
Atmospheric Science, 010504 meteorology & atmospheric sciences, Chemical composition, 010501 environmental sciences, 01 natural sciences, Environmental pollution, German, Meteorology. Climatology, 11. Sustainability, ddc:550, Aerosoles, AMS, ORGANIC AEROSOL, ComputingMilieux_MISCELLANEOUS, General Environmental Science, media_common, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Time resolution, Mass sprectrometry, TD172-193.5, SOURCE APPORTIONMENT, [SDE]Environmental Sciences, language, MONTSEC SOUTHERN PYRENEES, Phenomenology, Research center, Chemical compositions, Entrepreneurship, Higher education, [SDE.MCG]Environmental Sciences/Global Changes, AIR-QUALITY, European Regional Development Fund, Library science, 114 Physical sciences, SPECIATION MONITOR, Political science, media_common.cataloged_instance, European union, Aerosol, 1172 Environmental sciences, 0105 earth and related environmental sciences, RESOLVED MEASUREMENTS, Government, Mass spectrometry, business.industry, COMPONENTS, language.human_language, CARBONACEOUS AEROSOLS, 13. Climate action, MASS-SPECTROMETER, QC851-999, business
Abstract

Similarities and differences in the submicron atmospheric aerosol chemical composition are analyzed from a unique set of measurements performed at 21 sites across Europe for at least one year. These sites are located between 35 and 62°N and 10° W – 26°E, and represent various types of settings (remote, coastal, rural, industrial, urban). Measurements were all carried out on-line with a 30-min time resolution using mass spectroscopy based instruments known as Aerosol Chemical Speciation Monitors (ACSM) and Aerosol Mass Spectrometers (AMS) and following common measurement guidelines. Data regarding organics, sulfate, nitrate and ammonium concentrations, as well as the sum of them called non-refractory submicron aerosol mass concentration ([NR-PM1]) are discussed. NR-PM1 concentrations generally increase from remote to urban sites. They are mostly larger in the mid-latitude band than in southern and northern Europe. On average, organics account for the major part (36–64%) of NR-PM1 followed by sulfate (12–44%) and nitrate (6–35%). The annual mean chemical composition of NR-PM1 at rural (or regional background) sites and urban background sites are very similar. Considering rural and regional background sites only, nitrate contribution is higher and sulfate contribution is lower in mid-latitude Europe compared to northern and southern Europe. Large seasonal variations in concentrations (μg/m³) of one or more components of NR-PM1 can be observed at all sites, as well as in the chemical composition of NR-PM1 (%) at most sites. Significant diel cycles in the contribution to [NR-PM1] of organics, sulfate, and nitrate can be observed at a majority of sites both in winter and summer. Early morning minima in organics in concomitance with maxima in nitrate are common features at regional and urban background sites. Daily variations are much smaller at a number of coastal and rural sites. Looking at NR-PM1 chemical composition as a function of NR-PM1 mass concentration reveals that although organics account for the major fraction of NR-PM1 at all concentration levels at most sites, nitrate contribution generally increases with NR-PM1 mass concentration and predominates when NR-PM1 mass concentrations exceed 40 μg/m³ at half of the sites., This study was partially supported by the European Union's projects ACTRIS (EU FP7-262254) and ACTRIS-2 (EU Horizon 2020–654109). COST Action CA16109 COLOSSAL, Chemical On-Line cOmpoSition and Source Apportionment of fine aerosoL, is acknowledged. The ACSM observations at Birkenes was funded by the Norwegian Ministry of Climate and Environment Strategic Institute Program. IDAEA-CSIC (3 datasets: BCN, MSA, MSY) was partially supported by the Spanish Ministry of Economy and Competitiveness and FEDER funds under the PRISMA project (CGL 2012-39623-C02-1). The London measurements were supported by the UK National Research Council through the ClearfLo project and a PhD studentship (grant refs. NE/H008136/1 and NE/I528142/1) and the Department