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51. Isomerism Effects in the Collisional Excitation of Cyanoacetylene by Molecular Hydrogen

Author: Cheikh T. Bop, François Lique, Ernesto Quintas-Sánchez, Richard Dawes, Fidel A. Batista-Romero, Alexandre Faure, Laboratoire Ondes et Milieux Complexes (LOMC), Centre National de la Recherche Scientifique (CNRS)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Missouri University of Science and Technology (Missouri S&T), University of Missouri System, Centre National d'Études Spatiales [Toulouse] (CNES)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry, Missouri University of Science and Technology, 142 Schrenk Hall, 400 West 11th Street, Rolla, Missouri 65409, United States, University of Missouri System-University of Missouri System, Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: Atmospheric Science, Astrochemistry, 7. Clean energy, 01 natural sciences, Molecular processes, chemistry.chemical_compound, Geochemistry and Petrology, 0103 physical sciences, Molecule, Cyanoacetylene, [CHIM]Chemical Sciences, Physics::Chemical Physics, van der Waals complexes, Nuclear Experiment, 010303 astronomy & astrophysics, Collisional excitation, Quantum, Quantum Scattering, Astrophysics::Galaxy Astrophysics, ComputingMilieux_MISCELLANEOUS, Physics, 010304 chemical physics, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Hydrogen molecule, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry, Space and Planetary Science, Energy transfer, Scattering theory, Atomic physics, Excitation
Abstract: International audience; Rotational excitation of the interstellar HC 2 NC and HNC 3 molecules, two isomers of HC 3 N, induced by collisions with H 2 is investigated at low collision energy using a quantum time-independent approach. The scattering calculations are based on new high-level ab initio four-dimensional (4D) potential energy surfaces (PESs) computed at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12b] level of theory. The method of interpolating moving least squares (IMLS) was used to construct 4D analytical PESs. Rotationally inelastic cross sections among the low-lying rotational levels of HC 2 NC and HNC 3 were obtained using a pure quantum close-coupling approach for total energies up to ∼100 cm −1. The corresponding thermal rate coefficients were computed for temperatures ranging from 1 to 20 K. Propensity rules in favor of even Δj 1 transitions were found for both HC 2 NC and HNC 3 in collisions with para-H 2 (j 2 = 0), with j 1 being the rotational level of HC 2 NC and HNC 3 molecules. The new rate coefficients were compared to previously published HC 3 N−para-H 2 (j 2 = 0) rate coefficients. As expected, differences were found, especially for the rate coefficients corresponding to Δj 1 = 1 transitions. Such a comparison confirms the importance of having specific collisional data for the different isomers of a molecule. The new rate coefficients will be crucial to improve the estimation of the HC 3 N/ HC 2 NC/HNC 3 abundance ratio in the interstellar medium.
Published: 2019

52. Correction to: Agroforestry for soil health

Author: Jeanne Dollinger, Shibu Jose, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The School of Natural Resources, University of Missouri [Columbia], University of Missouri System-University of Missouri System, and University of Missouri [Columbia] (Mizzou)
Subjects: 2. Zero hunger, 0106 biological sciences, Soil health, business.industry, Agroforestry, [SDV]Life Sciences [q-bio], Forestry, 04 agricultural and veterinary sciences, 15. Life on land, 01 natural sciences, complex mixtures, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, business, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Correction to: Agroforest Syst (2018) 92:213–219 https://doi.org/10.1007/s10457-018-0223-9; Correction to: Agroforestry for soil health
Published: 2019

53. Density of fluids confined in nanopores

Author: Firlej, Lucyna, Kuchta, B, Pfeifer, P, Aigle, L2c, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], Physics::Fluid Dynamics, Quantitative Biology::Subcellular Processes, Quantitative Biology::Biomolecules, [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: Unlike macroscopic objects, any system of nanometric size shows characteristics that strongly depend on its size and geometric form.Here we focus on the influence of confinement on properties of fluids, when the confining volumes are of nanometric size.Using Grand Canonical Monte Carlo simulations we show that when a fluid is confined in nano-volume, delimited by non-attracting pore walls,its density is heterogeneous close to the pore wall, and, on average over the whole pore volume, it is smaller than the density of bulk fluid. Thisfluid heterogeneity, resulting from the nano-confinement, progressively weakens when the pore size increases, and totally disappears inside thepores larger than 5 nm. On the other side, in the limit of very small pores, the fluid density approaches the ideal gas value. This effect should bedistinguished from the well know heterogeneity of density of fluids adsorbed in nanopores, driven by the difference between the strength offluid-fluid and fluid-pore wall interactions, that varies with the distance from the pore wall.We show that the density distribution inside the non-attracting reservoir strongly depends the distance from the pore walls, and the pore size andshape. Such a behavior, although non-intuitive in macroscopic sample, has a simple physical explanation. The energy of a given gas moleculestrongly depends on the number of its nearest neighbors. In the nanopores this number decreases when the molecule is closer to the pore wall.Less intuitive is the observation that at higher pressures (p > 100 bar) the density of the gas close to the wall may be higher than in the middle ofthe pore, and even higher than the one of the bulk gas at the same thermodynamic conditions.
Published: 2019

54. The Cafa Challenge Reports Improved Protein Function Prediction And New Functional Annotations For Hundreds Of Genes Through Experimental Screens

Author: Heiko Schoof, Ahmet Sureyya Rifaioglu, Ian Sillitoe, Shanfeng Zhu, Marco Carraro, Naihui Zhou, Asa Ben-Hur, Rui Fa, Alice C. McHardy, David W. Ritchie, George Georghiou, Filip Ginter, Haixuan Yang, Alex A. Freitas, Constance J. Jeffery, Tapio Salakoski, Radoslav Davidovic, Huy N Nguyen, Devon Johnson, Yotam Frank, Alexandra J. Lee, Sean D. Mooney, Marco Falda, Marie-Dominique Devignes, Gianfranco Politano, David T. Jones, Silvio C. E. Tosatto, Renzhi Cao, Zihan Zhang, Sabeur Aridhi, Stefano Pascarelli, Vedrana Vidulin, Qizhong Mao, Balint Z. Kacsoh, Patricia C. Babbitt, Giovanni Bosco, Farrokh Mehryary, Florian Boecker, Alfonso E. Romero, Angela D. Wilkins, Saso Dzeroski, Richard Bonneau, Hans Moen, Chengxin Zhang, Prajwal Bhat, Giuliano Grossi, Martti Tolvanen, Matteo Re, Meet Barot, Mohammad R. K. Mofrad, Predrag Radivojac, Stefano Di Carlo, Tatyana Goldberg, Branislava Gemovic, Suyang Dai, Pier Luigi Martelli, Giorgio Valentini, Maxat Kulmanov, Maria Jesus Martin, Claire O'Donovan, Dallas J. Larsen, Alexandre Renaux, Alan Medlar, Jeffrey M. Yunes, Erica Suh, Volkan Atalay, Vladimir Gligorijević, Fran Supek, Elaine Zosa, Wei-Cheng Tseng, Nafiz Hamid, Marco Mesiti, Tunca Doğan, Petri Törönen, Hafeez Ur Rehman, Jose Manuel Rodriguez, Alessandro Petrini, Sayoni Das, Burkhard Rost, Miguel Amezola, Mateo Torres, Jianlin Cheng, Daisuke Kihara, Liisa Holm, Marco Frasca, Steven E. Brenner, Stefano Toppo, Adrian M. Altenhoff, Chenguang Zhao, Daniel B. Roche, Alperen Dalkiran, Alex W. Crocker, Marco Notaro, Iddo Friedberg, Michal Linial, Julian Gough, Damiano Piovesan, Slobodan Vucetic, Natalie Thurlby, Olivier Lichtarge, Jari Björne, Jonas Reeb, Rabie Saidi, Yuxiang Jiang, Christophe Dessimoz, Jie Hou, Ronghui You, Tomislav Šmuc, Paolo Fontana, Michele Berselli, Jia-Ming Chang, Deborah A. Hogan, Larry Davis, Ehsaneddin Asgari, Shuwei Yao, Zheng Wang, Fabio Fabris, Michael L. Tress, Caleb Chandler, Christine A. Orengo, Rengul Cetin Atalay, Castrense Savojardo, Danielle A Brackenridge, Peter W. Rose, Yang Zhang, Dane Jo, Gage S. Black, Shanshan Zhang, Aashish Jain, Liam J. McGuffin, Timothy Bergquist, Peter L. Freddolino, Robert Hoehndorf, Rita Casadio, Da Chen Emily Koo, Mark N. Wass, Hai Fang, Casey S. Greene, Suwisa Kaewphan, Magdalena Antczak, Wen-Hung Liao, Enrico Lavezzo, Neven Sumonja, Ashton Omdahl, José M. Fernández, Ilya Novikov, Jonathan B. Dayton, Feng Zhang, Vladimir Perovic, Cen Wan, Jonathan G. Lees, Kai Hakala, Weidong Tian, Alex Warwick Vesztrocy, Domenico Cozzetto, Nevena Veljkovic, Yi-Wei Liu, Imane Boudellioua, Po-Han Chi, Kimberley A. Lewis, Seyed Ziaeddin Alborzi, Giuseppe Profiti, Alberto Paccanaro, Itamar Borukhov, Alfredo Benso, Indika Kahanda, Rebecca L. Hurto, Bilgisayar Mühendisliği, National Science Foundation (United States), Gordon and Betty Moore Foundation, United States of Department of Health & Human Services, Cystic Fibrosis Foundation, Consejo Nacional de Ciencia y Tecnología (México), Deutsche Forschungsgemeinschaft (Alemania), European Research Council, Ministerio de Ciencia e Innovación (España), Unión Europea, University of Turku (Finlandia), Finlands Akademi (Finlandia), National Natural Science Foundation of China, Nanjing Agricultural University. The Academy of Science. National Key Research & Development Program of China, Ministero dell Istruzione, dell Universita e della Ricerca (Italia), Shanghai Municipal Science and Technology Major Project, Biotechnology and Biological Sciences Research Council (Reino Unido), Extreme Science and Engineering Discovery Environment, Ministry of Education, Science and Technological Development (Serbia), Ministry of Science and Technology, Ministry for Education (Baviera) (Alemania), Yad Hanadiv, University of Milan (Italia), Swiss National Science Foundation, Unión Europea. European Cooperation in Science and Technology (COST), Plataforma ISCIII de Bioinformática (España), Scientific and Technological Research Council of Turkey, Ministry of Education (China), University of Padua (Italia), Mühendislik ve Doğa Bilimleri Fakültesi -- Bilgisayar Mühendisliği Bölümü, Rifaioğlu, Ahmet Süreyya, Zhou N., Jiang Y., Bergquist T.R., Lee A.J., Kacsoh B.Z., Crocker A.W., Lewis K.A., Georghiou G., Nguyen H.N., Hamid M.N., Davis L., Dogan T., Atalay V., Rifaioglu A.S., Dalklran A., Cetin Atalay R., Zhang C., Hurto R.L., Freddolino P.L., Zhang Y., Bhat P., Supek F., Fernandez J.M., Gemovic B., Perovic V.R., Davidovic R.S., Sumonja N., Veljkovic N., Asgari E., Mofrad M.R.K., Profiti G., Savojardo C., Martelli P.L., Casadio R., Boecker F., Schoof H., Kahanda I., Thurlby N., McHardy A.C., Renaux A., Saidi R., Gough J., Freitas A.A., Antczak M., Fabris F., Wass M.N., Hou J., Cheng J., Wang Z., Romero A.E., Paccanaro A., Yang H., Goldberg T., Zhao C., Holm L., Toronen P., Medlar A.J., Zosa E., Borukhov I., Novikov I., Wilkins A., Lichtarge O., Chi P.-H., Tseng W.-C., Linial M., Rose P.W., Dessimoz C., Vidulin V., Dzeroski S., Sillitoe I., Das S., Lees J.G., Jones D.T., Wan C., Cozzetto D., Fa R., Torres M., Warwick Vesztrocy A., Rodriguez J.M., Tress M.L., Frasca M., Notaro M., Grossi G., Petrini A., Re M., Valentini G., Mesiti M., Roche D.B., Reeb J., Ritchie D.W., Aridhi S., Alborzi S.Z., Devignes M.-D., Koo D.C.E., Bonneau R., Gligorijevic V., Barot M., Fang H., Toppo S., Lavezzo E., Falda M., Berselli M., Tosatto S.C.E., Carraro M., Piovesan D., Ur Rehman H., Mao Q., Zhang S., Vucetic S., Black G.S., Jo D., Suh E., Dayton J.B., Larsen D.J., Omdahl A.R., McGuffin L.J., Brackenridge D.A., Babbitt P.C., Yunes J.M., Fontana P., Zhang F., Zhu S., You R., Zhang Z., Dai S., Yao S., Tian W., Cao R., Chandler C., Amezola M., Johnson D., Chang J.-M., Liao W.-H., Liu Y.-W., Pascarelli S., Frank Y., Hoehndorf R., Kulmanov M., Boudellioua I., Politano G., Di Carlo S., Benso A., Hakala K., Ginter F., Mehryary F., Kaewphan S., Bjorne J., Moen H., Tolvanen M.E.E., Salakoski T., Kihara D., Jain A., Smuc T., Altenhoff A., Ben-Hur A., Rost B., Brenner S.E., Orengo C.A., Jeffery C.J., Bosco G., Hogan D.A., Martin M.J., O'Donovan C., Mooney S.D., Greene C.S., Radivojac P., Friedberg I., Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Sciences and Bioengineering Sciences, Faculty of Engineering, Computational genomics, Institute of Biotechnology, Bioinformatics, Genetics, Helsinki Institute of Life Science HiLIFE, Discovery Research Group/Prof. Hannu Toivonen, Iowa State University (ISU), European Bioinformatics Institute, École Polytechnique de Montréal (EPM), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], University of Bologna, Max Planck Institute for Plant Breeding Research (MPIPZ), European Virus Bioinformatics Center [Jena], Université libre de Bruxelles (ULB), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Department of Computer Science, University of Bristol [Bristol], Department of Computer Science [Columbia], University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Yale School of Public Health (YSPH), Departamento de Geometría y Topología, Universidad de Granada (UGR), Tumor Biology Center, Centre for Nephrology [London, UK], University College of London [London] (UCL), Baylor College of Medicine (BCM), Baylor University, Department of Knowledge Technologies, Structural and Molecular Biology Department, University College London, Queen Mary University of London (QMUL), Spanish National Cancer Research Center (CNIO), Dipartimento di Informatica, Università degli Studi di Milano [Milano] (UNIMI), Dipartimento di Scienze dell'Informazione [Milano], United States Naval Academy, Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Medicine, Universita degli Studi di Padova, Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Physics Department, National Tsing Hua University [Hsinchu] (NTHU), Dipartimento di Automatica e Informatica [Torino] (DAUIN), Politecnico di Torino = Polytechnic of Turin (Polito), University of Turku, Bioinformatics Laboratory, University of Turku-Turku Center for Computer Science, Toyota Technological Institute at Chicago [Chicago] (TTIC), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Computer Science [Colorado State University], Colorado State University [Fort Collins] (CSU), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany., University of Bologna/Università di Bologna, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Università degli Studi di Milano = University of Milan (UNIMI), Università degli Studi di Padova = University of Padua (Unipd), and Université de Lausanne = University of Lausanne (UNIL)
Subjects: Library, Male, Identification, Candida-albicans, Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, Procedures, Genome, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 0302 clinical medicine, Candida albicans, Molecular genetics, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, Biological ontology, Settore BIO/11 - BIOLOGIA MOLECOLARE, 0303 health sciences, 318 Medical biotechnology, Biotechnology & applied microbiology, Ontology, Expectation, Genetics & heredity, Plant leaf, ddc, 3. Good health, Drosophila melanogaster, Human experiment, Fungal genome, Pseudomonas aeruginosa, Female, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Genome, Fungal, BIOINFORMATICS, Long-Term memory, Locomotion, Human, Adult, Memory, Long-Term, lcsh:QH426-470, Bioinformatics, Long term memory, Generation, Bacterial genome, Computational biology, Biology, Article, 03 medical and health sciences, Annotation, Big data, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Pseudomonas, Genetics, Animals, Humans, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Animal, Research, Experimental data, Molecular Sequence Annotation, Cell Biology, Nonhuman, Human genetics, lcsh:Genetics, lcsh:Biology (General), Biofilms, Proteins | Genes | Protein functions, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Function (biology), Genome, Bacterial
Abstract: Tosatto, Silvio/0000-0003-4525-7793; Zhang, Feng/0000-0003-3447-897X; Gonzalez, Jose Maria Fernandez/0000-0002-4806-5140; Devignes, Marie-Dominique/0000-0002-0399-8713; Wass, Mark/0000-0001-5428-6479; Falda, Marco/0000-0003-2642-519X; Thurlby, Natalie/0000-0002-1007-0286; Zosa, Elaine/0000-0003-2482-0663; Dessimoz, Christophe/0000-0002-2170-853X; Yunes, Jeffrey/0000-0003-1869-3231; Hamid, Md Nafiz/0000-0001-8681-6526; Hoehndorf, Robert/0000-0001-8149-5890; Dogan, Tunca/0000-0002-1298-9763; NOTARO, MARCO/0000-0003-4309-2200; Cozzetto, Domenico/0000-0001-6752-5432; Lewis, Kimberley/0000-0003-3010-8453; Roche, Daniel/0000-0002-9204-1840; Martin, Maria-Jesus/0000-0001-5454-2815; Tress, Michael/0000-0001-9046-6370; Tolvanen, Martti/0000-0003-3434-7646; Cheng, Jianlin/0000-0003-0305-2853; Rose, Peter/0000-0001-9981-9750; Renaux, Alexandre/0000-0002-4339-2791; Kacsoh, Balint/0000-0001-9171-0611; O'Donovan, Claire/0000-0001-8051-7429; Kulmanov, Maxat/0000-0003-1710-1820; Friedberg, Iddo/0000-0002-1789-8000; Zhou, Naihui/0000-0001-6268-6149, WOS: 000498615000001, PubMed ID: 31744546, Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens., National Science FoundationNational Science Foundation (NSF) [DBI1564756, DBI-1458359, DBI-1458390, DMS1614777, CMMI1825941, NSF 1458390]; Gordon and Betty Moore FoundationGordon and Betty Moore Foundation [GBMF 4552]; National Institutes of Health NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [P20 GM113132]; Cystic Fibrosis Foundation [CFRDP STANTO19R0]; BBSRCBiotechnology and Biological Sciences Research Council (BBSRC) [BB/K004131/1, BB/F00964X/1, BB/M025047/1, BB/M015009/1]; Consejo Nacional de Ciencia y Tecnologia Paraguay (CONACyT)Consejo Nacional de Ciencia y Tecnologia (CONACyT) [14-INV-088, PINV15-315]; NSFNational Science Foundation (NSF) [1660648, DBI 1759934, IIS1763246, DBI-1458477, 0965768, DMR-1420073, DBI-1458443]; NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01GM093123, DP1MH110234, UL1 TR002319, U24 TR002306]; Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy-EXC 2155 "RESIST"German Research Foundation (DFG) [39087428]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01GM123055, R01GM60595, R15GM120650, GM083107, GM116960, AI134678, NIH R35-GM128637, R00-GM097033]; ERCEuropean Research Council (ERC) [StG 757700]; Spanish Ministry of Science, Innovation and Universities [BFU2017-89833-P]; Severo Ochoa award; Centre of Excellence project "BioProspecting of Adriatic Sea"; Croatian Government; European Regional Development FundEuropean Union (EU) [KK.01.1.1.01.0002]; ATT Tieto kayttoon grant; Academy of FinlandAcademy of Finland; University of Turku; CSC-IT Center for Science Ltd.; University of Miami; National Cancer Institute of the National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [U01CA198942]; Helsinki Institute for Life Sciences; Academy of FinlandAcademy of Finland [292589]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [31671367, 31471245, 91631301, 61872094, 61572139]; National Key Research and Development Program of China [2016YFC1000505, 2017YFC0908402]; Italian Ministry of Education, University and Research (MIUR) PRIN 2017 projectMinistry of Education, Universities and Research (MIUR) [2017483NH8]; Shanghai Municipal Science and Technology Major Project [2017SHZDZX01, 2018SHZDZX01]; UK Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/N019431/1, BB/L020505/1, BB/L002817/1]; Elsevier; Extreme Science and Engineering Discovery Environment (XSEDE) award [MCB160101, MCB160124]; Ministry of Education, Science and Technological Development of the Republic of Serbia [173001]; Taiwan Ministry of Science and Technology [106-2221-E-004-011-MY2]; Montana State University; Bavarian Ministry for Education; Simons Foundation; NIH NINDSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [1R21NS103831-01]; University of Illinois at Chicago (UIC) Cancer Center award; UIC College of Liberal Arts and Sciences Faculty Award; UIC International Development Award; Yad Hanadiv [9660/2019]; National Institute of General Medical Science of the National Institute of Health [GM066099, GM079656]; Research Supporting Plan (PSR) of University of Milan [PSR2018-DIP-010-MFRAS]; Swiss National Science FoundationSwiss National Science Foundation (SNSF) [150654]; EMBL-European Bioinformatics Institute core funds; CAFA BBSRC [BB/N004876/1]; European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grantEuropean Union (EU) [778247]; COST ActionEuropean Cooperation in Science and Technology (COST) [BM1405]; NIH/NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01 GM071749]; National Human Genome Research Institute of the National of Health [U41 HG007234]; INB Grant (ISCIII-SGEFI/ERDF) [PT17/0009/0001]; TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [EEEAG-116E930]; KanSil [2016K121540]; Universita degli Studi di Milano; 111 ProjectMinistry of Education, China - 111 Project [B18015]; key project of Shanghai Science Technology [16JC1420402]; ZJLab; project Ribes Network POR-FESR 3S4H [TOPP-ALFREVE18-01]; PRID/SID of University of Padova [TOPP-SID19-01]; NIGMSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R15GM120650]; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/3454-01-01, URF/1/3790-01-01]; "the Human Project from Mind, Brain and Learning" of the NCCU Higher Education Sprout Project by the Taiwan Ministry of Education; National Center for High-performance ComputingIstanbul Technical University, The work of IF was funded, in part, by the National Science Foundation award DBI-1458359. The work of CSG and AJL was funded, in part, by the National Science Foundation award DBI-1458390 and GBMF 4552 from the Gordon and Betty Moore Foundation. The work of DAH and KAL was funded, in part, by the National Science Foundation award DBI-1458390, National Institutes of Health NIGMS P20 GM113132, and the Cystic Fibrosis Foundation CFRDP STANTO19R0. The work of AP, HY, AR, and MT was funded by BBSRC grants BB/K004131/1, BB/F00964X/1 and BB/M025047/1, Consejo Nacional de Ciencia y Tecnologia Paraguay (CONACyT) grants 14-INV-088 and PINV15-315, and NSF Advances in BioInformatics grant 1660648. The work of JC was partially supported by an NIH grant (R01GM093123) and two NSF grants (DBI 1759934 and IIS1763246). ACM acknowledges the support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy -EXC 2155 "RESIST" - Project ID 39087428. DK acknowledges the support from the National Institutes of Health (R01GM123055) and the National Science Foundation (DMS1614777, CMMI1825941). PB acknowledges the support from the National Institutes of Health (R01GM60595). GB and BZK acknowledge the support from the National Science Foundation (NSF 1458390) and NIH DP1MH110234. FS was funded by the ERC StG 757700 "HYPER-INSIGHT" and by the Spanish Ministry of Science, Innovation and Universities grant BFU2017-89833-P. FS further acknowledges the funding from the Severo Ochoa award to the IRB Barcelona. TS was funded by the Centre of Excellence project "BioProspecting of Adriatic Sea", co-financed by the Croatian Government and the European Regional Development Fund (KK.01.1.1.01.0002). The work of SK was funded by ATT Tieto kayttoon grant and Academy of Finland. JB and HM acknowledge the support of the University of Turku, the Academy of Finland and CSC -IT Center for Science Ltd. TB and SM were funded by the NIH awards UL1 TR002319 and U24 TR002306. The work of CZ and ZW was funded by the National Institutes of Health R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of PWR was supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. PR acknowledges NSF grant DBI-1458477. PT acknowledges the support from Helsinki Institute for Life Sciences. The work of AJM was funded by the Academy of Finland (No. 292589). The work of FZ and WT was funded by the National Natural Science Foundation of China (31671367, 31471245, 91631301) and the National Key Research and Development Program of China (2016YFC1000505, 2017YFC0908402]. CS acknowledges the support by the Italian Ministry of Education, University and Research (MIUR) PRIN 2017 project 2017483NH8. SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). PLF and RLH were supported by the National Institutes of Health NIH R35-GM128637 and R00-GM097033. JG, DTJ, CW, DC, and RF were supported by the UK Biotechnology and Biological Sciences Research Council (BB/N019431/1, BB/L020505/1, and BB/L002817/1) and Elsevier. The work of YZ and CZ was funded in part by the National Institutes of Health award GM083107, GM116960, and AI134678; the National Science Foundation award DBI1564756; and the Extreme Science and Engineering Discovery Environment (XSEDE) award MCB160101 and MCB160124.; The work of BG, VP, RD, NS, and NV was funded by the Ministry of Education, Science and Technological Development of the Republic of Serbia, Project No. 173001. The work of YWL, WHL, and JMC was funded by the Taiwan Ministry of Science and Technology (106-2221-E-004-011-MY2). YWL, WHL, and JMC further acknowledge the support from "the Human Project from Mind, Brain and Learning" of the NCCU Higher Education Sprout Project by the Taiwan Ministry of Education and the National Center for High-performance Computing for computer time and facilities. The work of IK and AB was funded by Montana State University and NSF Advances in Biological Informatics program through grant number 0965768. BR, TG, and JR are supported by the Bavarian Ministry for Education through funding to the TUM. The work of RB, VG, MB, and DCEK was supported by the Simons Foundation, NIH NINDS grant number 1R21NS103831-01 and NSF award number DMR-1420073. CJJ acknowledges the funding from a University of Illinois at Chicago (UIC) Cancer Center award, a UIC College of Liberal Arts and Sciences Faculty Award, and a UIC International Development Award. The work of ML was funded by Yad Hanadiv (grant number 9660/2019). The work of OL and IN was funded by the National Institute of General Medical Science of the National Institute of Health through GM066099 and GM079656. Research Supporting Plan (PSR) of University of Milan number PSR2018-DIP-010-MFRAS. AWV acknowledges the funding from the BBSRC (CASE studentship BB/M015009/1). CD acknowledges the support from the Swiss National Science Foundation (150654). CO and MJM are supported by the EMBL-European Bioinformatics Institute core funds and the CAFA BBSRC BB/N004876/1. GG is supported by CAFA BBSRC BB/N004876/1. SCET acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 778247 (IDPfun) and from COST Action BM1405 (NGP-net). SEB was supported by NIH/NIGMS grant R01 GM071749. The work of MLT, JMR, and JMF was supported by the National Human Genome Research Institute of the National of Health, grant numbers U41 HG007234. The work of JMF and JMR was also supported by INB Grant (PT17/0009/0001 - ISCIII-SGEFI/ERDF). VA acknowledges the funding from TUBITAK EEEAG-116E930. RCA acknowledges the funding from KanSil 2016K121540. GV acknowledges the funding from Universita degli Studi di Milano - Project "Discovering Patterns in Multi-Dimensional Data" and Project "Machine Learning and Big Data Analysis for Bioinformatics". SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). RY and SY are supported by the 111 Project (NO. B18015), the key project of Shanghai Science & Technology (No. 16JC1420402), Shanghai Municipal Science and Technology Major Project (No. 2018SHZDZX01), and ZJLab. ST was supported by project Ribes Network POR-FESR 3S4H (No. TOPP-ALFREVE18-01) and PRID/SID of University of Padova (No. TOPP-SID19-01). CZ and ZW were supported by the NIGMS grant R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of MK and RH was supported by the funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01 and URF/1/3790-01-01. The work of SDM is funded, in part, by NSF award DBI-1458443.
Published: 2019

