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627 results on '"FWF"'

251. Runtime Monitoring for Executable DSLs

Author: Benoit Combemale, Pierre Jeanjean, Erwan Bousse, Dorian Leroy, Manuel Wimmer, Johannes Kepler Universität Linz (JKU), Diversity-centric Software Engineering (DiverSe), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Smart Modeling for softw@re Research and Technology (IRIT-SM@RT), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), This work has been partially supported by the Austrian Federal Ministry for Digital and Economic Affairs, the National Foundation for Research,Technology and Development (CDG), and by the FWF under the grant numbers P28519-N31 and P30525-N31., Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Executable modeling, Domain-specific language, Computer science, Semantics (computer science), executable DSLs, media_common.quotation_subject, Complex event processing, 02 engineering and technology, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], computer.software_genre, domain-specific languages, 0202 electrical engineering, electronic engineering, information engineering, Overhead (computing), runtime monitoring, media_common, business.industry, Programming language, Runtime verification, 020207 software engineering, temporal property language, computer.file_format, 021001 nanoscience & nanotechnology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Debugging, Analytics, Executable, 0210 nano-technology, business, computer, Software
Abstract: International audience; Runtime monitoring is a fundamental technique used throughout the lifecycle of a system for many purposes, such as debugging, testing, or live analytics. While runtime monitoring for general purpose programming languages has seen a great amount of research, developing such complex facilities for any executable Domain Specific Language (DSL) remains a challenging, reoccurring and error prone task. A generic solution must both support a wide range of executable DSLs (xDSLs) and induce as little execution time overhead as possible. Our contribution is a fully generic approach based on a temporal property language with a semantics tailored for runtime verification. Properties can be compiled to efficient runtime monitors that can be attached to any kind of executable discrete event model within an integrated development environment. Efficiency is bolstered using a novel combination of structural model queries and complex event processing. Our evaluation on 3 xDSLs shows that the approach is applicable with an execution time overhead of 121% (on executions shorter than 1s), to 79% (on executions shorter than 20s) making it suitable for model testing and debugging.
Published: 2020
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252. Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection

Author: Michael Mentges, Ana Lilia Martínez-Rocha, Jörg Bormann, Marc-Henri Lebrun, Anika Glasenapp, Marike Johanne Boenisch, Rasmus John Normand Frandsen, Bernard Henrissat, Ulrich Güldener, Sascha Malz, Wilhelm Schäfer, Martin Münsterkötter, University of Hamburg, Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Tech Univ Munich, TUM Sch Life Sci Weihenstephan, Dept Bioinformat, Inst Bioinformat & Syst Biol, Sopron Univ, Funct Genom & Bioinformat, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Austrian Science Fund (FWF) F3705/DFGME1682/6-1, German Research Foundation (DFG) BO4098/2-1, Universitat Hamburg, and Tech Univ Denmark, Dept Biotechnol & Biomed
Subjects: 0106 biological sciences, 0301 basic medicine, Fusarium, Hypha, Infection cushion, Soil Science, Virulence, effector proteins, Runner hyphae, Plant Science, Fungus, runner hyphae, 01 natural sciences, Microbiology, 03 medical and health sciences, Fusarium graminearium, RNA-Seq, wheat infection, Secondary metabolism, Molecular Biology, Mycelium, Triticum, Plant Diseases, Plant Proteins, 2. Zero hunger, Appressorium, biology, infection cushion, secondary metabolites, Gene Expression Profiling, Secondary metabolites, food and beverages, Original Articles, biology.organism_classification, Effector proteins, Wheat infection, Reverse genetics, Fusarium graminearum, 030104 developmental biology, [SDE]Environmental Sciences, Original Article, Agronomy and Crop Science, transcriptome, 010606 plant biology & botany
Abstract: Fusarium graminearum is one of the most destructive plant pathogens worldwide, causing fusarium head blight (FHB) on cereals. F. graminearum colonizes wheat plant surfaces with specialized unbranched hyphae called runner hyphae (RH), which develop multicelled complex appressoria called infection cushions (IC). IC generate multiple penetration sites, allowing the fungus to enter the plant cuticle. Complex infection structures are typical for several economically important plant pathogens, yet with unknown molecular basis. In this study, RH and IC formed on the surface of wheat paleae were isolated by laser capture microdissection. RNA‐Seq‐based transcriptomic analyses were performed on RH and IC and compared to mycelium grown in complete medium (MY). Both RH and IC displayed a high number of infection up‐regulated genes (982), encoding, among others, carbohydrate‐active enzymes (CAZymes: 140), putative effectors (PE: 88), or secondary metabolism gene clusters (SMC: 12 of 67 clusters). RH specifically up‐regulated one SMC corresponding to aurofusarin biosynthesis, a broad activity antibiotic. IC specifically up‐regulated 248 genes encoding mostly putative virulence factors such as 7 SMC, including the mycotoxin deoxynivalenol and the newly identified fusaoctaxin A, 33 PE, and 42 CAZymes. Furthermore, we studied selected candidate virulence factors using cellular biology and reverse genetics. Hence, our results demonstrate that IC accumulate an arsenal of proven and putative virulence factors to facilitate the invasion of epidermal cells., Transcriptome analyses on epiphytic runner hyphae (RH) and penetrating infection cushions (IC) of Fusarium graminearum grown on wheat palea compared to in culture‐grown mycelium (MY) reveal that IC are fungal arsenals for infection.
Published: 2020
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253. Uniform Birkhoff