of Environment, Food and Rural Affairs (DEFRA). ECPL personel, namely Nikolaos Mihalopoulos, Aikaterini Bougiatioti and Iasonas Stavroulas acknowledge support by the project “Panhellenic infrastructure for atmospheric composition and climate change, PANACEA” (MIS 5021516) which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure”, funded by the Operational Programme” Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the European Union (European Regional Development Fund). IMT Lille Douai acknowledges financial support from the CaPPA (Chemical and Physical Properties of the Atmosphere) project funded by the French National Research Agency (ANR) through the PIA (Programme d'Investissement d'Avenir) under contract ANR-11-LABX-0005-01, and two CPER projects funded by the French Ministry of Higher Education and Research, the CNRS, the Regional Council “Hauts-de-France” and the European Regional Development Fund (ERDF): Climibio, and IRENI (additionally financed by the Communauté Urbaine de Dunkerque). S. Zhang thanks IMT Lille Douai and the Regional Council “Hauts-de-France” for her PhD grant. Prague co-authors would like to acknowledge a Czech MEYS's project under INTER-EXCELENCE INTERCOST program under grant agreement LTC18068 and from European Regional Development Fund-Project under the grant ACTRIS-CZ RI (CZ.02.1.01/0.0/0.0/16_013/0001315). EPA Ireland, Department of Communications, Climate Action and Environment (DCCAE) and the European Union's Seventh Framework Programme (FP7/2007–2013) project BACCHUS under grant agreement n_603445 are acknowledged for research support at Mace Head. The physical measurements were also funded by the German Ultrafine Aerosol Network GUAN, which was jointly established with help of the German Federal Environment Ministry (BMU) grants F&E 370343200 (German title: “Erfassung der Zahl feiner und ultrafeiner Partikel in der Auβenluft”), 2008–2010, and F&E 371143232 (German title: “Trendanalysen gesundheitsgefährdender Fein-und Ultrafeinstaubfraktionen unter Nutzung der im German Ultrafine Aerosol Network (GUAN) ermittelten Immissionsdaten durch Fortführung und Interpretation der Messreihen”) 2012–2014. We also acknowledge the WCCAP (World Calibration Center for Aerosol Physics) as part of the WMO-GAW program. The WCCAP is base-funded by the German Federal Environmental Agency (Umweltbundesamt), Germany. Support by the European Regional Development Funds (EFRE – Europe funds Saxony) is gratefully acknowledged. Atmospheric measurements performed in Corsica is part of the ChArMEx project supported by CNRS-INSU, ADEME, Météo-France and CEA in the framework of the multidisciplinary programme MISTRALS (Mediterranean Integrated Studies aT Regional And Local Scales; http://mistrals-home.org/, last access: June 10, 2020). Final data processing of these measurements has been supported by the EMME-CARE (Eastern Mediterranean and Middle East Climate and Atmosphere Research Center) which has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 856612 and the Cyprus Government. The measurements in Switzerland were supported by the Federal Office for the Environment. We thank the International Foundation High Altitude Research Stations Jungfraujoch and Gornergrat (HFSJG) for the opportunity to perform experiments on the Jungfraujoch.

Published
2021
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42. In Vitro Hair Dermal Papilla Cells Induction by Fagraea berteroana, a Tree of the Marquesan Cosmetopoeia (French Polynesia)

Author

Claire Chazaud, Jean-François Butaud, Phila Raharivelomanana, Stéphanie Hermitte, Raimana Ho, Edwige Ranouille, Stéphane Greff, Edith Filaire, Kristelle Hughes, Jean-Yves Berthon, Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), GREENTECH, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Forestry and Polynesian Botany, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), French Ministry of Higher Education and Research at the University of French Polynesia ED 469Greentech, GREFF, Stéphane, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), and Institut de Recherche pour le Développement (IRD)