55. Interferon tau-dependent and independent effects of the bovine conceptus on the endometrial transcriptome

Author: Claudia Passaro, Thomas E. Spencer, Gilles Charpigny, José María Sánchez, Daniel J Mathew, Susanta K. Behura, Patrick Lonergan, UCD School of Agriculture and Food Science, Division of Animal and Nutritional Sciences, West Virginia University, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Division of Animal Sciences, University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: 0301 basic medicine, Superovulation, Pregnancy Proteins, Biology, Endometrium, Gonadotropin-Releasing Hormone, Transcriptome, Andrology, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, In vivo, medicine, Animals, Conceptus, endometrium, Receptor, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Insemination, Artificial, Progesterone, reproductive and urinary physiology, Estrous cycle, Regulation of gene expression, 030219 obstetrics & reproductive medicine, uterus, urogenital system, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Cell Biology, General Medicine, Interferon tau, 030104 developmental biology, medicine.anatomical_structure, Gene Expression Regulation, Reproductive Medicine, conceptus, Interferon Type I, embryonic structures, Pregnancy, Animal, IFNt, Cattle, Female, bovine reproduction, Estrus Synchronization, Research Article
Abstract: This study investigated bovine conceptus-induced modifications to the endometrial transcriptome related to effects of interferon tau (IFNT), conceptus origin (in vivo vs. in vitro), and conceptus sex. In vitro (IVF) or in vivo (superovulation and artificial insemination, AI) produced blastocysts were transferred into recipient heifers on day 7 of the estrous cycle. On day 15, IVF- or AI-derived conceptuses were obtained by uterine flushing and individually placed on endometrial explants in media for 6 h. Explants were also cultured with media alone as a control or media containing 100 ng/mL IFNT. Total explant RNA was analyzed by RNA-Seq. Incubation of endometrium with IFNT or IVF- or AI-derived conceptuses changed (P ≤ 0.001) expression of 491, 498, and 576 transcripts, respectively, compared to the control. Further, 369 differentially expressed genes (DEGs) were common between explants exposed to IFNT or a conceptus. A total of 240 DEGs were uniquely altered by conceptuses (IVF- and AI-derived) but not IFNT. Of these transcripts, 46 were shared between the IVF and AI groups, while 61 and 133 were specific to IVF and AI conceptuses, respectively. Five genes [melanophilin (MLPH), prominin-2 (PROM2), myeloid associated differentiation marker (MYADM), vomeronasal 1 receptor 4 like (VN1R4L) and 5-hydroxytryptamine receptor 1A (HTR1A)] were more abundant in endometrium exposed to female compared to male conceptuses (P < 0.001). A single gene [ADP-ribosylation factor like GTPase 4C (ARL4C)] was more abundant in response to male conceptuses (P < 0.001) than female conceptuses. These data support the hypothesis that conceptus regulation of gene expression in the endometrium is complex and involves factors other than IFNT that may have a biological role in pregnancy establishment.Summary SentenceElongating bovine conceptuses modify the adjacent endometrial transcriptome in a manner dependent and independent of interferon tau and related to conceptus origin and sex.
Published: 2019

56. Redox transients of P680 associated with the incremental chlorophyll‐ a fluorescence yield rises elicited by a series of saturating flashes in diuron‐treated photosystem II core complex of Thermosynechococcus vulcanus

Author: Gábor Sipka, Qingjun Zhu, Petar H. Lambrev, László Kovács, Pavel Müller, Melinda Magyar, Guangye Han, Yanan Xiao, Győző Garab, Jian Ren Shen, Klaus Brettel, Biological Research Centre [Budapest] (BRC), Hungarian Academy of Sciences (MTA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS), Okayama University, Ostravská univerzita / University of Ostrava, Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Photocatalyse et Biohydrogène (LPB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Dept Biol, University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: 0106 biological sciences, Pheophytin, Photosystem II, Physiology, [SDV]Life Sciences [q-bio], p-680, Kinetics, pheophytin, Analytical chemistry, Primary charge separation, Plant Science, Cyanobacteria, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, absorbency changes, reduction kinetics, Ultrafast laser spectroscopy, recombination pathways, Genetics, primary-charge separation, 030304 developmental biology, particles, 0303 health sciences, Chemistry, Chlorophyll A, absorption-spectroscopy, Photosystem II Protein Complex, primary electron-donor, excitation, P680, Cell Biology, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Fluorescence, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Yield (chemistry), Oxidation-Reduction, 010606 plant biology & botany
Abstract: International audience; Recent chlorophyll-a fluorescence yield measurements, using single-turnover saturating flashes (STSFs), have revealed the involvement of a rate-limiting step in the reactions following the charge separation induced by the first flash (Magyar et al. 2018). As also shown here, in diuron-inhibited PSII core complexes isolated from Thermosynechococcus vulcanus the fluorescence maximum could only be reached by a train of STSFs. In order to elucidate the origin of the fluorescence yield increments in STSF series, we performed transient absorption measurements at 819 nm, reflecting the photooxidation and re-reduction kinetics of the primary electron donor P680. Upon single flash excitation of the dark-adapted sample, the decay kinetics could be described with lifetimes of 17 ns (~50%) and 167 ns (~30%), and a longer-lived component (~20%). This kinetics are attributed to re-reduction of P680•+ by the donor side of PSII. In contrast, upon second-flash (with Δt between 5 μs and 100 ms) or repetitive excitation, the 819 nm absorption changes decayed with lifetimes of about 2 ns (~60%) and 10 ns (~30%), attributed to recombination of the primary radical pair P680•+ Pheo•- , and a small longer-lived component (~10%). These data confirm that only the first STSF is capable of generating stable charge separation - leading to the reduction of QA ; and thus, the fluorescence yield increments elicited by the consecutive flashes must have a different physical origin. Our double-flash experiments indicate that the rate-limiting steps, detected by chlorophyll-a fluorescence, are not correlated with the turnover of P680. This article is protected by copyright. All rights reserved.
Published: 2019

57. Synthesis and characterization of B-substitutednanoporous carbons for hydrogen adsorption

Author: Walczak, Katarzyna, Journet-Gautier, Catherine, Llewellin, P, Neisius, Thomas, Pfeifer, P, Kuchta, B, Firlej, Lucyna, Aigle, L2c, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; Here we explored the possibility to prepare boron-substituted nanoporous carbons, cheap, light and save material that wassupposed [2,3] to reversibly store hydrogen by physisorption at room temperatures and moderated pressure (< 120 bar). Weshowed that electric arc discharge between graphite electrodes may be optimized to produce graphitized structures with avariety of graphene fragment sizes, forms, and interconnections between them. It also allows to introduce boron heteroatominto graphite-like structure. The as-synthetized material shows the hydrogen binding energy twice as high as unsubstitutedcarbons, but requires post-treatment (activation) as the its surface is low (~200 m2/g).
Published: 2019