Subjects
Aging, Fagraea berteroana, ethnocosmetology, Pharmaceutical Science, Dermatology, 01 natural sciences, Bone morphogenetic protein 2, lcsh:Chemistry, 03 medical and health sciences, hair growth, Hair cycle, Gene expression, medicine, Chemical Engineering (miscellaneous), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 0303 health sciences, biology, 010405 organic chemistry, Cell growth, Wnt signaling pathway, Marquesas islands, Transforming growth factor beta, Gentianaceae, Hair follicle, 0104 chemical sciences, Cell biology, Dermal papillae, medicine.anatomical_structure, lcsh:QD1-999, biology.protein, Surgery
Abstract

Fagraea berteroana is a tree used in traditional medicine in various islands of the South Pacific. Here, we studied its hair growth-inducing properties as suggested by one of its Marquesan ethno-uses in haircare. The ethyl acetate extract of the fruits of F. berteroana (FEAE) and four resulting fractions (FEAE-F0, FEAE-F1, FEAE-F2, and FEAE-F3) were tested on hair follicle dermal papilla cells to determine their cell proliferative activity. Furthermore, RT-qPCR analysis enabled gene modulation analysis, while immunostaining of the β-catenin protein was used to follow protein regulation. We found that the plant extracts induced a controlled, dose-dependent cell proliferation. FEAE-F0 simultaneously down-regulated Bone Morphogenetic Protein 2 (BMP2) mRNA expression and upregulated Cyclin-D1 (CCND1) gene expression, which suggests an involvement in the regulation of the Wnt and Transforming Growth Factor beta (TGFβ) pathways that control the hair cycle. FEAE-F0 exhibited a 1.34-fold increase of nuclear β-catenin protein. This is indicative of an active hair growth state. Thus, we conclude that FEAE-F0 could be an innovative candidate in hair care, which opens interesting leads to promote the Marquesan cosmetopoeia.

Published
2021
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43. Degradation of Exogenous Fatty Acids in Escherichia coli

Author

Viola Pavoncello, Frédéric Barras, Emmanuelle Bouveret, Adaptation au stress et Métabolisme chez les entérobactéries - Stress adaptation and metabolism in enterobacteria (SAMe), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and This research was funded by the Centre National de la Recherche Scientifique (CNRS) and the Pasteur Institute. V.P. was supported by a doctoral fellowship from the French Ministry of Higher Education and Research.

Subjects
fad genes, FadR, Escherichia coli, fatty acids, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Biology, Biochemistry, beta-oxidation
Abstract

Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.

Published
2022
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44. Pentadecaibins I–V: 15-Residue Peptaibols Produced by a Marine-Derived Trichoderma sp. of the Harzianum Clade

Author

Franck Bastide, Thibaut Robiou du Pont, Soizic Prado, Anne-Isaline Van Bohemen, Laurence Meslet-Cladiere, Lea Atanasova, Bastien Cochereau, Aurore Zalouk-Vergnoux, Yves François Pouchus, Thomas Guillemette, Irina S. Druzhinina, Nicolas Ruiz, Bernard Bodo, Corentin Maslard, Muriel Marchi, Aurore Michaud, Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Vienna University of Technology (TU Wien), University of Natural Resources and Life Sciences (BOKU), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French Ministry of Higher Education and Research, Region Ile-de-France, Museum National d'Histoire Naturelle (Paris, France), and Centre National de la Recherche Scientifique (CNRS).