58. Influence of agroforestry plant species on the infiltration of S-Metolachlor in buffer soils

Author: Chung-Ho Lin, Jeanne Dollinger, Ranjith P. Udawatta, Valérie Pot, Shibu Jose, Pierre Benoit, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), The Center for Agroforestry, Anheuser Busch Natural Resources Bldg, University of Missouri [Columbia], University of Missouri System-University of Missouri System, The School of Natural Resources, Anheuser Busch Natural Resources Bldg, and University of Missouri [Columbia] (Mizzou)
Subjects: [SDV]Life Sciences [q-bio], 0207 environmental engineering, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, chemistry.chemical_compound, Soil, Hydraulic conductivity, Acetamides, Environmental Chemistry, Soil Pollutants, Agroforestry, 020701 environmental engineering, 0105 earth and related environmental sciences, Water Science and Technology, 2. Zero hunger, Rhizosphere, Herbicides, food and beverages, 15. Life on land, Non-point source pollution, 6. Clean water, Infiltration (hydrology), chemistry, Plant Soil, Soil water, Leaching, DNS root zone, Environmental science, Herbicide, Microcosm, Surface runoff, Metolachlor
Abstract: Agroforestry practices have been acknowledged for reducing pesticide losses while maintaining land productivity. Pesticide removal from overland flow results from great infiltration capacities of the buffer soils. This can in turn threaten the quality of groundwater in case of poor pesticide sorption and degradation in the root-influenced zone. These mechanisms and their balance are likely to be influenced by plant species. However, little is known about the role of agroforestry species in the infiltration of herbicides. The aim of this study was thereby to evaluate how popular agroforestry species modulate the infiltration of water and of a widely used herbicide. We established large buffer microcosms by planting Brome grass, Black walnut, Pin oak and Poplar trees in repacked soil columns. After a growth season of 4 months, we performed ponded infiltration experiments with bromide and S-Metolachlor. We used then the HYDRUS 1D model to compare the hydrodynamic properties and S-Metolachlor transport patterns between the microcosms. In addition, we compared the sorption properties of the rhizosphere and bulk soils. We found that the tree species increased the sorption of S-Metolachlor in soil with Kd being 3 times greater than in the un-vegetated and Brome grass microcosms. Poplar trees increased the hydraulic conductivity (Ksat) compared to the control and was associated to a low retardation of S-metolachlor, which increases the risk of groundwater contamination. With slightly reduced Ksat and retardation factor in the root zone, 1.6 to 1.8 times greater than in the control treatment, Black walnut appears as an optimal species for mitigating S-Metolachlor. The Brome grass and oak microcosms had the lowest Ksat of all treatments and S-Metolachlor retardation factors were equal and slightly increased compared to the control, respectively. These results show that agroforestry buffer's efficiency can be optimized by selecting appropriate species.
Published: 2018

59. Textural, thermal, and topographic constraints on lava flow system structure: the December 2010 eruption of Piton de la Fournaise

Author: Arianna Soldati, Andrew J. L. Harris, Lucia Gurioli, Nicolas Villeneuve, Francisco Gomez, M. Rhéty, Alan G. Whittington, Department of Geological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Laboratoire Magmas et Volcans (LMV), Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Observatoire Volcanologique du Piton de la Fournaise (OVPF), Institut de Physique du Globe de Paris, Laboratoire GéoSciences Réunion (LGSR), Université de La Réunion (UR)-Institut de Physique du Globe de Paris, ANR-10-LABX-0006,CLERVOLC,Clermont-Ferrand centre for research on volcanism(2010), ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016), Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut de Physique du Globe de Paris (IPG Paris), and Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)
Subjects: 010504 meteorology & atmospheric sciences, Lava, Stable channel, Flow (psychology), Front (oceanography), Channelized, Crystallization, 010502 geochemistry & geophysics, 01 natural sciences, Open-channel flow, Dispersed flow, Braided flow, Geochemistry and Petrology, Underlying slope, Confluence, [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, lava flow, Sedimentology, Petrology, Cooling, Channel network, Geology, 0105 earth and related environmental sciences, Communication channel
Abstract: co-auteur étranger; International audience; In this study, we examine the channel-fed ‘a‘ā lava flow system that was emplaced during a very short (less than 15 h long) eruptionat Piton de la Fournaise (La Réunion) in December 2010. The system had four branches, the longest of which was 1100 m long.Three brancheswere emplaced over a smooth-surfaced pāhoehoe flow fieldwith a vertical relief of 1–2mand did not undergo burialby subsequent events. The fourth branch erupted from the same vent as the 1957 eruption and re-used the pre-existing channels ofthat eruption. In the proximal–medial sections of the three systems that were unconfined, we identified channelized flow sectionsthat were characterized by the presence of either a single channel or multiple braided channels. These fed short (30–260 m long)zones of dispersed flow in the distal sections. We subsequently investigated the role of lava rheology (as controlled by downflowvariations in crystal and bubble content) and pre-existing topography in triggering the transitions between single-channel andbraided channel flow sections. Crystal content was 10 to 70 vol% and vesicle content was 18 to 55 vol%; cooling rates overdistance (derived from glass chemistry) were 11 °C/km to 27 °C/km. However, downflow textural and thermal evolution appearedto neither affect, nor be affected by, whether the channel was single or braided. Instead, the channel network architecture could berelated to even modest underlying slope variations. Here, a slope increase resulted in channel confluence, and a slope decreaseresulted in channel bifurcation. This process was reversible, in that downflow slope variation could drive the channel networkarchitecture to switch back and forth between a single channel and multiple braided channels several times along its length.Dispersed flow is always present immediately behind the flow front, irrespective of underlying topography. Three previous studiesof basaltic lava flows found that steeper slopes favored braided channels, the opposite of what was observed here.We suggest thatthe underlying substrate and lava type may exert a control on this behavior, but further studies remain necessary.
Published: 2018

60. Structure‐Property Relationships in Tricyanoferrate(III) Building Blocks and Trinuclear Cyanide‐Bridged Complexes

Author: Stephen M. Holmes, Uma P. Malik, Hung Nguyen, Benjamin Quiggins, Alexey E. Kovalev, Stephen Hill, Rodolphe Clérac, Christopher C. Beedle, Benjamin J. Bythell, Yuan-Zhu Zhang, University of Missouri [St. Louis], University of Missouri System, National High Magnetic Field Laboratory, Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Florida State University [Tallahassee] (FSU), Center for Nanoscience, and University of Missouri System-University of Missouri System
Subjects: Cyanides, 010405 organic chemistry, Stereochemistry, Chemistry, Heisenberg model, Cyanide, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, law.invention, Ion, Clusters, Inorganic Chemistry, Magnetic anisotropy, Crystallography, chemistry.chemical_compound, Magnetization, Ferromagnetism, Ferromagnetic compounds, law, Single-molecule magnets, Pyrazolylborate, Electron paramagnetic resonance, Spin (physics)
Abstract: The preparation, structures, and magnetic properties of two tricyanoferrates, [NEt4]2[(Tp*Me)FeII(CN)3]·MeCN (1) and [NEt4][(Tp*Me)FeIII(CN)3]·H2O (2), and three trinuclear derivatives, {[(Tp*Me)FeIII(CN)3]2[NiII(L)2]}·n(solvent) (L = bpy, 3; tren, 4; DETA, 5) are described. Magnetic measurements show that 2 is an S = 1/2 complex [g = 2.65(1)], while 3–5 display ST = 2 spin ground states, owing to cyanide-mediated ferromagnetic exchange between FeIIILS (S = 1/2) and NiII (S = 1) ions. The χT vs. T data for 3–5 were modelled using an isotropic Heisenberg model and give J/kB and gavg values of +11.1(1) K and 2.48(1) for 3, 9.1(1) K and 2.6(1) for 4, and +11.2(1) K and 2.41(5) for 5 (with zJ′ = –0.28 K). High-field/frequency EPR data indicates significant g-anisotropy in 2 (gz = 3.6, gy = 2.2, gx = 2.0) and [NEt4][(Tp*)FeIII(CN)3]·H2O (6) (gz = 3.5, gy = 2.0, gx = 1.3), while 5 shows D = –2.09 cm–1, E = 0.08 cm–1, and B40 = –2.3 × 10–3 cm–1 with gz = 2.4 and gx = gy = 1.95. Despite significant magnetic anisotropy in 3–5, frequency-dependent behavior is only seen for 5 above 1.8 K, suggesting that rapid quantum tunnelling of the magnetization is operative.
Published: 2016

61. A global spectral library to characterize the world's soil

Author: David J. Brown, Carolyn Hedley, Cécile Gomez, Bo Stenberg, Suk Young Hong, P. Sanborn, H.J.M. Morrás, R. A. Viscarra Rossel, Youssef Fouad, Martial Bernoux, Adrian Chappell, Pierre Roudier, Harm Bartholomeus, César Guerrero, Viacheslav I. Adamchuk, Valérie Genot, Zhou Shi, Bernard Barthès, Leigh A. Winowiecki, Eyal Ben-Dor, L. Brodský, Kenneth A. Sudduth, Christian Walter, Anita D. Bayer, Wenjun Ji, Hamouda Aichi, José Alexandre Melo Demattê, Sabine Grunwald, Leonardo Ramirez-Lopez, Barry G. Rawlins, Andreas Gubler, E.M. Rufasto Campos, Changwen Du, Keith D. Shepherd, V.M. Sellitto, Kristin Böttcher, Antoine Stevens, Marco Nocita, Thorsten Behrens, Maria Knadel, CSIRO Land and Water, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Tübingen, Tel Aviv University [Tel Aviv], Washington State University (WSU), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), World Agroforestry Center [CGIAR, Mali] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Zhejiang University, Swedish University of Agricultural Sciences (SLU), Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain = Catholic University of Louvain (UCL), McGill University = Université McGill [Montréal, Canada], SPADD Laboratory, Higher School of Agriculture of Mograne, Université de Tunis Carthage, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Karlsruhe Institute of Technology (KIT), JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC), Finnish Environment Institute (SYKE), Czech University of Life Sciences Prague (CZU), State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Sol Agro et hydrosystème Spatialisation (SAS), 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), Université de Liège, Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Florida [Gainesville] (UF), Agroscope FAL Reckenholz (AGROSCOPE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universidad Miguel Hernández [Elche] (UMH), Manaaki Whenua – Landcare Research [Lincoln], Aarhus University [Aarhus], INTA Castelar CIRN, Instituto Nacional de Tecnología Agropecuaria (INTA), BÜCHI Labortechnik AG, Partenaires INRAE, Universidad Nacional Pedro Ruiz Gallo, University of Northern British Columbia [Prince George] (UNBC), University of Molise [Campobasso] (UNIMOL), University of Molise, USDA-ARS Cropping Systems and Water Quality Research Unit (USDA), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, British Geological Survey (BGS), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), National Institute of Agricultural Sciences, Remote Sensing and GIS Laboratory, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), CSIRO - Land & Water National Research Flagship, Tissu Osseux et Contraintes Mecaniques (LBTO), Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universidad de Sevilla, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Tel Aviv University (TAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Università degli Studi del Molise = University of Molise (UNIMOL)
Subjects: Vis–NIR spectroscopy, 010504 meteorology & atmospheric sciences, Earth and Planetary Sciences(all), Soil Science, Soil science, Land cover, Silt, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Global soil dataset, Wavelets, 01 natural sciences, Ecosystem services, Laboratory of Geo-information Science and Remote Sensing, Machine learning, Cation-exchange capacity, machine teaming, Laboratorium voor Geo-informatiekunde en Remote Sensing, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Agricultural Science, 0105 earth and related environmental sciences, 2. Zero hunger, Soil vis-NIR spectra, Food security, business.industry, Scale (chemistry), Environmental resource management, Vis-NIR spectroscopy, Soil vis–NIR spectra, 04 agricultural and veterinary sciences, 15. Life on land, PE&RC, Soil spectral library, Multivariate statistics, Environmental Sciences related to Agriculture and Land-use, 13. Climate action, Greenhouse gas, Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, General Earth and Planetary Sciences, Environmental science, business
Abstract: Soil provides ecosystemservices, supports human health and habitation, stores carbon and regulatesemissions ofgreenhouse gases. Unprecedented pressures on soil from degradation and urbanization are threatening agroecologicalbalances and food security. It is important that we learn more about soil to sustainably manage andpreserve it for future generations. To this end, we developed and analyzed a global soil visible–near infrared(vis–NIR) spectral library. It is currently the largest and most diverse database of its kind. We show that the informationencoded in the spectra can describe soil composition and be associated to land cover and its global geographic distribution, which acts as a surrogate for global climate variability. We also show the usefulness ofthe global spectra for predicting soil attributes such as soil organic and inorganic carbon, clay, silt, sand andiron contents, cation exchange capacity, and pH. Usingwavelets to treat the spectra, whichwere recorded in differentlaboratories using different spectrometers and methods, helped to improve the spectroscopic modelling.We found that modelling a diverse set of spectra with a machine learning algorithm can find the local relationshipsin the data to produce accurate predictions of soil properties. The spectroscopic models that we derivedare parsimonious and robust, and using them we derived a harmonized global soil attribute dataset, whichmight serve to facilitate research on soil at the global scale. This spectroscopic approach should help to dealwith the shortage of data on soil to better understand it and to meet the growing demand for information to assessandmonitor soil at scales ranging fromregional to global.New contributions to the library are encouraged sothat this work and our collaboration might progress to develop a dynamic and easily updatable database withbetter global coverage. We hope that this work will reinvigorate our community's discussion towards larger,more coordinated collaborations. We also hope that use of the database will deepen our understanding of soilso that we might sustainably manage it and extend the research outcomes of the soil, earth and environmentalsciences towards applications that we have not yet dreamed of.
Published: 2016

62. Synthesis and characterization of B-substituted nanoporous carbons with high energy of hydrogen adsorption.'

Author: Katarzyna Walczak, Coulet, M. V., Thomas Neisius, Catherine Journet, Llewellin, P., Gillespie, A., Pfeifer, P., Kuchta, B., Lucyna Firlej, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des Matériaux, de Microélectronique et des Nanosciences de Provence (IM2NP), Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; The systematic usage of fossil fuels and the emission of their combustion products (mostly CO2) in the air have already impacted global climate. Therefore, new technological solutions to drug the global energy economy towards cleaner and renewable fuels, in particular for mobile applications, are urgently needed. In particular the efficient storage of hydrogen, a clean energy vector, requires to develop an adequate sorbent operating at ambient temperature and moderated pressures, with simultaneously optimized specific surface and hydrogen binding energy. In this project we explore the potential effectiveness of arc-discharge procedure to synthesize carbon-based nanoporous sorbents with characteristics fulfilling the requirements of vehicular applications. We show that by adjusting the synthesis parameters is possible to prepare numerous graphene-based structures of different forms, sizes, and interconnections between them. The arc-discharge technique provides also a relatively easy way to incorporate heteroatoms (like boron or nitrogen) into pure carbon structures. The as-synthesized boron-substituted carbon nanostructures are characterized in term of texture (using nitrogen adsorption and spectroscopic measurements) and homogeneity of boron (using energy filtered transmission electron microscopy). The calorimetric study at different temperatures were performed to quantify the material’s capacity to adsorb hydrogen.The obtained results are promising. The energy of hydrogen adsorption in our samples is the highest ever observed experimentally in carbon-based sorbents. However, the specific surface of as prepared samples is low. Therefore, the thermal and chemical activation procedure have been applied to increase the surface accessible for adsorption and micropore volume, and in consequence, the samples’ capacity to store hydrogen.
Published: 2018

63. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment

Author: Lensink, Marc F., Brysbaert, Guillaume, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Gerguri, Tereza, Bates, Paul A., Laine, Elodie, Carbone, Alessandra, Grudinin, Sergei, Kong, Ren, Liu, Ran-Ran, Xu, Xi-Ming, Shi, Hang, Chang, Shan, Eisenstein, Miriam, Karczynska, Agnieszka, Czaplewski, Cezary, Lubecka, Emilia, Lipska, Agnieszka, Krupa, Paweł, Mozolewska, Magdalena, Golon, Łukasz, Samsonov, Sergey, Liwo, Adam, Crivelli, Silvia, Pagès, Guillaume, Karasikov, Mikhail, Kadukova, Maria, Yan, Yumeng, Huang, Sheng-You, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Romero-Durana, Miguel, Díaz-Bueno, Lucía, Fernandez-Recio, Juan, Christoffer, Charles, Terashi, Genki, Shin, Woong-Hee, Aderinwale, Tunde, Maddhuri Venkata Subraman, Sai Raghavendra, Kihara, Daisuke, Kozakov, Dima, Vajda, Sandor, Porter, Kathryn, Padhorny, Dzmitry, Desta, Israel, Beglov, Dmitri, Ignatov, Mikhail, Kotelnikov, Sergey, Moal, Iain H., Ritchie, David W., Chauvot de Beauchêne, Isaure, Maigret, Bernard, Devignes, Marie-Dominique, Ruiz Echartea, Maria E., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Cao, Yue, Shen, Yang, Baek, Minkyung, Park, Taeyong, Woo, Hyeonuk, Seok, Chaok, Braitbard, Merav, Bitton, Lirane, Scheidman-Duhovny, Dina, Dapkūnas, Justas, Olechnovič, Kliment, Venclovas, Česlovas, Kundrotas, Petras J., Belkin, Saveliy, Chakravarty, Devlina, Badal, Varsha D., Vakser, Ilya A., Vreven, Thom, Vangaveti, Sweta, Borrman, Tyler, Weng, Zhiping, Guest, Johnathan D., Gowthaman, Ragul, Pierce, Brian G., Xu, Xianjin, Duan, Rui, Qiu, Liming, Hou, Jie, Ryan Merideth, Benjamin, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Koukos, Panagiotis I., Roel-Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li, Jiménez-García, Brian, van Noort, Charlotte W., Honorato, Rodrigo V., Bonvin, Alexandre M. J. J., Wodak, Shoshana J., 0000-0003-3957-9470, 0000-0003-2759-2088, 0000-0003-0621-0925, 0000-0003-2098-5743, 0000-0001-7169-9398, 0000-0002-0294-3403, 0000-0002-4209-4565, 0000-0002-7787-8896, 0000-0002-3986-7686, 0000-0002-6163-6323, 0000-0003-4091-6614, 0000-0003-0464-4500, 0000-0002-4960-5487, 0000-0002-7035-3042, 0000-0002-1703-7796, 0000-0002-1419-9888, 0000-0002-0496-6107, 0000-0002-4215-0213, 0000-0002-5743-2934, 0000-0003-3413-806X, 0000-0002-3032-7966, 0000-0002-1409-8358, 0000-0001-7369-1322, 0000-0002-0701-6545, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Francis Crick Institute [London], School of Geographical Sciences [Bristol], University of Bristol [Bristol], Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), JiangSu University, Chemical Research Support [Rehovot], Weizmann Institute of Science [Rehovot, Israël], University of Gdańsk (UG), Department of Environmental Analytics [Univ Gdańsk], Faculty of Chemistry [Univ Gdańsk], University of Gdańsk (UG)-University of Gdańsk (UG), Institute of Physics [Warsaw] (IFPAN), Polish Academy of Sciences (PAN), Department of Computer Science [Davis] (UC Davis), University of California [Davis] (UC Davis), University of California-University of California, Moscow Institute of Physics and Technology [Moscow] (MIPT), Huazhong University of Science and Technology [Wuhan] (HUST), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Purdue University [West Lafayette], Kitasato University, Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Department of Biomedical Engineering [Boston], Boston University [Boston] (BU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II, Service des Recherches Métallurgiques Appliquées (SRMA), Département des Matériaux pour le Nucléaire (DMN), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Chemistry, Seoul National University [Seoul] (SNU), The Hebrew University of Jerusalem (HUJ), Vilnius University [Vilnius], Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] (KU), University of Kansas [Kansas City], University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), University of Maryland [Baltimore], Beijing University of Technology, University of Missouri [Columbia] (Mizzou), University of Missouri System, Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], University of Missouri System-University of Missouri System, Shandong University, Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI), Université Paris-Sud - Paris 11 (UP11)-Sorbonne Université - UFR d'Ingénierie (UFR 919), Sorbonne Université (SU)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Saclay (COmUE), University of California [Santa Cruz] (UCSC), University of California, The Hospital for sick children [Toronto] (SickKids), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut des Hautes Etudes Scientifiques (IHES), IHES, The Francis Crick Institute, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut National Polytechnique de Grenoble (INPG), Weizmann Institute of Science, University of Gdańsk, Department of Environmental Analytics [Gdańsk], Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Technische Universität München [München] (TUM), CEA-Direction de l'Energie Nucléaire (CEA-DEN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction de l'Energie Nucléaire (CEA-DEN), University of Missouri [Columbia], Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Sorbonne Université - UFR d'Ingénierie (UFR 919), Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Saclay (COmUE), Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Agence Nationale de la Recherche (France), Cancer Research UK, European Commission, Medical Research Council (UK), National Institutes of Health (US), National Natural Science Foundation of China, National Research Foundation of Korea, National Science Foundation (US), Ministerio de Economía y Competitividad (España), Università degli Studi di Napoli PARTHENOPE, Wellcome Trust, Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Algorithms for Modeling and Simulating Nanosystems [2018-...] (NANO-D-POST [2018-2020]), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California (UC)-University of California (UC), University of Naples Federico II = Università degli studi di Napoli Federico II, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), and Grudinin, Sergei
Subjects: Models, Molecular, Computer science, Protein Conformation, Protein complexes, Template‐based modeling, Oligomeric state, Biochemistry, Docking, protein-protein interaction, Structural Biology, Protein Interaction Mapping, Taverne, Blind prediction, Protein assemblies, Databases, Protein, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, oligomeric state, 030302 biochemistry & molecular biology, protein assemblies, computer.file_format, 3. Good health, CASP, docking, blind prediction, Protein‐protein interaction, CAPRI, proteincomplexes, Algorithms, Protein Binding, protein complexes, template-based modeling, Computational biology, Article, Protein–protein interaction, 03 medical and health sciences, protein‐protein interaction, template‐based modeling, Molecular Biology, 030304 developmental biology, Binding Sites, Computational Biology, Proteins, Protein Data Bank, Docking (molecular), Structural Homology, Protein, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements., Agence Nationale de la Recherche, Grant/Award Number: ANR‐15‐CE11‐0029‐03; Cancer Research UK, Grant/Award Number: FC001003; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Lietuvos Mokslo Taryba, Grant/Award Number: S‐MIP‐17‐60; Medical Research Council, Grant/Award Number: FC001003; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM123055, R35GM124952; National Natural Science Foundation of China, Grant/Award Number: 31670724; National Research Foundation of Korea, Grant/Award Number: 2016M3C4A7952630; National Science Foundation, Grant/Award Number: DBI1565107; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Grant/Award Number: 718.015.001; Spanish >Programma Estatal I+D+i>, Grant/Award Number: BIO2016‐79930‐R; University Parthenope, Grant/Award Number: Finanziamento per il Sostegno alla Ricerca Individ; Wellcome Trust, Grant/Award Number: FC001003
Published: 2019

64. On Palaeolithic coloring agents: epistemological analysis of scientific process

Author: CHANTERAUD, C., Chalmin, Emilie, Salomon, Hélène, Monney, Julien, Génuite, Kim, Pradeau, Jean-Victor, delannoy, jean-jacques, University of Missouri Research Reactor [Columbia] (MURR), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), and Union International des Science Préhistoriques et Protohistoriques
Subjects: Colouring materials, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, geochemical analysis, [SDE]Environmental Sciences, Epistemology, Palaeolithic
Abstract: International audience; What were the coloring agents used during the Palaeolithic? How to recognize, define and describe them? What kind of information may they have recorded?In the past decade, these questions have become essential since coloring agents take a central place in current researches on modern human behaviors and emerging of figurative expressions. Typically, coloring agents are found in various archaeological/sedimentological/economical/cultural contexts: open air and rock-shelter dwellings (settlements?), graves, drawings and paintings in caves.As a consequence, this topic needs interdisciplinary approaches. There is a crucial challenge to overcome which starts from sharing semantics adapted from geosciences, archeology and material sciences. This allows to strengthen the fundamental knowledge to build the working hypothesis and the methodology. Notably, as for the flaked industry, the “chaîne opératoire” (processing sequence) analysis has proven to be an efficient tool. It provides i) a path to a dynamic comprehension of coloring material processing and ii) a way to include this productions within a systemic framework of Palaeolithic activities. Applied to the coloring agents, it concerns:1- The qualification of their sensitive (visual and mechanical) properties: color tone, texture, proneness to be ground to powder.2- The procurement strategies which require the setting up of geological references (Project Pigmentothèque), and combine information concerning geological contexts, availability and sensitive properties. With a combined and reproducible documentation and characterization procedure of the raw coloring rocks, we identify the signature with different scales of information (petrography, mineralogy, geochemistry). This gives robust data in order to compare raw materials to coloring agents used during the Palaeolithic, even if they were transformed by heating or mixing, as well as if they were ground to powder, or strongly modified through taphonomic processes.3- Techniques implemented to use the coloring agents are corollaries of sensitive properties, supply strategies, as well as the objectives of the production. Thus, techniques are systematically documented (powder production, hue control, grain size of the powder, mixing with other substances).4- As a synthesis of the three previous stages of analysis, the objectives of the production are questioned with regard to sensitive, availability and cultural concerns.At this point, by studying current scientific methods and discourses on past human activities related to coloring agent exploitation, we can focus on the possible weaknesses in the scientific procedures.
Published: 2018

65. Intelligent Monte Carlo:A New Paradigm for Inverse Polymerization Engineering

Author: Mohammad Reza Saeb, Florian J. Stadler, Philippe Zinck, Esmaiel Jabbari, Krzysztof Matyjaszewski, Yousef Mohammadi, Alexander Penlidis, ENSCL, CNRS, Centrale Lille, Univ. Artois, Université de Lille, Institute for Color Science and Technology, Department of Chemical Engineering [Waterloo], Department of Chemical Engineering [Columbia], Unité de Catalyse et Chimie du Solide - UMR 8181 [UCCS], Shenzhen University [Shenzhen], Carnegie Mellon University [Pittsburgh] [CMU], University of Waterloo [Waterloo], University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), Centrale Lille Institut (CLIL)-Université d'Artois (UA)-Centrale Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Lille, Carnegie Mellon University [Pittsburgh] (CMU), and Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: artificial intelligence, chain shuttling polymerization, inverse polymerization engineering, Monte Carlo simulation, Polymers and Plastics, Computer science, Organic Chemistry, Monte Carlo method, Inverse, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Chain shuttling polymerization, 01 natural sciences, 0104 chemical sciences, Inorganic Chemistry, [CHIM.POLY]Chemical Sciences/Polymers, Polymerization, Materials Chemistry, Statistical physics, 0210 nano-technology
Abstract: International audience; Traditional computational methods simulate the microstructure of polymer chains from input reaction conditions, but a need exists for predicting optimum reaction conditions in a computationally demanding multivariable space leading to the synthesis of predesigned microstructures and architectures. Herein, the intelligent Monte Carlo (IMC) approach, able to predict optimum reaction conditions for synthesizing copolymers with predefined, complex microstructures as input is introduced. This is rendered possible by a combination of kinetic Monte Carlo (KMC) simulation with artificial intelligence concepts, which enables a reasonably enhanced convergence to optimum reactions conditions. Chain shuttling polymerization is chosen as a first test case due to its complexity and the intricate multiblock microstructures that are formed; whose tailoring requires multiple parameters. The IMC approach locates optimum reaction conditions for the synthesis of olefinic multiblock copolymers with specific microstructures. This approach provides a new platform for identifying complex reaction conditions to “produce” and “tailor‐make” materials with precisely predefined microstructures and facilitates the development of meaningful structure‐property relationships.
Published: 2018

66. Ab initio model of optical properties of two-temperature warm dense matter

Author: Behunin, R., Dalvit, D., Decca, R., Genet, C., Jung, I., Lambrecht, A., Liscio, A., López, D., Reynaud, S., Schnoering, G., Voisin, G., Zeng, Y., Holst, B., Recoules, V., Mazevet, S., Torrent, M., Ng, A., Chen, Z., Kirkwood, S., Sametoglu, V., Reid, M., Tsui, Y., DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire pour l'utilisation des lasers intenses (LULI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Univers et Théories (LUTH (UMR_8102)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, University of Alberta, Université d'Ottawa [Ontario] (uOttawa), University of Northern British Columbia [Prince George] (UNBC), ANR-09-BLAN-0206,OEDYP(2009), Service des Maladies infectieuses et tropicales [CHU Limoges], CHU Limoges, Universität Erlangen-Nürnberg - Erlangen, Laboratoire Kastler Brossel (LKB (Jussieu)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Organic Synthesis and Photoreactivity (ISOF), Consiglio Nazionale delle Ricerche [Roma] (CNR), CETIAT, Centre Technique des Industries Aérauliques et Thermiques, Institut de Science et d'ingénierie supramoléculaires (ISIS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut d'électronique fondamentale (IEF), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Physics [Graz], Graz University of Technology [Graz] (TU Graz), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), University of Quebec (INRS-EMT), Swedish Institute of Space Physics [Kiruna] (IRF), CTVR/Stokes Institute, Engineering Research Building, and University of Limerick (UL)
Subjects: Materials science, PACS number(s): 52.50.Jm, 52.27.Gr, 71.15.−m, 72.80.−r, Ab initio, FOS: Physical sciences, Physics::Optics, Electron, 01 natural sciences, Molecular physics, 010305 fluids & plasmas, law.invention, Ion, law, 0103 physical sciences, 010306 general physics, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], Computational Physics (physics.comp-ph), Warm dense matter, Condensed Matter Physics, Laser, Physics - Plasma Physics, Electronic, Optical and Magnetic Materials, Plasma Physics (physics.plasm-ph), Femtosecond, Density functional theory, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Ultrashort pulse, Physics - Computational Physics
Abstract: International audience; We present a model to describe thermophysical and optical properties of two-temperature systems consisted ofheated electrons and cold ions in a solid lattice that occur during ultrafast heating experiments. Our model is basedon ab initio simulations within the framework of density functional theory. The optical properties are obtainedby evaluating the Kubo-Greenwood formula. By applying the material parameters of our ab initio model to atwo-temperature model we are able to describe the temperature relaxation process of femtosecond-laser-heatedgold and its optical properties within the same theoretical framework. Recent time-resolved measurements ofoptical properties of ultrafast heated gold revealed the dynamics of the interaction between femtosecond laserpulses and solid state matter. Different scenarios obtained from simulations of our study are compared withexperimental data [Chen, Holst, Kirkwood, Sametoglu, Reid, Tsui, Recoules, and Ng, Phys. Rev. Lett. 110,135001 (2013)]
Published: 2018

67. Infinite Dilution Activity Coefficients and Gas-to-Liquid Partition Coefficients of Organic Solutes Dissolved in 1-Benzylpyridinium Bis(Trifluoromethylsulfonyl)Imide and 1-Cyclohexylmethyl-1-Methylpyrrolidinium Bis(Trifluoromethylsulfonyl)Imide

Author: Xin Tong, William E. Acree, Delani Woods, Gary A. Baker, Sudhir Ravula, Fabrice Mutelet, Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry [Columbia] (Mizzou Chemistry), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Microsoft Research, and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)
Subjects: Activity coefficient, Biophysics, Solvation, Analytical chemistry, 02 engineering and technology, Atmospheric temperature range, 010402 general chemistry, 01 natural sciences, Biochemistry, 0104 chemical sciences, Dilution, Partition coefficient, chemistry.chemical_compound, [SPI]Engineering Sciences [physics], 020401 chemical engineering, chemistry, Ionic liquid, Inverse gas chromatography, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 0204 chemical engineering, Physical and Theoretical Chemistry, Imide, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: Infinite dilution activity coefficients and gas-to-ionic liquid partition coefficients were measured for a chemically diverse set of 48 or more organic solute probes dissolved in the ionic liquids 1-benzylpyridinium bis(trifluoromethylsulfonyl)imide ([BzPy][Tf2N]) and 1-cyclohexylmethyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([ChxmPyrr][Tf2N]) in the temperature range from 323.15 to 373.15 K using inverse gas chromatography. Selectivities and capacities for different separation problems were calculated from the measured chromatographic data. The measured partition coefficients were correlated using mathematical equations based on the Abraham general solvation parameter model. The derived Abraham model correlations back-calculated the observed partition coefficients to within 0.12 log10 units.
Published: 2018

68. Formation of thorium and uranium - phosphorano - stabilized carbene

Author: Rungthanaphatsophon, Pokpong, Maron, Laurent, Walensky, Justin, Department of Chemistry, Missouri University of Science and Technology, 142 Schrenk Hall, 400 West 11th Street, Rolla, Missouri 65409, United States, Missouri University of Science and Technology (Missouri S&T), University of Missouri System-University of Missouri System, Laboratoire de physique et chimie des nano-objets (LPCNO), 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)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-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 Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), 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 Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract: International audience
Published: 2018

69. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Author: Phil J. Bowman, Johanna Vilkki, Mehdi Sargolzaei, Robert D. Schnabel, Didier Boichard, Frank Panitz, Chris Hozé, Kay Uwe Götz, D. C. Purfield, Christian Bendixen, Lars-Erik Holm, Carla Hurtado Ponce, Ben J. Hayes, Alessandro Bagnato, J. J. Crowley, Cord Drögemüller, Jeremy F. Taylor, Aniek C. Bouwman, Aurélien Capitan, Jesse L. Hoff, Marie Pierre Sanchez, Thierry Tribout, Hubert Pausch, Dorian J. Garrick, Michael E. Goddard, Mekki Boussaha, Min Wang, Anna A. E. Vinkhuyzen, Ruedi Fries, Hans D. Daetwyler, Roel F. Veerkamp, Curtis P. Van Tassell, Ingolf Russ, Amanda J. Chamberlain, Reiner Emmerling, R.F. Brøndum, Mirjam Frischknecht, Vidhya Jagannathan, Marlies Dolezal, Paul Stothard, Bo Thomsen, Bertrand Servin, Simon Boitard, Donagh P. Berry, James M. Reecy, Dominique Rocha, Anna Bieber, Birgit Gredler, Johann Sölkner, Mogens Sandø Lund, Christy J. Vander Jagt, Pascal Croiseau, Goutam Sahana, Anne Barbat, Armelle Govignon-Gion, Flavio S Schenkel, Bernt Guldbrandtsen, Department of Agriculture, Food and the Marine, Ireland, Science Foundation Ireland, German Federal Ministry of Education and Research, Deutsche Forschungsgemeinschaft, Breed4Food, European Commission, Dairy Futures Cooperative Research Centre, Genome Canada project, 11/S/112, 14/IA/2576, 0315527B, PA 2789/1-1, BO-22.04-011-001-ASG-LR, Wageningen University and Research Centre (WUR), Dept Econ Dev Jobs Transport & Resources, La Trobe University, University of Melbourne, University of Guelph, Semex Alliance, Partenaires INRAE, Aarhus University [Aarhus], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-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, University of Veterinary Medicine [Vienna] (Vetmeduni), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), ETH, Dept Anim Sci, University Fed Rural Semi Arido, Natural Resources Institute Finland (LUKE), Dept Vet Med, University of California [Davis] (UC Davis), University of California-University of California, Div Anim Sci, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Inst Mol Biosci, Karl-Franzens-Universität [Graz, Autriche], University of Queensland [Brisbane], Qualitas AG, Allice, Inst Genet, University of Bern, Canadian Beef Breeds Council, Research Institute of Organic Agriculture - Forschungsinstitut für biologischen Landbau (FiBL), Teagasc Agriculture and Food Development Authority (Teagasc), Bavarian State Res Ctr Agr, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), USDA-ARS : Agricultural Research Service, University of Alberta, and AgriBio
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Genome-wide association study, Conserved Sequence, condition score, Mammals, 2. Zero hunger, Genetics, 04 agricultural and veterinary sciences, Body size, plag1, Phenotype, Animal Breeding & Genomics, Cattle stature, Quantitative Trait Loci, selection, Genomics, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, milk-yield, Genetic variation, Animals, Humans, Life Science, Dairy cattle, [INFO]Computer Science [cs], Human height, Fokkerij & Genomica, Genetic Association Studies, [SDV.GEN]Life Sciences [q-bio]/Genetics, missense mutation, 0402 animal and dairy science, Genetic Variation, Beef cattle, weight, 040201 dairy & animal science, Body Height, Genetic architecture, Breeding and genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, human height, Expression quantitative trait loci, genome-wide association studies, angus, Cattle, Human genome, hereford, Genome-Wide Association Study
Abstract: peer-reviewed H.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B). H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato acknowledges the European Union (EU) Collaborative Project LowInputBreeds (grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge the German Holstein Association (DHV) and the Confederación de Asociaciones de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft (DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576). M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the Holstein genotypes. P.S. acknowledges funding from the Genome Canada project entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing computing resources. J.F.T. was supported by the National Institute of Food and Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and 2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011- 001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V. acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and New Zealand Holstein and Jersey bulls. Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
Published: 2018

70. B-substituted nanoporous carbons for hydrogen storage: from computer simulations to experimental verification

Author: Firlej, Lucyna, Kuchta, B, Pfeifer, P, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Aigle, L2c
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; Hydrogen is considered to be the preferred successor to gasoline due to its clean combustion, but its efficient and save storage remains the bottle-neck and one of the main challenges in hydrogen based technologies, especially those addressing mobile applications. Among different storage methods, reversible physical adsorption of molecular hydrogen in nanoporous materials is considered as the one of most attractive options. However, despite of more than 20 years of intensive experimental research no existing porous structures – from traditional activated carbons to porous polymer networks or metal organic frameworks - possess the required adsorbing properties.Therefore, we used computer simulations to explore the experimental options toward the most promising solutions. We showed that boron substituted graphene-based nanoporous structures may reach necessary storage performance if both key parameters defining the storage capacity of a sorbent (its specific surface and the energy of hydrogen adsorption) will be optimized. A potentially effective way to synthetize such optimized structures is arc-discharge procedure, successfully used in the past to synthetize fullerenes and nanotubes. We have assumed that the synthesis parameters can be modified to prepare graphene-based structures with a variety of substitution sites, shapes, sizes, and interconnections between graphene fragments.The first boron-substituted carbons prepared in this way show promising properties: they contain a variety of organized, graphene based structures decorated with boron nanoclusters, partially incorporated into graphene layers. The strongest adsorption occurs with the binding energy higher than 10 kJ/mol, and at least 10 % of adsorption sites adsorb hydrogen with the energy higher than 6.5 kJ/mol, significantly larger than in activated carbons (~4.5 kJ/mol). The specific surface of as-prepared samples is low (~ 200 m2/g). To increase it, both physical (heating in O2 reach atmosphere) and chemical (with KOH) activation are currently in progress.
Published: 2017

71. Review of hydrogen adsorption modeling in porous systems

Author: Kuchta, B, FIRLEJ, Lucyna, Pfeifer, P, Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Aigle, L2c
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; Hydrogen storage is a key technology for the fuel applications. Hydrogen has the highest energy density of any fuel; however, its low ambient temperature density results in a low energy per unit volume. High density hydrogen storage is a challenge for stationary and portable applications and remains a significant challenge for transportation applications. Presently available storage options typically require large-volume systems that store hydrogen in gaseous form. On a mass basis, hydrogen has nearly three times the energy content of gasoline—120 MJ/kg for hydrogen versus 44 MJ/kg for gasoline. On a volume basis, however, the situation is reversed; liquid hydrogen has a density of 8 MJ/L whereas gasoline has a density of 32 MJ/L, as shown in the figure (https://energy.gov/eere/fuelcells/hydrogen-storage) comparing energy densities of fuels based on lower heating values. Onboard hydrogen storage capacities of 5–13 kg hydrogen will be required to meet the driving range for the full range of light-duty vehicle platforms. One of alternative methods is storage by adsorption in porous materials.The numerical modeling of hydrogen adsorption has been a part of research with the goal to provide adequate hydrogen storage for onboard light-duty vehicle, material-handling equipment, and portable power. Here we discuss how this methodology has been used for the last 20 years and what is it contribution towards final solution. The discussion will be focused on three aspects. First, we will discuss why the existing high-surface porous materials are not promising hydrogen sorbents. Then, we will show how chemical modifications of the adsorbing surface may increase the binding energy between the hydrogen molecule and the surface. Finally, we will present the “universal” limits of hydrogen adsorption in porous structures and discuss the resulting problems and future research perspectives.
Published: 2017

72. High density hydrogen films adsorbed in engineered carbon nanospaces

Author: Pfeifer, P, Gillespie, A., Dohnke, E., Firlej, Lucyna, Kuchta, B, Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Aigle, L2c
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; The search for sustainable automotive fuels has driven numerous studies of sorption-based hydrogen storage for hydrogen fuel cell vehicles. Storage by adsorption is fully reversible, achieves fast fill/discharge demands by simple pressurization/depressurization, and operates at much lower pressure than compressed hydrogen and at much less demanding temperatures than liquid hydrogen. In support of the DOE 2020 storage capacity target of 40 g hydrogen/L system, we have investigated the density of the adsorbed hydrogen films in a variety of porous carbons synthesized at the University of Missouri. The investigation decomposes storage into a high-density adsorbed film and low-density non-adsorbed gas and determines the fraction of pore volume occupied by the two phases.We find exceptionally dense H2 films at liquid nitrogen temperature, 77 K. Saturated film densities are 100-120 g/L across all samples at pressures as low as 35-70 bar. This is 1.4-1.7 times the density of liquid hydrogen at its normal boiling point, 71 g/L (20 K). Experimental film thicknesses are 0.30-0.32 nm, and fractions of total pore volume filled with high-density film are 0.25-0.53. Thus high storage capacities, well in excess of the DOE target and even in excess of liquid hydrogen, can be achieved at 77 K in appropriately engineered nanoporous carbons.The dense films occur at a temperature more than twice the liquid-gas critical temperature of hydrogen, 33 K, above which no bulk liquid exists at any pressure. The high-density film above 33 K does not contradict the non-existence of bulk liquid: the film is not a bulk, 3D phase, but a monomolecular 2D phase. Monte Carlo simulations confirm the observed high density and small film thickness. The film density and volume remain constant up to gas densities ~80% of the film density. A discussion in terms of competing forces acting on adsorbed molecules will be given.
Published: 2017

73. Effect of conceptus size on embryo-maternal communication during early pregnancy in cattle

Author: Sanchez, J.M., Mathew, D.J., Passaro, C., Charpigny, Gilles, Behura, S., Butler, S.T., Spencer, T.E., Lonergan, P., School of Agriculture, Food Science and Veterinary Medicine, University College Dublin [Dublin] (UCD), Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Division of Animal Sciences, University of Missouri [Columbia], University of Missouri System-University of Missouri System, Animal Research Department, Animal and Grassland Research and Innovation Centre (AGRICE), Irish Department of Agriculture, Food and The Marine through the Research Stimulus Fund (Grant number: 13/S/528), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), University of Missouri [Columbia] (Mizzou), and Association Européenne de Transfert Embryonnaire - European Embryo Transfer Association (AETE). FRA.
Subjects: animal structures, bovin, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, cow, Biotechnologies, uterine-explant, conceptus, transcriptome, gestation, embryonic structures, vache, endomètre, endometrium, relation mère-embryon, reproductive and urinary physiology
Abstract: Effect of conceptus size on embryo-maternal communication during early pregnancy in cattle. 33. Annual Meeting of the European Embryo Transfer Association (AETE)
Published: 2017

74. A giant among dwarfs: a new species of galago (Primates: Galagidae) from Angola

Author: Svensson, Magdalena S., Bersacola, Elena, Mills, Michael S.L., Munds, Rachel A., Nijman, Vincent, Perkin, Andrew, Masters, Judith C., Couette, Sébastien, Nekaris, K. Anne-Isola, Bearder, Simon K., Nocturnal Primate Research Group, Oxford Brookes University, A. P. Leventis Ornithological Research Institute, University of Jos, Department of Anthropology, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Tanzania Forest Conservation Group, African Primate Initiative for Ecology and Speciation, Africa Earth Observatory Network-Earth Stewardship Science Research Institute-Nelson Mandela Metropolitan University [Port Elizabeth, South Africa], Laboratoire Paléobiodiversité et Evolution (PALEVO), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), University of Missouri-Columbia, Laboratoire Paléobiodiversité et Evolution ( PALEVO ), École pratique des hautes études ( EPHE ), Biogéosciences [Dijon] ( BGS ), and 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 )
Subjects: Male, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, cryptic species, Skull, Galago, [SDV.BID]Life Sciences [q-bio]/Biodiversity, strepsirrhine, Angola, Species Specificity, morphology, Animals, Body Size, Female, Galagoides, Bushbaby, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: 14 pages; International audience; ObjectivesBased on vocalization recordings of an unknown galago species, our main objectives were to compare morphology and call structure with known closely-related taxa and describe a new species of galago.Materials and methodsWe conducted field surveys in three forest habitats along the escarpment region in western Angola (Kumbira Forest, Bimbe Area, and Northern Scarp Forest), and examined galago specimens from museums worldwide. We digitized and analyzed calls using Avisoft SASLab Pro software. We also compared museum specimens from Angola with other Galago and Galagoides specimens, and conducted comparative analyses (ANOVA and between group principle component analysis) based on a set of twelve linear measurements of skulls and teeth.ResultsWe describe the new species to which we give the name Angolan dwarf galago, Galagoides kumbirensis sp. nov. The new species has a loud and characteristic crescendo call, used by other Galagoides spp. (sensu stricto) in West Africa to attract companions and repel rivals. However, this call shows species-typical differences from its closest relatives. Galagoides kumbirensis sp. nov. is also distinguished by differences in the skull morphology, pelage color and facial markings, as well as a larger body size, similar to that of Galago moholi, which is not known to be sympatric.ConclusionThis discovery points to the importance of Angolan forests as refuges for endemic biodiversity. These forests are under severe threat from overexploitation, and there is an urgent need to establish conservation measures and designate protected areas.
Published: 2017

75. Small RNA profiles in soybean primary root tips under water deficit

Author: Martin Crespi, Yun Zheng, Henry T. Nguyen, Babu Valliyodan, Christine Lelandais-Brière, Vandana Hivrale, Ramanjulu Sunkar, Gregory D. May, Andrew Farmer, Xiaotuo Zhang, Faculty of Information Engineering and Automation, Kunming University of Science and Technology (KMUST), Department of Biochemistry and Molecular Biology, Mayo Clinic, National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri [Columbia], University of Missouri System-University of Missouri System, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), National Center for Genome Resources, Pioneer Hi-Bred International, University of Missouri [Columbia] (Mizzou), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and National center for genome resources (NCGR)
Subjects: 0301 basic medicine, Small RNA, Genotype, [SDV]Life Sciences [q-bio], Population, Drought tolerance, Meristem, Primary root tips, Biology, 03 medical and health sciences, Structural Biology, Auxin, Gene Expression Regulation, Plant, Stress, Physiological, Modelling and Simulation, microRNA, Botany, Drought, miRNAs, Post-transcriptional gene regulation, Soybean, education, Molecular Biology, Gene, 2. Zero hunger, Regulation of gene expression, chemistry.chemical_classification, education.field_of_study, Base Sequence, Sequence Analysis, RNA, Applied Mathematics, Research, fungi, food and beverages, High-Throughput Nucleotide Sequencing, Water, Computer Science Applications, Cell biology, Droughts, MicroRNAs, 030104 developmental biology, chemistry, Modeling and Simulation, Soybeans
Abstract: Background Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling. Methods Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips. Results Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others. Conclusions These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0374-0) contains supplementary material, which is available to authorized users.
Published: 2017

76. Azoospermia and Testicular Hypoplasia in a Boar Carrier of a Novel Y-Autosome Translocation

Author: Manuel Palomino, W. Allan King, D.A.F. Villagómez, Samira Rezaei, Awang Junaidi, Tamas Revay, Brendan Donaldson, Alain Pinton, Ali Honaramooz, Dept Biomed Sci, University of Missouri [Columbia], University of Missouri System-University of Missouri System, Dept Prod Anim, Universidad Jesuita de Guadalajara (ITESO), University of Guelph, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-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-École nationale supérieure agronomique de Toulouse [ENSAT], Dept Vet Biomed Sci, University of Saskatchewan [Saskatoon] (U of S), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and University of Missouri [Columbia] (Mizzou)
Subjects: 0301 basic medicine, Male, pig, Embryology, Swine, Endocrinology, Diabetes and Metabolism, [SDV]Life Sciences [q-bio], Spermatogenesis arrest, Semen, Chromosomal translocation, Biology, Y chromosome, Translocation, Genetic, 03 medical and health sciences, Meiosis, Y Chromosome, medicine, Animals, meiosis, Spermatogenesis, Genetics, Azoospermia, fish, urogenital system, azoospermia, Chromosome, y-autosome translocation, medicine.disease, Sperm, 030104 developmental biology, Developmental Biology
Abstract: Few sex-autosome chromosome abnormalities have been documented in domestic animal species. In humans, Y-autosome chromosome abnormalities may occur at a rate of 1/2,000 live births, whereas in the domestic pig only 2 Y-autosome reciprocal translocations have been previously described. During a routine cytogenetic screening of young boars, we identified a new Y-autosome translocation carrier, which after puberty showed semen devoid of sperm and testicular hypoplasia with spermatogenesis arrest. Whole chromosome painting by FISH analysis corroborated the reciprocal nature of the chromosomal exchanges between the Y chromosome and SSC13. The possible causes for the observed meiotic arrest of the carrier are reviewed.
Published: 2017

77. Determination of fumonisin B1 levels in body fluids and hair from piglets fed fumonisin B -contaminated diets

Author: Souto, Pollyana C.M.C., Jager, Alessandra V., Tonin, Fernando G., Petta, Tânia, Di Gregório, Mayra C., Cossalter, Anne Marie, Pinton, Philippe, Oswald, Isabelle, Rottinghaus, George E., Oliveira, Carlos A.F., Department of Food Engineering, School of Animal Science and Food Engineering, University of São Paulo, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirao Preto, Department of Biosystems Engineering, School of Animal Science and Food Engineering, Plateforme Ezop (Ezop), ToxAlim (ToxAlim), 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-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-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 la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), Veterinary Medical Diagnostic Laboratory, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and University of Missouri [Columbia]
Subjects: exposure assessment, [SDV]Life Sciences [q-bio], biomarker, hair, FB(1), urine, plasma
Abstract: The levels of fumonisin B1 (FB1) residues in plasma, urine, feces and hair from 24 piglets fed FB1-contaminated diets containing 3.1, 6.1 or 9.0 μg FB1.g-1 for 28 days were determined using liquid chromatography coupled to mass spectrometry (LC-MS/MS). The levels of FB1 in plasma, urine, feces and pooled hair (n = 3) samples varied from 0.15 to 1.08 μg.L-1, 16.09-75.01 μg.L-1, 1.87-13.89 μg.g-1 and 2.08-8.09 ng.g-1, respectively. Significant correlations (r = 0.808-0.885; P < 0.001; N = 18) were found between FB1 intake and plasma FB1 on days 7, 14, 21 and 28. However, urinary FB1 correlated with FB1 intake only on days 7 and 14 (r = 0.561-572; P = 0.02; N = 18). A significant correlation (r = 0.509; P = 0.02; N = 24) was also found for the first time between FB1 in hair samples and FB1 intake. Plasma and urinary FB1 are good biomarkers of early exposure of pigs to low dietary FB1 levels, although plasma is recommended to assess prolonged exposure (>14 days). The possibility to evaluate hair as a biomarker of fumonisin exposure was established, although further studies are needed to provide physiologically based toxicokinetics of residual FB1 in the pig hair.
Published: 2017

78. Synthesis and characterisation of B-substituted nanoporous carbons with high energy of hydrogen adsorption

Author: WALCZAK, Katarzyna, Coulet, M.V., Neisius, T., Jiurnet, C., GOZE-BAC, Christophe, Llewellin, P, Gilespie, A., Pfeifer, P, Kuchta, B, FIRLEJ, Lucyna, Aigle, L2c, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], ComputingMilieux_MISCELLANEOUS, [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience;
Published: 2017

79. Formation of Methane versus Benzene in the Reactions of (C5Me5)(2)Th(CH3)(2) with [CH3PPh3]X (X=Cl, Br, I) Yielding Thorium-Carbene or Thorium-Ylide Complexes

Author: Rungthanaphatsophon, Pokpong, Bathelier, Adrien, Castro, Ludovic, Behrle, Andrew C., Barnes, Charles L., Maron, Laurent, Walensky, Justin R., Department of Chemistry, Missouri University of Science and Technology, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Laboratoire de physique et chimie des nano-objets (LPCNO), 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)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-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 Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), 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 Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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 des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)
Subjects: carbenes, [PHYS]Physics [physics], ylides, multiple bonding, [CHIM]Chemical Sciences, organometallics, thorium
Abstract: bibtex: ISI:000412189700021 bibtex\location:'POSTFACH 101161, 69451 WEINHEIM, GERMANY',publisher:'WILEY-V C H VERLAG GMBH',type:'Article',affiliation:'Walensky, JR (Reprint Author), Univ Missouri, Dept Chem, Columbia, MO 65211 USA. Maron, L (Reprint Author), Univ Toulouse, 135 Ave Rangueil, F-31077 Toulouse, France. Maron, L (Reprint Author), LPCNO, CNRS, INSA, UPS,UMR,UMR 5215, 135 Ave Rangueil, F-31077 Toulouse, France. Rungthanaphatsophon, Pokpong; Bathelier, Adrien; Barnes, Charles L.; Walensky, Justin R., Univ Missouri, Dept Chem, Columbia, MO 65211 USA. Bathelier, Adrien; Castro, Ludovic; Maron, Laurent, Univ Toulouse, 135 Ave Rangueil, F-31077 Toulouse, France. Bathelier, Adrien; Castro, Ludovic; Maron, Laurent, LPCNO, CNRS, INSA, UPS,UMR,UMR 5215, 135 Ave Rangueil, F-31077 Toulouse, France.','author-email':'laurent.maron@irsamc.ups-tlse.fr walenskyj@missouri.edu',da:'2018-12-05','doc-delivery-number':'FI7PR',eissn:'1521-3773','funding-acknowledgement':'U.S. Department of Energy, Office of Science, Early Career Research Program [DE-SC-0014174]; Humboldt Foundation; Chinese Academy of Science; CalMip','funding-text':'J.R.W. gratefully acknowledges support for this work from the U.S. Department of Energy, Office of Science, Early Career Research Program under Award Number DE-SC-0014174. L.M. is member of the Instiut Universitaire de France. The Humboldt Foundation, the Chinese Academy of Science and CalMip is acknowledged for either financial support or computing time.','journal-iso':'Angew. Chem.-Int. Edit.','keywords-plus':'CARBON MULTIPLE BOND; MOLECULAR-STRUCTURE; METALLA-ALLENES; URANIUM COMPLEX; TRANS-INFLUENCE; U-IV=C; REACTIVITY; LIGAND; CHEMISTRY; PH2PNSIME3','number-of-cited-references':'42',oa:'Bronze','orcid-numbers':'Walensky, Justin/0000-0003-0221-2675','research-areas':'Chemistry','times-cited':'5','unique-id':'ISI:000412189700021','usage-count-last-180-days':'0','usage-count-since-2013':'9','web-of-science-categories':'Chemistry, Multidisciplinary'\; International audience; The reaction of (C5Me5)(2)Th(CH3)(2) with the phosphonium salts [CH3PPh3]X (X=Cl, Br, I) was investigated. When X=Br and I, two equivalents of methane are liberated to afford (C5Me5)(2)Th[CHPPh3]X, rare terminal phosphorano-stabilized carbenes with thorium. These complexes feature the shortest thorium-carbon bonds (approximate to 2.30 angstrom) reported to date, and electronic structure calculations show some degree of multiple bonding. However, when X = Cl, only one equivalent of methane is lost with concomitant formation of benzene from an unstable phosphorus(V) intermediate, yielding (C5Me5)(2)Th[kappa(2)-(C,C')-(CH2)(CH2)PPh2]Cl. Density functional theory (DFT) investigations of the reaction energy profiles for [CH3PPh3]X, X = Cl and I showed that in the case of iodide, thermodynamics prevents the production of benzene and favors formation of the carbene.
Published: 2017

80. Temperate agroforestry research: considering multifunctional woody polycultures and the design of long-term field trials

Author: Christian Dupraz, Sarah Taylor Lovell, Ronald S. Revord, Kevin J. Wolz, Shibu Jose, Michael A. Gold, Erik Christian Stanek, Department of Crop Sciences, Institute for Sustainability, Energy, and Environment, Plant Science Lab, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), School of Natural Resources, The Center for Agroforestry, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Department of Crop Sciences, Institute for Sustainability, Energy, and Environment, Department of Crop Sciences, University of Göttingen - Georg-August-Universität Göttingen, Program in Ecology, Evolution and Conservation Biology, Institute for Sustainability, Energy, and Environment, Institute for Sustainability, Energy, and Environment at the University of Illinois, National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch project : ILLU-802-938, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Missouri [Columbia], and University of Goettingen
Subjects: 0106 biological sciences, agroecology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 01 natural sciences, Sustainable agriculture, Permaculture, Temperate climate, amérique du nord, Agroecology, 2. Zero hunger, agroforesterie, permaculture, Food security, Agroforestry, business.industry, Forestry, 04 agricultural and veterinary sciences, 15. Life on land, sustainable agriculture, Geography, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, polyculture, Monoculture, business, multifunctional landscape, Agronomy and Crop Science, 010606 plant biology & botany, Woody plant
Abstract: The many benefits of agroforestry are well-documented, from ecological functions such as biodiversity conservation and water quality improvement, to cultural functions including aesthetic value. In North American agroforestry, however, little emphasis has been placed on production capacity of the woody plants themselves, taking into account their ability to transform portions of the landscape from annual monoculture systems to diversified perennial systems capable of producing fruits, nuts, and timber products. In this paper, we introduce the concept of multifunctional woody polycultures (MWPs) and consider the design of long-term experimental trials for supporting research on agroforestry emphasizing tree crops. Critical aspects of long-term agroforestry experiments are summarized, and two existing well-documented research sites are presented as case studies. A new long-term agroforestry trial at the University of Illinois, “Agroforestry for Food,” is introduced as an experiment designed to test the performance of increasingly complex woody plant combinations in an alley cropping system with productive tree crops. This trial intends to address important themes of food security, climate change, multifunctionality, and applied solutions. The challenges of establishing, maintaining, and funding long-term agroforestry research trials are discussed.
Published: 2017

81. The 67P/Churyumov-Gerasimenko observation campaign in support of the Rosetta mission

Author: Benoit Carry, M. F. A'Hearn, Sebastien Besse, Michaël Gillon, M. J. Mumma, Galin Borisov, B. Rajkumar, Janet E. Drew, Olga Muñoz, Viktor Afanasiev, Tarik Zegmott, Lucas Paganini, D. Bodewits, Rita Schulz, Emily Kramer, Adam J. McKay, Diane H. Wooden, J. de León, Michael Schmidt, Geraint H. Jones, S. Haque, Andrew McNeill, Fernando Moreno, Sara Faggi, P. J. Gutiérrez, Jérémie Lasue, Aurélie Guilbert-Lepoutre, J. M. Sunshine, Javier Licandro, Zhong-Yi Lin, Pedro Lacerda, Philippe Rousselot, Jose Luis Ortiz, Nicolas Biver, Marco Micheli, J. J. López-Moreno, Matthew M. Knight, Jon Marchant, Detlef Koschny, Dominik R. G. Schleicher, F. Aceituno, Michael S. P. Kelley, Colin Snodgrass, G. P. Tozzi, Michael A. DiSanti, Karen J. Meech, Olivier Hainaut, Alfredo Sota, Niklas J. T. Edberg, Edith Hadamcik, Rene Duffard, Rosita Kokotanekova, Erika L. Gibb, Damien Hutsemekers, E. Ramos, Y. Ramanjooloo, A. Guijarro, Ulrich Hopp, Luisa Lara, Stephen C. Lowry, Tim Lister, Anita L. Cochran, V. Casanova, Pablo Santos-Sanz, J. Kleyna, R. Hedrosa, M. Pajuelo, A. K. Sen, Cyrielle Opitom, Emmanuel Jehin, A. Thompson, Alan Fitzsimmons, Geronimo L. Villanueva, E. J. W. de Mooij, Stefano Bagnulo, C. Ries, Boncho P. Bonev, O. Ivanova, Amy Mainzer, John K. Davies, Blair C. Conn, Anny Chantal Levasseur-Regourd, P. Nikolov, Auni Somero, Nikolai Kiselev, Lori M. Feaga, Maria Monguió, Francisco J. Pozuelos, A. Stinson, M. Delacruz, Björn Davidsson, Jacqueline V. Keane, M. Kluge, Dean C. Hines, Simon F. Green, Jean Manfroid, James Bauer, Silvia Protopapa, M. de Val-Borro, T. Pursimo, Xiaobin Wang, Cecilia Tubiana, Hermann Boehnhardt, Masafumi Yagi, I. Mohammed, Vera Rosenbush, F. Hoyo, Harry Lehto, G. Bergond, B. Yang, Méabh Hyland, Arno Riffeser, Hideaki Fujiwara, Erin L. Ryan, B. Zaprudin, School of Physical Sciences [Milton Keynes], The Open University [Milton Keynes] ( OU ), Department of Astronomy [College Park], University of Maryland [College Park], Instituto de Astrofísica de Andalucía ( IAA ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Special Astrophysical Observatory of the Russian Academy of Sciences ( SAO ), Russian Academy of Sciences [Moscow] ( RAS ), Armagh Observatory [Armagh], Jet Propulsion Laboratory ( JPL ), NASA-California Institute of Technology ( CALTECH ), Centro Astronómico Hispano Alemán, European Space Astronomy Center ( ESAC ), European Space Agency ( ESA ), Laboratoire d'études spatiales et d'instrumentation en astrophysique ( LESIA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Max-Planck-Institut für Sonnensystemforschung ( MPS ), Department of Physics [Washington], American University Washington D.C. ( AU ), Institute of Astronomy and National Astronomical Observatory, Bulgarian Academy of Sciences, Joseph Louis LAGRANGE ( LAGRANGE ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Observatoire de la Côte d'Azur, Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Mécanique Céleste et de Calcul des Ephémérides ( IMCCE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), McDonald Observatory, University of Texas at Austin [Austin], Research School of Astronomy and Astrophysics [Canberra] ( RSAA ), Australian National University ( ANU ), Gemini Observatory [Southern Operations Center], Association of Universities for Research in Astronomy ( AURA ), UK Astronomy Technology Centre ( UK ATC ), Science and Technology Facilities Council ( STFC ), Universidad de La Laguna ( ULL ), Instituto de Astrofisica de Canarias ( IAC ), Astrophysics Research Centre [Belfast] ( ARC ), Queen's University [Belfast] ( QUB ), Catholic University of America, Astrochemistry Laboratory [Greenbelt], NASA Goddard Space Flight Center ( GSFC ), Department of Astrophysical Sciences [Princeton], Princeton University, Institute for Astronomy [Honolulu], University of Hawaii at Manoa ( UHM ), School of Physics, Astronomy and Mathematics [Hatfield], University of Hertfordshire [Hatfield] ( UH ), Swedish Institute of Space Physics [Uppsala] ( IRF ), National Astronomical Observatory of Japan ( NAOJ ), Department of Physics and Astronomy [Columbia], University of Missouri-Columbia, Institut d'Astrophysique et de Géophysique [Liège], Université de Liège, Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules ( UTINAM ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), IMPEC - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales ( LATMOS ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), European Southern Observatory ( ESO ), Department of Physics [Trinidad], The University of the West Indies, Space Telescope Science Institute ( STSci ), Ludwig-Maximilians University [Munich] ( LMU ), Astronomical Institute of the Slovak Academy of Sciences, Slovak Academy of Science [Bratislava] ( SAS ), Mullard Space Science Laboratory ( MSSL ), University College of London [London] ( UCL ), Centre for Planetary Sciences [UCL/Birkbeck] ( CPS ), Main Astronomical Observatory of NAS of Ukraine ( MAO ), National Academy of Sciences of Ukraine ( NASU ), Research and Scientific Support Department, ESTEC ( RSSD ), European Space Research and Technology Centre ( ESTEC ), European Space Agency ( ESA ) -European Space Agency ( ESA ), Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Tuorla Observatory, University of Turku, Institute of Astronomy [Taiwan] ( IANCU ), National Central University [Taiwan] ( NCU ), Las Cumbres Observatory ( LCO ), Centre for Astrophysics and Planetary Science [Canterbury] ( CAPS ), University of Kent [Canterbury], Astrophysics Research Institute [Liverpool] ( ARI ), Liverpool John Moores University ( LJMU ), ESA SSA-NEO Coordination Centre, Caribbean Institute of Astronomy ( CARINA ), Pontificia Universidad Católica del Perú ( PUCP ), Nordic Optical Telescope ( NOT ), SETI Institute, Lowell Observatory [Flagstaff], European Space Agency, Scientific Support Office, Assam University, INAF - Osservatorio Astrofisico di Arcetri ( OAA ), Istituto Nazionale di Astrofisica ( INAF ), Key Laboratory for the Structure and Evolution of Celestial Objects, Chinese Academy of Sciences [Beijing] ( CAS ), Yunnan Observatories, Chinese Academy of Sciences [Changchun Branch] ( CAS ), NASA Ames Research Center ( ARC ), Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), University of Maryland System-University of Maryland System, Instituto de Astrofísica de Andalucía (IAA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Special Astrophysical Observatory of the Russian Academy of Sciences (SAO), Russian Academy of Sciences [Moscow] (RAS), Jet Propulsion Laboratory (JPL), California Institute of Technology (CALTECH)-NASA, Centro Astronómico Hispano Alemán, Observatorio de Calar Alto (CAHA), European Space Astronomy Centre (ESAC), European Space Agency (ESA), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Sonnensystemforschung (MPS), Max-Planck-Gesellschaft, American University Washington D.C. (AU), Institute of Astronomy of the Bulgarian Academy of Sciences, Bulgarian Academy of Sciences (BAS), Joseph Louis LAGRANGE (LAGRANGE), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Research School of Astronomy and Astrophysics [Canberra] (RSAA), Australian National University (ANU), Association of Universities for Research in Astronomy (AURA), UK Astronomy Technology Centre (UK ATC), Science and Technology Facilities Council (STFC), Universidad de La Laguna [Tenerife - SP] (ULL), Instituto de Astrofisica de Canarias (IAC), Astrophysics Research Centre [Belfast] (ARC), Queen's University [Belfast] (QUB), NASA Goddard Space Flight Center (GSFC), University of Hawai‘i [Mānoa] (UHM), University of Hertfordshire [Hatfield] (UH), Swedish Institute of Space Physics [Uppsala] (IRF), National Astronomical Observatory of Japan (NAOJ), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), European Southern Observatory (ESO), Space Telescope Science Institute (STSci), Ludwig-Maximilians-Universität München (LMU), Slovak Academy of Science [Bratislava] (SAS), Mullard Space Science Laboratory (MSSL), University College of London [London] (UCL), Centre for Planetary Sciences [UCL/Birkbeck] (CPS), Main Astronomical Observatory of NAS of Ukraine (MAO), National Academy of Sciences of Ukraine (NASU), Research and Scientific Support Department, ESTEC (RSSD), European Space Research and Technology Centre (ESTEC), European Space Agency (ESA)-European Space Agency (ESA), Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institute of Astronomy [Taiwan] (IANCU), National Central University [Taiwan] (NCU), Las Cumbres Observatory (LCO), Centre for Astrophysics and Planetary Science [Canterbury] (CAPS), Astrophysics Research Institute [Liverpool] (ARI), Liverpool John Moores University (LJMU), Caribbean Institute of Astronomy (CARINA), Pontificia Universidad Católica del Perú (PUCP), Nordic Optical Telescope (NOT), ESA Scientific Support Office, INAF - Osservatorio Astrofisico di Arcetri (OAA), Istituto Nazionale di Astrofisica (INAF), Chinese Academy of Sciences [Beijing] (CAS), Chinese Academy of Sciences [Changchun Branch] (CAS), NASA Ames Research Center (ARC), NASA-California Institute of Technology (CALTECH), Agence Spatiale Européenne = European Space Agency (ESA), Pôle Planétologie du LESIA, Laboratoire d'études spatiales et d'instrumentation en astrophysique = Laboratory of Space Studies and Instrumentation in Astrophysics (LESIA), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Max-Planck-Institut für Sonnensystemforschung = Max Planck Institute for Solar System Research (MPS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Agence Spatiale Européenne = European Space Agency (ESA)-Agence Spatiale Européenne = European Space Agency (ESA), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and Pontificia Universidad Católica del Perú = Pontifical Catholic University of Peru (PUCP)
Subjects: Future studies, History, 010504 meteorology & atmospheric sciences, General Mathematics, Comet, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], General Physics and Astronomy, FOS: Physical sciences, Context (language use), 01 natural sciences, Astrobiology, Jupiter, 0103 physical sciences, 010303 astronomy & astrophysics, QC, 0105 earth and related environmental sciences, QB, Earth and Planetary Astrophysics (astro-ph.EP), comet 67P/Churyumov?Gerasimenko, Rosetta, solar system, observational astronomy, ta115, Spacecraft, business.industry, [SDU.ASTR.SR]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Solar and Stellar Astrophysics [astro-ph.SR], General Engineering, Articles, [ SDU.ASTR.EP ] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Early results, business, [ SDU.ASTR.SR ] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Solar and Stellar Astrophysics [astro-ph.SR], Astrophysics - Earth and Planetary Astrophysics
Abstract: We present a summary of the campaign of remote observations that supported the European Space Agency's Rosetta mission. Telescopes across the globe (and in space) followed comet 67P/Churyumov-Gerasimenko from before Rosetta's arrival until nearly the end of mission in September 2016. These provided essential data for mission planning, large-scale context information for the coma and tails beyond the spacecraft, and a way to directly compare 67P with other comets. The observations revealed 67P to be a relatively `well behaved' comet, typical of Jupiter family comets and with activity patterns that repeat from orbit-to-orbit. Comparison between this large collection of telescopic observations and the in situ results from Rosetta will allow us to better understand comet coma chemistry and structure. This work is just beginning as the mission ends -- in this paper we present a summary of the ground-based observations and early results, and point to many questions that will be addressed in future studies., Comment: Author prepared version; final published version available at journal. 22 pages
Published: 2017