Subjects
Mathematical methods, Stereochemistry, Lineage (evolution), Peptaibol, Pharmaceutical Science, Peptides and proteins, 01 natural sciences, DNA sequencing, Analytical Chemistry, chemistry.chemical_compound, Fragmentation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Discovery, Gene, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Pharmacology, chemistry.chemical_classification, Ions, biology, Phylogenetic tree, Strain (chemistry), 010405 organic chemistry, Organic Chemistry, Genomics, biology.organism_classification, 0104 chemical sciences, Amino acid, 010404 medicinal & biomolecular chemistry, Complementary and alternative medicine, chemistry, Trichoderma, Molecular Medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; In the course of investigations on peptaibol chemodiversity from marine-derived Trichoderma spp., five new 15-residue peptaibols named pentadecaibins I–V (1–5) were isolated from the solid culture of the strain Trichoderma sp. MMS1255 belonging to the T. harzianum species complex. Phylogenetic analyses allowed precise positioning of the strain close to T. lentiforme lineage inside the Harzianum clade. Peptaibol sequences were elucidated on the basis of their MS/MS fragmentation and extensive 2D NMR experiments. Amino acid configurations were determined by Marfey’s analyses. The pentadecaibins are based on the sequences Ac-Aib1-Gly2-Ala3-Leu4-Aib/Iva5-Gln6-Aib/Iva7-Val/Leu8-Aib9-Ala10-Aib11-Aib12-Aib13-Gln14-Pheol15. Characteristic of the pentadecaibin sequences is the lack of the Aib-Pro motif commonly present in peptaibols produced by Trichoderma spp. Genome sequencing of Trichoderma sp. MMS1255 allowed the detection of a 15-module NRPS-encoding gene closely associated with pentadecaibin biosynthesis. Pentadecaibins were assessed for their potential antiproliferative and antimicrobial activities.

Published
2021
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45. Characterization and source apportionment of single particles from metalworking activities

Author

Karine Deboudt, Saliou Mbengue, Jovanna Arndt, Robert M. Healy, Véronique Riffault, Laurent Y. Alleman, John C. Wenger, Ari Setyan, Pascal Flament, University College Cork (UCC), Ontario Ministry of the Environment and Climate Change, Laboratoire de Physico-Chimie de l'Atmosphère (LPCA), Université du Littoral Côte d'Opale (ULCO), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT), Centre for Energy and Environment (CERI EE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), ADEME, Regional Council 'Hauts-de-France', French Ministry of Higher Education and Research, CNRS, European Regional Development Fund (ERDF), Communauté Urbaine de Dunkerque, Irish Research Council, NANO-INDUS project (1181C0089), CPER CLIMIBIO, CPER IRENI, and ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011)

Subjects
010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, 010501 environmental sciences, Raw material, Toxicology, 01 natural sciences, Ferromanganese, Air Pollution, Particle Size, Polycyclic Aromatic Hydrocarbons, Air quality index, Chemical composition, 0105 earth and related environmental sciences, Vehicle Emissions, Aerosols, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Air Pollutants, General Medicine, Particulates, Pollution, Aerosol, 13. Climate action, Environmental chemistry, Metalworking, [SDE]Environmental Sciences, Particle, Environmental science, Particulate Matter, France, Environmental Monitoring
Abstract

International audience; Industrial metalworking facilities emit a variety of air toxics including volatile organic compounds, polycyclic aromatic hydrocarbons (PAHs) and heavy metals. In order to investigate these emissions, a 1-month multi-instrument field campaign was undertaken at an industrial site in Grande-Synthe, Dunkirk (France), in May and June 2012. One of the main objectives of the study was to provide new information on the chemical composition of particulate matter with aerodynamic diameters smaller than 2.5 μm (PM2.5) in the vicinity of metalworking facilities. An aerosol time-of-flight mass spectrometer (ATOFMS) was deployed to provide size-resolved chemical mixing state measurements of ambient single particles at high temporal resolution. This mixing state information was then used to apportion PM2.5 to local metalworking facilities influencing the receptor site. Periods when the site was influenced by metalworking sources were characterised by a pronounced increase in particles containing toxic metals (manganese, iron, lead) and polycyclic aromatic hydrocarbons (PAHs) with a variety of chemical mixing states. The association of specific particle classes with a nearby ferromanganese alloy manufacturing plant was confirmed through comparison with previous analysis of raw materials (ores) and chimney filter particle samples collected at the facility. Particles associated with emissions from a nearby steelworks were also identified. The contribution of local metalworking activities to PM2.5 at the receptor site for the period when the ATOFMS was deployed ranged from 1 to 65% with an average contribution of 17%, while the remaining mass was attributed to other local and regional sources. These findings demonstrate the impact of metalworking facilities on air quality downwind and provide useful single particle signatures for future source apportionment studies in communities impacted by metalworking emissions.

Published
2021
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46. Can HIV epidemics among men who have sex with men be eliminated through participation in PrEP rollouts?

Author

Jijón, Sofía, Molina, Jean-Michel, Costagliola, Dominique, Supervie, Virginie, Breban, Romulus, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Evolution et pathogenèses virales, Institut National de la Santé et de la Recherche Médicale (INSERM)-Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), SJ was supported by an ANRS fellowship and a PhD fellowship from the French Ministry of Higher Education and Research, obtained via the Public Health Doctoral Network coordinated by the EHESP, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Breban, Romulus

Subjects
behavioral epidemiology, game theory, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, prevention coverage, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, HIV, men who have sex with men, Pre-exposure prophylaxis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

International audience; Objectives: To study the conditions under which PrEP coverage can eliminate HIV among men who have sex with men (MSM) in the Paris region.Design: Mathematical modeling.Methods: We propose an innovative approach, combining a transmission model with a game-theoretic model, for decision-making about PrEP use. Individuals at high risk of HIV infection decide to use PrEP, depending on their perceived risk of infection and the relative cost of using PrEP versus antiretroviral treatment (ART), which includes monetary and/or non-monetary aspects, such as price and access model of PrEP, consequences of being infected and lifelong ART.Results: If individuals assessed correctly their infection risk, and the cost of using PrEP were sufficiently low, then the PrEP rollout could lead to elimination. Specifically, assuming 86% PrEP effectiveness, as observed in two clinical trials, a minimum PrEP coverage of 55% (95% CI:43%–64%) among high-risk MSM would achieve elimination in the Paris region. A complete condom drop by MSM using PrEP slightly increases the minimum PrEP coverage required for elimination, by ∼1%, while underestimation of their own HIV infection risk would require PrEP programs reduce the cost of using PrEP by a factor ∼2 to achieve elimination.Conclusions: Elimination conditions are not yet met in the Paris region, where at most 47% of high-risk MSM were using PrEP as of mid-2019. Further lowering the cost of PrEP and promoting a fair perception of HIV risk are required and should be maintained in the long run, to maintain elimination status.

Published
2021
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47. Probing the effects of redox conditions and dissolved Fe2+ on nanomagnetite stoichiometry by wet chemistry, XRD, XAS and XMCD

Author

Khalil Hanna, Mathieu Pasturel, Frank Heberling, Marawit Tesfa, Rémi Marsac, Mathieu Pédrot, Phoomipat Jungcharoen, Fadi Choueikani, Géosciences Rennes (GR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Ecole Nationale Supérieure de Chimie de Rennes (ENSCR), Institut für Nukleare Entsorgung (INE), Karlsruher Institut für Technologie (KIT), Région Bretagne, Campus France, Khon Kaen University (Thailand), GeOHeLiS analytical platform of Rennes University, French Region of Rennes Metropole, French Ministry of Higher Education and Research, SURFNANO project - CNRS-INSU EC2CO program, SynFeSol project - Brittany Region (AAP TRANSFERT 2019), ANR-18-CE01-0008,C-FACTOR,Le devenir des contaminants est contrôlé par la spéciation de la matière organique colloïdale(2018), European Project: FEDER, Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
X-ray absorption spectroscopy, Materials science, Recrystallization (geology), Aqueous solution, Materials Science (miscellaneous), Maghemite, 02 engineering and technology, engineering.material, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Redox, 0104 chemical sciences, chemistry.chemical_compound, Chemical engineering, chemistry, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, engineering, 0210 nano-technology, Wet chemistry, General Environmental Science, Magnetite, Spin canting
Abstract