82. New carbon-hybrid nanoporous materials for enhanced hydrogen storage: synthesis and characterization

Author: WALCZAK, Katarzyna, Coulet, M.V., Neisius, Thomas, Journet, C., GOZE-BAC, Christophe, Llewellin, P, Smith, A.J., Pfeifer, P, Kuchta, B, FIRLEJ, Lucyna, Aigle, L2c, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; The world is running out of fossil fuels and the products of their burning in air (mostly CO2) have already impacted global climate. Therefore, we still need a lot effort to search how to convert the global energy economy towards cleaner and renewable fuels (like hydrogen), in particular, for mobile applications. It is clear now, that to efficiently store hydrogen at ambient temperature and not too high pressures, we need to develop hydrogen sorbent and optimize simultaneously both its specific surface and adsorption energy. In this project we propose to explore the potential effectiveness of arc-discharge procedure to synthetize nanoporous, carbon based sorbents with characteristics required in vehicular applications. The technique was successfully used in the past to synthetize fullerenes and nanotubes. Therefore we have assumed that we can adjust the synthesis parameters to prepare other graphene-based structures, with a variety graphene fragment sizes, forms, and interconnections between them. In addition, arc-discharge technique provides a relatively easy way to incorporate heteroatoms into pure carbon structures.The first characterizations of boron-substituted carbons obtained by this method are promising: the energy of hydrogen adsorption is the highest ever observed experimentally in carbon-based sorbents. However, the specific surface is relatively low, ~ 200 m2/g, suggesting that the samples need to be activated to increase their accessible for adsorption surface and, in consequence, their capacity to store hydrogen.
Published: 2017

83. Methane confined in nanopores: heterogeneity and structural transformations

Author: Kuchta, B, Dundar, E, Firlej, Lucyna, Wexler, C, Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aigle, L2c, and Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; It is well known that the nano-systems exhibit properties different from their bulk analogs. Typically, the phase diagrams are redefined because the position of coexistence lines depends on the size and shape of the nano-objects. This is related to the fact that nano-systems are characterized by high surface-to-volume ratio. The surface atoms are weakly bonded and their contribution to the latent heat is smaller. Consequently, the surface usually transforms at lower temperature and the whole transition may happen smoothly over a finite range of temperatures. This observation suggests that there is no temperature of melting (or any other struc-tural change) in the conventional sense because the structural (phase) changes are gradual and phases are no longer distinguishable.Here we discuss mechanism of methane melting [1-3] and its structural transformations when adsorbed in nanoporous systems. The general analysis of methane melting in slit pores was already discussed by Mi-yahara and Gubbins [1]. In this paper, we emphasize the influence of structural heterogeneity on the mecha-nism of structural transformations. As an example, we discuss the mechanism of melting of methane con-fined in two different structures: first, in 3 and 4 nm slit pores, then, in 2.8 nm square channels of SURMOF porous structure. Mechanism of melting transformation in both cases will be compared and the correlation between the nano-scale and heterogeneity will be emphasized and discussed. Fig. 1 presents an order pa-rameter calculated in different layers of the confined system as a function of temperature.Structural transformations of adsorbate are interesting phenomena from both fundamental and practical point of view. The mechanism of transformations is defined by the characteristic nanosize of the system and the influence of the interactions with the pore framework. This defines the unusual properties of the confined system which can be used for the system characterization.
Published: 2016

84. High density hydrogen adsorption in carbon nanopores

Author: FIRLEJ, Lucyna, Kuchta, B, Gillespie, A, Pfeifer, P, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aigle, L2c, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; Hydrogen is very likely the ultimate future of the energetic economy of the world: it is ubiquitous in the en-vironment, it can be sustainably produced, and it holds the highest energy per unit mass of any fuel (except nuclear). If combusted, it produces only water. Therefore hydrogen, when used as energy vector, enters the natural water cycle of the Earth, with no impact on the planet’s climate. Today the major issue of the wide-spread hydrogen use is its low mass and low volume storage, as the energy density of hydrogen gas is low. Physisorption in nanoporous materials seems to be the most promising way of storage, as it does not release much energy during adsorption and in principle do not require the energy input when hydrogen is released.In this paper we will present the Grand Canonical Monte Carlo simulations of hydrogen adsorption in slit-shaped carbon nanopores. Our calculations confirm the very controversial experimental results [1-3] showing that under confinement the density of hydrogen film adsorbed on the carbon wall exceeds that of the bulk liquid at low temperature and approaches that of solid hydrogen at extreme pressures. The densification of hydrogen is restricted to the layer in direct contact with the adsorbent, and does not depend significantly on the pore size (at least for the pores of the width from 0.6 to 3.0 nm) nor on the temperature (for 77 K< T < 180 K).The simulations are confronted with the experimental isotherms of hydrogen adsorption in KOH - activat-ed nanoporous carbons [3] obtained from biomass waste [4]. The numerical and experimental results are coherent and prove that the interaction between hydrogen molecules and carbon surface is strong enough to produce adsorbed layer with solid hydrogen density.We also show that the gas confined in nanopores is structured, and its density is not uniform across the whole pore volume (Fig.1). In addition, the gas density depends on the pore size (Fig.2). This fact, never re-ported before, should be taken into account when the total (excess) amount stored is estimated from the excess (total) values.
Published: 2016

85. Infinite dilution activity coefficients of solutes dissolved in anhydrous alkyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide ionic liquids containing functionalized- and nonfunctionalized-alkyl chains

Author: Dominique Alonso, Sudhir Ravula, William E. Acree, Gary A. Baker, Bihan Jiang, Fabrice Mutelet, Laboratoire Réactions et Génie des Procédés (LRGP), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Department of Chemistry [Columbia] (Mizzou Chemistry), University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: Activity coefficient, Inorganic chemistry, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, [SPI]Engineering Sciences [physics], 020401 chemical engineering, Polymer chemistry, Materials Chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 0204 chemical engineering, Physical and Theoretical Chemistry, Imide, Spectroscopy, Alkyl, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Chemistry, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Dilution, Partition coefficient, Ionic liquid, Anhydrous, Predictive methods
Abstract: Infinite dilution activity coefficients and gas-to-liquid partition coefficients have been determined for at least 42 different organic solutes of varying polarity and hydrogen-bonding character dissolved in anhydrous ionic liquids comprising propyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, hexyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, 2-hydroxyethyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, cyanomethyl(dimethyl)isopropylammonium bis(trifluoromethylsulfonyl)imide, and N , N , N ′, N ′-tetramethyl- N , N ′-diisopropyl-1,9-nonanediaminium di[bis(trifluoromethylsulfonyl)imide]. The measured gas-to-liquid partition coefficient data were converted to water-to-liquid partition coefficients using standard thermodynamic relationships. Abraham model predictive correlations were developed from both sets of partition coefficients. The derived correlations describe the observed partitioning behavior to within 0.14 (or fewer) log units.
Published: 2016

86. Understanding Universal Adsorption Limits for Hydrogen Storage in Nano Porous Systems

Author: Bogdan Kuchta, Peter Pfeifer, Lucyna Firlej, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)
Subjects: Materials science, Cryo-adsorption, Mechanical Engineering, Inorganic chemistry, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Hydrogen adsorption, 0104 chemical sciences, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], Nano porous, Physical limitations, Hydrogen storage, Adsorption, Mechanics of Materials, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], General Materials Science, 0210 nano-technology, Porous medium, ComputingMilieux_MISCELLANEOUS
Abstract: Despite of more than 15 years of research, no materials possess the adsorbing properties required for mobile storage. At this time of state-of-the-art technology, the essential question should be asked: why is it so difficult to prepare a material with the desired properties? Here, we discuss the sources of physical limitations of existing materials and indicate the directions for further material research.
Published: 2013

87. A cyanido-bridged trinuclear {FeIII2NiII} complex decorated with organic radicals

Author: Yuan-Zhu Zhang, Dongfeng Li, Rodolphe Clérac, Stephen M. Holmes, Department of Chemistry & Biochemistry, Missouri, University of Missouri [St. Louis], University of Missouri System-University of Missouri System, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Central China Normal University [Wuhan, China], Centre de recherches Paul Pascal (CRPP), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Center for Nanoscience
Subjects: Polynuclear complexes, 010405 organic chemistry, Radical, Relaxation (NMR), Crystal structures Magnetic, chemistry.chemical_element, [CHIM.MATE]Chemical Sciences/Material chemistry, Crystal structure, 010402 general chemistry, 01 natural sciences, Cyanometalates, 0104 chemical sciences, Inorganic Chemistry, Crystallography, Nickel, Magnetization, Paramagnetism, Magnetic anisotropy, chemistry, Materials Chemistry, Physical and Theoretical Chemistry, Trifluoromethanesulfonate
Abstract: Reaction of [NEt 4 ][(pzTp)Fe III (CN) 3 ], nickel(II) trifluoromethanesulfonate and 4,4,5,5-tetramethylimidazoline-1-oxyl-2-(2′-pyridyl) (IM-2Py) affords {[(pzTp)Fe III (CN) 3 ] 2 Ni II (IM-2Py) 2 }·2DMF·H 2 O·0.5Et 2 O ( 1 ) as a bent cyanide-bridged trinuclear complex. As judged from simulations of the magnetic data, the magnetic exchange between the {Fe III 2 Ni II } ( S = 2) and both IM-2Py ( S = ½) radical ligands are negligible, or in other words, each radical imparts a Curie contribution to the overall paramagnetism of the complex; the best set of parameters are g iso = 2.53(5), g rad = 2 (fixed), and J iso / k B = 3.9(1) K. ac susceptibility and M versus H data show that 1 does not exhibit slow relaxation of the magnetization above 1.8 K. Consistent with the magnetic data, we conclude that bent cyanide bridges, an improper alignment of the Fe III LS anisotropy tensors, and/or small IM-2Py ring distortions conspire to bring insufficient magnetic anisotropy to the complex, and prevent observation of single-molecule magnet behavior.
Published: 2013

88. Relationship between the Synthesis of Prussian Blue Pigments, Their Color, Physical Properties, and Their Behavior in Paint Layers

Author: Fernande Grandjean, Pauline Martinetto, Pierre Bordet, David Strivay, Gary J. Long, Louise Samain, Faculty of Sciences, University of Liège, Université de Liège, Department of Chemistry, Missouri University of Science and Technology, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Department of Chemistry & Biochemistry, Missouri, University of Missouri [St. Louis], Matériaux, Rayonnements, Structure (MRS), Institut Néel (NEEL), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), and Centre Européen d'Archéométrie, University of Liège
Subjects: Analytical chemistry, 02 engineering and technology, Crystal structure, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, Pigment, Mössbauer spectroscopy, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, Prussian blue, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Thermogravimetry, General Energy, chemistry, visual_art, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], visual_art.visual_art_medium, Ferricyanide, Ferrocyanide, 0210 nano-technology, Stoichiometry, Nuclear chemistry
Abstract: Prussian blue pigments, highly insoluble mixed-valence iron(III) hexacyanoferrate(II) complexes of typical stoichiometry Fe-4(III)[Fe-II(CN)(6)](3)center dot xH(2)O or KFeIII[Fe-II(CN)(6)]center do ...
Published: 2013

89. Synthesis and fading of eighteenth-century Prussian blue pigments: a combined study by spectroscopic and diffractive techniques using laboratory and synchrotron radiation sources

Author: Louise Samain, Pauline Martinetto, David Strivay, Fernande Grandjean, Jana Sanyova, Gary J. Long, Pierre Bordet, Centre Européen d'Archéométrie, University of Liège, Université de Liège, Faculty of Sciences, University of Liège, Department of Chemistry, Missouri University of Science and Technology, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Matériaux, Rayonnements, Structure (MRS), Institut Néel (NEEL), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), and Institut Royal du Patrimoine Artistique
Subjects: Nuclear and High Energy Physics, Inorganic chemistry, Analytical chemistry, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Cobalt blue, chemistry.chemical_compound, Ferrihydrite, Pigment, X-Ray Diffraction, Materials Testing, Paint, Mössbauer spectroscopy, Instrumentation, Prussian blue, Radiation, Spectrometry, X-Ray Emission, Equipment Design, 021001 nanoscience & nanotechnology, humanities, Nanocrystalline material, 0104 chemical sciences, Equipment Failure Analysis, chemistry, visual_art, visual_art.visual_art_medium, Colorimetry, [PHYS.COND.CM-SCE]Physics [physics]/Condensed Matter [cond-mat]/Strongly Correlated Electrons [cond-mat.str-el], Absorption (chemistry), Ferrocyanide, 0210 nano-technology, Synchrotrons, Ferrocyanides
Abstract: Prussian blue, a hydrated iron(III) hexacyanoferrate(II) complex, is a synthetic pigment discovered in Berlin in 1704. Because of both its highly intense color and its low cost, Prussian blue was widely used as a pigment in paintings until the 1970s. The early preparative methods were rapidly recognized as a contributory factor in the fading of the pigment, a fading already known by the mid-eighteenth century. Herein two typical eighteenth-century empirical recipes have been reproduced and the resulting pigment analyzed to better understand the reasons for this fading. X-ray absorption and Mössbauer spectroscopy indicated that the early syntheses lead to Prussian blue together with variable amounts of an undesirable iron(III) product. Pair distribution functional analysis confirmed the presence of nanocrystalline ferrihydrite, Fe10O14(OH)2, and also identified the presence of alumina hydrate, Al10O14(OH)2, with a particle size of ∼15 Å. Paint layers prepared from these pigments subjected to accelerated light exposure showed a tendency to turn green, a tendency that was often reported in eighteenth- and nineteenth-century books. The presence of particles of hydrous iron(III) oxides was also observed in a genuine eighteenth-century Prussian blue sample obtained from a polychrome sculpture.
Published: 2013

90. Aging: Somatic Mutations, Epigenetic Drift and Gene Dosage Imbalance

Author: James A. Birchler, Samuel Bottani, Reiner A. Veitia, Diddahally R. Govindaraju, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (USPC), Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Department of Human Evolutionary Biology, Harvard University [Cambridge], Division of Biological Sciences [Columbia], University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, University Paris Diderot, Centre National de la Recherche Scientifique, Fondation pour le Recherche Medicale, National Science Foundation grant I05-1545780, ANR-10-BINF-0006,Iceberg,Des modèles de population aux populations de modèles: observation, modélisation et contrôle de l'expression génique au niveau de la cellule unique(2010), Department of Human Evolutionary Biology, Cambridge, University of Missouri [Columbia], and ANR-10-BINF-06-11,Iceberg,Des modèles de population aux populations de modèles: observation, modélisation et contrôle de l’expression génique au niveau de la cellule unique(2011)
Subjects: 0301 basic medicine, Senescence, Aging, senescence, Degenerative Disorder, Somatic cell, Gene Dosage, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, medicine.disease_cause, Gene dosage, Models, Biological, dosage imbalance, Epigenesis, Genetic, epigenetic drift, 03 medical and health sciences, medicine, Animals, Humans, Epigenetics, mutational load, Epigenomics, Genetics, genomic integrity, Mutation, [SDV.GEN]Life Sciences [q-bio]/Genetics, Cell Biology, Phenotype, 030104 developmental biology, epigenetic clock
Abstract: International audience; Aging involves a progressive decline of metabolic function and an increased incidence of late-onset degenerative disorders and cancer. To a large extent, these processes are influenced by alterations affecting the integrity of genome architecture and, ultimately, its phenotypic expression. Despite the progress made towards establishing causal links between genomic and epigenomic changes and aging, mechanisms underlying metabolic dysregulation and age-related phenotypes remain obscure. Here, we present a model linking genome-wide changes and their age-related phenotypic consequences via the alteration of macromolecular complexes and cellular networks. This approach may provide a better understanding of the dynamically changing genome-phenome map with age, but also deeper insights to developing more targeted therapies to prevent and/or manage late-onset degenerative disorders as well as decelerate aging.
Published: 2016

91. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016

92. Modeling of low temperature adsorption of hydrogen in carbon nanopores

Author: Bogdan Kuchta, Lucyna Firlej, Justyna Rogacka, Wroclaw University of Science and Technology, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and Aigle, L2c
Subjects: Hydrogen, [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], Monte Carlo method, Analytical chemistry, chemistry.chemical_element, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Catalysis, Inorganic Chemistry, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], Hydrogen storage, Adsorption, Atom, Fugacity, Physical and Theoretical Chemistry, Chemistry, Organic Chemistry, Microporous material, 021001 nanoscience & nanotechnology, [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0104 chemical sciences, Computer Science Applications, Computational Theory and Mathematics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology, Carbon
Abstract: International audience; During the last two decades a lot of effort has been devoted to develop a material that could store an applicable amount of hydrogen by physisorption. All these attempts have failed. Therefore, computer simulations have been used to guide the experiment and to determine in advance the potential storage capacity of a particular structure.Usually, to simplify the interaction model and to spare the computation time, the simulations of hydrogen adsorption in nanoporous materials use the superatom representation of H2 molecule with semi-empirical values of interaction model. This approach totally neglects the non-spherical shape of the molecule. However, this information may be crucial for the precise evaluation of the amount stored and the structure of the adsorbed layers, as packing of the spherical and elongated molecules is not the same. Therefore in the present work we compare the structure and storage of H2 in slit-shaped, infinite carbon pores of nanometric width (from 0.6 nm to 2.5 nm), modeled using united atom (UA) and all atom (AA) representation of H2 molecule.We used Grand Canonical Monte Carlo technique to simulate H2 adsorption isotherms at T = 77 K, either within Material Studio software (for AA model) or home-made code (for UA model). We shows that in both models the calculated amount of stored hydrogen is similar. This results confirm the validity of previous UA model-based estimations of storage capacity reported in the literature. Moreover, our simulation shows that UA model slightly overestimates the stored amount in narrowest pores (0.6 – 0.8 nm) and underestimates it in pores of width of 1.0 -1.2 nm. For pores larger than 1.5nm both models give the same results, at least at the adsorption pressure range studied here (1 – 700 bar). In particular, these observations do not depend on pressure.Both models shows that the H2 layer directly in contact with the pore wall is dense, with density largely exceeding the bulk density of liquid hydrogen at 33 K. This results confirm the recent experimental observations of hydrogen densification under confinement in carbon-based nanospaces [1, 2].
Published: 2016

93. Modeling of methane confined in carbon nanopores

Author: Kuchta, B, Dundar, E, Firlej, Lucyna, Wexler, C, Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aigle, L2c, and Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci]
Abstract: International audience; It is well known that the nano-systems exhibit properties different from their bulk analogs. Typically, the phase diagrams are redefined because the position of coexistence lines depends on the size and shape of the nano-objects. This is related to the fact that nano-systems are characterized by high surface-to-volume ratio. The surface atoms are weakly bonded and their contribution to the latent heat is smaller. Consequently, the surface usually transforms at lower temperature and the whole transition may happen smoothly over a finite range of temperatures. This observation suggests that there is no temperature of melting (or any other structural change) in the conventional sense because the structural (phase) changes are gradual and phases are no longer distinguishable.Here we discuss mechanism of methane melting [1-3] in confined nanoporous systems. The general analysis of methane in slit pores was already discussed by Miyahara and Gubbins [1]. In this paper, we emphasize the influence of structural heterogeneity on the mechanism of structural transformations. As an example, we discuss the differences in mechanism of melting of methane confined in two different structures: first, in 3 and 4 nm slit pores, then, in 2.8 nm square channels of SURMOF porous structure. Mechanism of melting transformation in both cases will be compared and the correlation between the nano-scale and heterogeneity will be emphasized and discussed.
Published: 2016

94. Activity coefficients at infinite dilution for organic solutes dissolved in two 1-alkylquinuclidinium bis(trifluoromethylsulfonyl)imides bearing alkyl side chains of six and eight carbons

Author: Durgesh V. Wagle, Amel Ayad, Amber Lu, William E. Acree, Fabrice Mutelet, Gary A. Baker, Amina Negadi, Bihan Jiang, Laboratoire de Thermodynamique Appliquée et Modélisation Moléculaire (LATA2M), Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry [Columbia] (Mizzou Chemistry), University of Missouri [Columbia] (Mizzou), and University of Missouri System-University of Missouri System
Subjects: Activity coefficient, Analytical chemistry, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, [SPI]Engineering Sciences [physics], 020401 chemical engineering, Materials Chemistry, Inverse gas chromatography, Organic chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 0204 chemical engineering, Physical and Theoretical Chemistry, Imide, Spectroscopy, Alkyl, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Dilution, Solvent, Partition coefficient, chemistry, Ionic liquid
Abstract: Infinite dilution activity coefficients and gas-to-liquid partition coefficients are reported for 47 and 45 organic probe molecules dissolved in 1-hexylquinuclidinium bis(trifluoromethylsulfonyl)imide ([Quin6] + [Tf 2 N] − ) and 1-octylquinuclidinium bis(trifluoromethylsulfonyl)imide ([Quin8] + [Tf 2 N] − ), respectively, as determined by inverse gas chromatography in the temperature range of 313 K to 353 K. The measured partition coefficient data were converted to water-to-liquid partition coefficients using standard thermodynamic relationships and published gas-to-water partition coefficient data. Both sets of calculated partition coefficient data for each ionic liquid solvent were analyzed in terms of the Abraham general solvation model. Mathematical correlations derived from the Abraham model described the measured partition coefficient data to within 0.14 or fewer log units.
Published: 2016

95. A Bayesian model for xylem vessel length accommodates subsampling and reveals skewed distributions in species that dominate seasonal habitats

Author: Kiona Ogle, Amy E. Zanne, Juan Carlos Penagos Zuluaga, Jonathan Sweeney, Brad Oberle, The George Washington University (GW), Northern Arizona University [Flagstaff], Department of Biology, Missouri, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and JPH, Editor
Subjects: 0106 biological sciences, 0303 health sciences, Water stress, Sampling (statistics), Xylem, 15. Life on land, Seasonality, Biology, Bayesian inference, medicine.disease, 010603 evolutionary biology, 01 natural sciences, Length variation, 03 medical and health sciences, Habitat, 13. Climate action, Statistics, Data analysis, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology
Abstract: Vessel length is an important but understudied dimension of variation in angiosperm vascular anatomy. Among other traits, vessel length mediates an important tradeoff between hydraulic efficiency and safety that could influence how plants respond to extreme weather with climate change. However, the functional significance of vessel length variation within individual stems is poorly known, in part because existing data analysis methods handle uncertainty in a way that makes vessel length distributions difficult to compare. We provide a solution to this problem through a hierarchical Bayesian framework for estimating vessel lengths and we demonstrate the flexibility of this method by applying it to data from serial cross sections of dye injected stems. Our approach can accelerate data collection and accommodate associated uncertainties by statistically correcting for bias and error that result from subsampling images. We illustrate our analytical framework by estimating and comparing vessel length distributions for 21 woody species characteristic of a North American forest. The best-fit model corrected for both bias due to secondary growth and sampling error within and among species. Vessel length estimates from this model varied by almost an order of magnitude and parameters of these distributions correlated with point estimates derived from a different, commonly used method. Furthermore, we show how key contrasts can be estimated with the Bayesian framework, and in doing so, we show that the shape of the vessel length distribution differed between ring- and diffuse-porous species, suggesting that within-stem vessel length variation corresponds to water stress seasonality and contributes to landscape-level habitat segregation. Our analysis method revealed the importance of within-stem variation in vessel length, and our results complement work on between-species variation in average vessel length, further illuminating how vascular anatomy can influence woody plants’ responses to water stress.
Published: 2016

96. Simulation and Characterization of Tetracosane on Graphite: Molecular Dynamics Beyond the Monolayer

Author: Carlos Wexler, M.W. Roth, E. Maldonado, M. J. Connolly, Lucyna Firlej, Bogdan Kuchta, Centre IRMf de Marseille, Université de la Méditerranée - Aix-Marseille 2, Laboratoire Charles Coulomb ( L2C ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Matériaux divisés, interfaces, réactivité, électrochimie ( MADIREL ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Physics, University of Northern Iowa, Cedar Falls, Department of Physics and Astronomy [Columbia], University of Missouri-Columbia, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Cedar Falls], University of Northern Iowa (UNI), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)
Subjects: Materials science, Nanotechnology, 02 engineering and technology, Carbon nanotube, 010402 general chemistry, 01 natural sciences, CARBON NANOTUBES, law.invention, Molecular dynamics, chemistry.chemical_compound, law, Monolayer, Perpendicular, Tetracosane, Graphite, Physical and Theoretical Chemistry, Bilayer, Intermolecular force, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, General Energy, chemistry, Chemical physics, [ CHIM.MATE ] Chemical Sciences/Material chemistry, 0210 nano-technology
Abstract: International audience; We present the results of extensive fully atomistic molecular dynamics (MD) simulations of tetracosane (C24H50) bilayer and trilayer systems adsorbed onto the basal plane of graphite. At low temperature, both layers of the bilayer exist in well-defined solid phases. With increasing temperature, the system exhibits separated smectic phases that eventually lead to melting. During this process, we observed a strong interlayer translational correlation and mobility between layers; however, the upper layer presents more intra- (chain) and intermolecular disorder because of a lack of confinement and a greater distance to the graphite substrate. Simulations of the perpendicular trilayer patch show that gauche defects provide the main mechanism for spreading of the bottom and outer perimeter of the patch in the solid, leading to the ultimate collapse of the patch with increasing temperature and formation of a flat (parallel) trilayer that melts at a higher temperature than the bilayer structure. The wide variety of structural order parameters, thermodynamic functions, and probability distributions we employed provide a clear picture of the roles of gauche defects, confinement, and interlayer correlation in the phases and phase transitions exhibited by these confined organic layers.
Published: 2016

97. Low temperature mechanism of adsorption of methane: Comparison between homogenous and heterogeneous pores

Author: Bogdan Kuchta, Lucyna Firlej, Carlos Wexler, Ege Dundar, Pascal Boulet, Philip L. Llewellyn, Justyna Rogacka, Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Wroclaw University of Science and Technology, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Columbia] (Mizzou Physics), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC), Matériaux divisés, interfaces, réactivité, électrochimie ( MADIREL ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Charles Coulomb ( L2C ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Physics and Astronomy [Columbia], University of Missouri-Columbia, and Aix Marseille Université ( AMU )
Subjects: Chemical substance, Inorganic chemistry, [ PHYS.COND.CM-MS ] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Methane, chemistry.chemical_compound, Colloid and Surface Chemistry, Adsorption, Molecule, Intermolecular force, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry, Chemical engineering, 13. Climate action, [ CHIM.MATE ] Chemical Sciences/Material chemistry, [ CHIM.THEO ] Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Layering, 0210 nano-technology, Science, technology and society, Carbon
Abstract: International audience; ! abstract The mechanisms of methane adsorption in (i) homogeneous carbon slit pores of widths between 1 nm and 2 nm and (ii) heterogeneous MOF pores of similar unit cell sizes have been compared. We discuss the mechanism of layering transition in subcritical conditions, for temperatures between 80 K and 180 K. The layer formation is strongly temperature-dependent. In slit pores it varies from a sharp adsorption at low temperatures to a more continuous uptake at higher temperatures. The pore size defines the number of adsorbed layers: the 1 nm pore allows adsorption of 2 layers while the 2 nm pore allows adsorption of 5 layers of methane molecules. We compare this behavior with the mechanism of adsorption in two MOFs, IRMOF-1 and IRMOF-16, with strongly heterogeneous walls (both structurally and energetically). This comparison allows us to discuss separately the influence of wall topology and intermolecular interactions on the mechanism of layering.
Published: 2016

98. Key genes involved in desiccation tolerance and dormancy across life forms

Author: Henk M.W. Hilhorst, Julia Buitink, Jill M. Farrant, Maria Cecília D. Costa, Wilco Ligterink, Melvin J. Oliver, HilhorstaaWageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University and Research [Wageningen] (WUR), Department of Molecular and Cell Biology, University of Cape Town, U.S. Department of Agriculture-ARS-MWA-PGRU, Missouri University of Science and Technology (Missouri S&T), University of Missouri System-University of Missouri System, 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), Wageningen University and Research Centre [Wageningen] (WUR), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Key genes, Arabidopsis thaliana, ABI3, Climate Change, Desiccation tolerance, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Species Specificity, Stress, Physiological, Genetics, Dormancy, Laboratorium voor Plantenfysiologie, Desiccation, Conserved genes, Gene, Conserved Sequence, 2. Zero hunger, Ecology, fungi, food and beverages, General Medicine, 15. Life on land, biology.organism_classification, Plant Dormancy, Phenotype, Droughts, 030104 developmental biology, Evolutionary biology, Seeds, Trait, Mutagenesis, Site-Directed, Adaptation, EPS, Energy Metabolism, Agronomy and Crop Science, Laboratory of Plant Physiology, 010606 plant biology & botany
Abstract: Desiccation tolerance (DT, the ability of certain organisms to survive severe dehydration) was a key trait in the evolution of life in terrestrial environments. Likely, the development of desiccation-tolerant life forms was accompanied by the acquisition of dormancy or a dormancy-like stage as a second powerful adaptation to cope with variations in the terrestrial environment. These naturally stress tolerant life forms may be a good source of genetic information to generate stress tolerant crops to face a future with predicted higher occurrence of drought. By mining for key genes and mechanisms related to DT and dormancy conserved across different species and life forms, unique candidate key genes may be identified. Here we identify several of these putative key genes, shared among multiple organisms, encoding for proteins involved in protection, growth and energy metabolism. Mutating a selection of these genes in the model plant Arabidopsis thaliana resulted in clear DT-, dormancy- and other seed-associated phenotypes, showing the efficiency and power of our approach and paves the way for the development of drought-stress tolerant crops. Our analysis supports a co-evolution of DT and dormancy by shared mechanisms that favour survival and adaptation to ever-changing environments with strong seasonal fluctuations.
Published: 2016

99. Milk Production and Fertility in Cattle

Author: Berry, D. P., Friggens, Nicolas C., Lucy, M., Roche, J. R., Animal & Grassland Research and Innovation Centre,Teagasc, Moorepark, Animal and Grassland Research and Innovation Centre (AGRICE), Modélisation Systémique Appliquée aux Ruminants (MoSAR), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Division of Animal Science, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, New Zealand, DairyNZ, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and University of Missouri [Columbia]
Subjects: reproduction, nutrition, [SDV]Life Sciences [q-bio], dairy, genetics, beef
Abstract: Evolutionary biology provides reasons for why the intensive selection for milk production reduces reproductive success rates. There is considerable exploitable genetic variation in reproductive performance in both dairy and beef cattle, and examination of national genetic trends demonstrates that genetic gain for both reproductive performance and milk production is possible in a well-structured breeding program. Reproductive failure is often postulated to be a consequence of the greater negative energy balance associated with the genetic selection for increased milk production. However, experimental results indicate that the majority of the decline in reproductive performance cannot be attributed to early lactation energy balance, per se; reproductive success will, therefore, not be greatly improved by nutritional interventions aimed at reducing the extent of negative energy balance. Modeling can aid in better pinpointing the key physiological components governing reproductive success and, also, the impact of individual improvements on overall fertility, helping to prioritize variables for inclusion in breeding programs.
Published: 2016

100. The evolution of HD2 proteins in green plants

Author: D. W. Stevenson, J. C. Pires, Valérie Nicolas-Francès, Michael Melkonian, D. E. Soltis, Nóra Lehotai, Carl J. Rothfels, Eric J. Carpenter, David Wendehenne, Mark W. Chase, Patrick P. Edger, Shuangxiu Wu, V. Grandperret, Gane Ka-Shu Wong, Z. Yan, Xuhao Wang, Sean W. Graham, Yinlong Xie, S. Bourque, Michael K. Deyholos, Sébastien Aimé, Nicholas W. Miles, Jim Leebens-Mack, Sylvain Jeandroz, Agroécologie [Dijon], 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-Université Bourgogne Franche-Comté [COMUE] (UBFC), Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Department of Biology, Florida Museum of Natural History, Genetics Institute, Emek Medical Center, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Botanical Institute, University of Cologne, Northern Arizona University [Flagstaff], Department of Plant Biology, The Royal Veterinary and Agricultural University, Plant Biology, Università degli Studi di Roma 'La Sapienza' [Rome], Jodrell Laboratory, Royal Botanic Garden , Kew, University Herbarium and Department of Integrative Biology, New York Botanical Garden (NYBG), Department of Botany, National University of Ireland [Galway] (NUI Galway), Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences [Changchun Branch] (CAS), Division of Biological Sciences and Bond Life Sciences Center, University of Missouri [Columbia], University of Missouri System-University of Missouri System, Department of Horticulture, University of Wisconsin-Madison, Beishan Industrial Zone, Beijing Genomics Institute, Department of Medicine, Imperial College London, Association pour la Recherche sur les Nicotianees, Conseil Regional de Bourgogne, University of Burgundy, 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, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], University of Missouri [Columbia] (Mizzou), Beijing Genomics Institute [Shenzhen] (BGI), 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-Université Bourgogne Franche-Comté ( UBFC ), The Open University [Milton Keynes] ( OU ), Royal Botanic Gardens Kew, University of California Berkeley, New York Botanical Garden, National University of Ireland [Galway] ( NUI Galway ), Chinese Academy of Sciences [Changchun Branch] ( CAS ), UNIVERSITY OF MISSOURI, and University of Wisconsin-Madison [Madison]
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Science, Viridiplantae, 01 natural sciences, Histone Deacetylases, 03 medical and health sciences, Gene Expression Regulation, Plant, Arabidopsis, Gene duplication, Ovule, Gene, Plant Proteins, Genetics, Zinc finger, Plant evolution, biology, [ SDV ] Life Sciences [q-bio], fungi, food and beverages, biology.organism_classification, 030104 developmental biology, Histone deacetylase, 010606 plant biology & botany, Protein deacetylation
Abstract: In eukaryotes, protein deacetylation is carried out by two well-conserved his tone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.
Published: 2016

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