International audience; Magnetite nanoparticles, commonly found in subsurface environments, are extensively used in various applications such as environmental remediation, catalysis, electronics and medicine. However, the oxidative transformation of magnetite (mixed-valent Fe-oxide) into maghemite (Fe(III)-oxide) that drastically affects magnetic, catalytic and redox properties of the mineral, is still poorly understood. In the present study, a thorough characterization of both particle core and surface of magnetite was performed to accurately assess the relationship between mineral composition and reactivity within the magnetite/maghemite core-shell structure. Previous work showed that X-ray absorption spectra (XAS) and X-ray magnetic circular dichroism (XMCD) can provide key insights into magnetite stoichiometry (R = Fe(II)/Fe(III)) of 10 nm sized particles, as compared to wet chemistry and X-ray diffraction (XRD). In the present study, XMCD signals have been used to further characterize the complex reactions involved in the magnetite/maghemite system upon oxidation and recharge processes, e.g. decreasing R from 0.5 to 0.1 using H2O2 or increasing from 0.1 to 0.5 through dissolved Fe2+ amendment. Indeed, surface recrystallization processes, induced by oxidation as well as Fe2+ diffusion into the solid phase and/or redistribution of electron equivalents between the aqueous solution and the magnetite bulk, led to decreased spin canting effects, altering XMCD signals. This study provides a fundamental understanding of the processes occurring in the magnetite/maghemite system upon the alteration of the redox conditions and offers a more accurate method for the determination of magnetite stoichiometry by XMCD.

Published
2021
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48. Deprivation of direct adult contact during development affects social representation in a songbird

Author

Marion Coulon, Audrey Perret, Martine Hausberger, Hugo Cousillas, Isabelle George, Laurence Henry, Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), This study was supported by a grant from the French A.N.R. (Agence Nationale pour la Recherche) entitled 'Intermodality and Imitation: Behavioral and Neuronal Aspects (Studies in Human Newborns and Birds).' All authors were supported by the University of Rennes 1 and by the French CNRS. A. P. was funded by a doctoral fellowship of the French Ministry of Higher Education and Research., ANR-09-BLAN-0319,INTERIMIT(2009), and Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
social cognition, Social stimuli, social motivation, 03 medical and health sciences, Behavioral Neuroscience, [SCCO]Cognitive science, Developmental Neuroscience, operant conditioning, Social cognition, Social representation, Developmental and Educational Psychology, Social experience, Animals, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Social Behavior, adult influences, 030304 developmental biology, 0303 health sciences, Motivation, social representation, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, 05 social sciences, biology.organism_classification, Songbird, social deprivation, Social deprivation, Sturnus, Starlings, Conditioning, Operant, Psychology, Social motivation, Developmental Biology, Cognitive psychology
Abstract

International audience; Social cognition involves a wide array of skills that are built largely through interactions with conspecifics and therefore depend upon early social experience. Motivation for social stimuli is a key feature of social behavior and an operant conditioning task showed that isolated wild-caught adult starlings (Sturnus vulgaris) are highly motivated to access pictures of other starlings. Here, we show that hand-raised adult starlings maintained in groups of peers throughout development but without any contact with adult models were not or only poorly motivated to access pictures of conspecifics. Moreover, they did not prefer pictures of starlings to pictures of landscapes, unlike birds wild-caught as adults. These results raise questions about the role of social experience during development, particularly with adult models, in the development of social motivation and of social representation in general.

Published
2021
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49. Group behaviours and individual spatial sorting before departure predict the dynamic of collective movements in horses

Author

Jean-Louis Deneubourg, Léa Briard, Odile Petit, Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-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 libre de Bruxelles (ULB), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was financially supported by the French Ministry of Higher Education and Research, the Foundation des Treilles, David et Alice van Buuren, de Meurs-François and Groupement de Recherche en Ethologie 2822 (to LB)., and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Identity (social science), 010603 evolutionary biology, 01 natural sciences, decision making, predeparture, Group cohesiveness, Orientation (mental), [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Ecology, Evolution, Behavior and Systematics, Event (probability theory), density, Group (mathematics), Movement (music), local interactions, 05 social sciences, Outcome (probability), Equusferuscaballus, recruitment, Dynamics (music), MESH: decision-making, dispersion, Equus ferus caballus, joining order, Animal Science and Zoology, Psychology, Cognitive psychology
Abstract

International audience; Establishing how collective decisions emerge is central to our understanding of animal societies. A frequent approach in collective behaviour studies is to seek for leaders that will trigger and direct group movements. Relatively few studies on collective movements, notably in mammals, took into account the events preceding group departures. Success in recruitment can depend on the arousal state, the behaviour and the spatial distribution of animals before departure. We tested the effect of such factors on recruitment process in two groups of 9 domestic mares, Equus ferus caballus , at pasture. Predeparture periods were compared to control periods to identify their unique characteristics and to understand how they can predict the following collective outcome. We found that predeparture periods were characterized by the simultaneous increase in the number of active and goal-oriented individuals as well as in group cohesion. However, while the temporal patterns of activity and dispersion were unique to predeparture periods, those of orientation were not different from control periods. We also found that before departure individuals started to move towards the future goal area and to position themselves along the front-back axis. Moreover, the front-to-back position of group members was linked to the order in which they joined a collective movement. Finally, the duration of the joining process was positively correlated to the group dispersion. Our findings demonstrate that decision making is a continuous process and emphasize the necessity, in the study of collective decisions, to look beyond the event of initiation itself and the identity of the initiator as recruitment depends on group state before and at departure.

Published
2021
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50. Fast active learning for pure exploration in reinforcement learning

Author

Ménard, Pierre, Domingues, Omar Darwiche, Kaufmann, Emilie, Jonsson, Anders, Leurent, Edouard, Valko, Michal, Valko, Michal, Au delà de l'apprentissage séquentiel pour de meilleures prises de décisions - - BOLD2019 - ANR-19-CE23-0026 - AAPG2019 - VALID, Otto-von-Guericke University [Magdeburg] (OVGU), Scool (Scool), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), RENAULT, DeepMind [Paris], The research presented was supported by European CHIST-ERA project DELTA, French Ministry of Higher Education and Research, Nord-Pas-de-Calais Regional Council, French National Research Agency project BOLD (ANR-19-CE23-0026-04). Anders Jonsson is partially supported by the Spanish grants TIN2015-67959 and PCIN-2017-082., ANR-19-CE23-0026,BOLD,Au delà de l'apprentissage séquentiel pour de meilleures prises de décisions(2019), Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg] (OVGU), Sequential Learning (SEQUEL), Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS), and DeepMind

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Statistics - Machine Learning, Machine Learning (stat.ML), [STAT.ML] Statistics [stat]/Machine Learning [stat.ML], Machine Learning (cs.LG)
Abstract

International audience; Realistic environments often provide agents with very limited feedback. When the environment is initially unknown, the feedback, in the beginning, can be completely absent, and the agents may first choose to devote all their effort on exploring efficiently. The exploration remains a challenge while it has been addressed with many hand-tuned heuristics with different levels of generality on one side, and a few theoretically backed exploration strategies on the other. Many of them are incarnated by intrinsic motivation and in particular explorations bonuses. A common rule of thumb for exploration bonuses is to use 1/ √ n bonus that is added to the empirical estimates of the reward, where $n$ is a number of times this particular state (or a state-action pair) was visited. We show that, surprisingly, for a pure-exploration objective of reward-free exploration, bonuses that scale with 1/n bring faster learning rates, improving the known upper bounds with respect to the dependence on the horizon $H$. Furthermore, we show that with an improved analysis of the stopping time, we can improve by a factor $H$ the sample complexity in the best-policy identification setting, which is another pure-exploration objective, where the environment provides rewards but the agent is not penalized for its behavior during the exploration phase.

Published
2021

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