Author: Mai Gehrke, Michael Pinsker, LJAD, Laboratoire Jean Alexandre Dieudonné (JAD), 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)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and The research of Mai Gehrke has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 670624). The research of Michael Pinsker has been funded through project P27600 of the Austrian Science Fund (FWF).
Subjects: Pointwise convergence, Pure mathematics, Algebra and Number Theory, Natural mapping, [MATH.MATH-RA]Mathematics [math]/Rings and Algebras [math.RA], 010102 general mathematics, Structure (category theory), Mathematics - Logic, Mathematics - Rings and Algebras, Term (logic), 01 natural sciences, Uniform continuity, Mathematics::Group Theory, Clone (algebra), Rings and Algebras (math.RA), Free algebra, 0103 physical sciences, FOS: Mathematics, [INFO]Computer Science [cs], 010307 mathematical physics, Finitely-generated abelian group, [MATH]Mathematics [math], 0101 mathematics, Logic (math.LO), Mathematics
Abstract: We show that pseudovarieties of finitely generated algebras, i.e., classes $C$ of finitely generated algebras closed under finite products, homomorphic images, and subalgebras, can be described via a uniform structure $U$ on the free algebra for $C$: the members of $C$ then are precisely those finitely generated algebras $A$ for which the natural mapping from the free algebra onto the term clone of $A$ is well-defined and uniformly continuous with respect to the uniformity $U$ and the uniformity of pointwise convergence on the term clone of $A$, respectively. Our result unifies earlier theorems describing pseudovarieties of finite algebras and the pseudovariety generated by a single oligomorphic algebra., Comment: 10 pages. (This material contains old results from 2014 published in 2018 (see reference), but so far not on arXiv)
Published: 2020
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254. Pseudo-Ranks: How to Calculate Them Efficiently in R

Author: Arne C. Bathke, Georg Zimmermann, Martin Happ, Edgar Brunner, and FWF
Subjects: Statistics and Probability, Computer science, Statistics, Nonparametric statistics, 01 natural sciences, pseudo-ranks, Mathematics, Mathematical statistics, HA1-4737, Interpretation (model theory), nonparametric statistics, 010104 statistics & probability, Resampling, Independent samples, ranks, R, 0101 mathematics, Statistics, Probability and Uncertainty, Algorithm, Software
Abstract: Many popular nonparametric inferential methods are based on ranks. Among the most commonly used and most famous tests are for example the Wilcoxon-Mann-Whitney test for two independent samples, and the Kruskal-Wallis test for multiple independent groups. However, recently, it has become clear that the use of ranks may lead to paradoxical results in case of more than two groups. Luckily, these problems can be avoided simply by using pseudo-ranks instead of ranks. These pseudo-ranks, however, suffer from being (a) at first less intuitive and not as straightforward in their interpretation, (b) computationally much more expensive to calculate. The computational cost has been prohibitive, for example, for large-scale simulative evaluations or application of resampling-based pseudorank procedures. In this paper, we provide different algorithms to calculate pseudo-ranks efficiently in order to solve problem (b) and thus render it possible to overcome the current limitations of procedures based on pseudo-ranks.
Published: 2020
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255. Gaia Early Data Release 3: Acceleration of the solar system from Gaia astrometry

Author: Vincenzo Ripepi, P. Gavras, M. Vaillant, Mathias Schultheis, László Molnár, E. Poujoulet, Mark Cropper, C. Babusiaux, D. Molina, J. Fernández-Hernández, G. Jevardat de Fombelle, A. de Torres, Aldo Dell'Oro, J. Castañeda, Z. Kostrzewa-Rutkowska, A. Bombrun, André Moitinho, Marcella Marconi, Rossella Cancelliere, M. Hauser, M. Ajaj, C. M. Raiteri, L. Eyer, Michał Pawlak, H. I. Siddiqui, C. Ducourant, Tatiana Muraveva, Tsevi Mazeh, A. Panahi, Federico Marocco, Stefano Bertone, D. Vicente, Patrick Charlot, A. Guerrier, R. De March, Mario Gai, J. Souchay, H. E. P. Lindstrøm, Nicoletta Sanna, Agnes Fienga, Giovanni Comoretto, Jon Marchant, A. Lorca, E. Utrilla, A. Garcia-Gutierrez, Ilaria Musella, L. Balaguer-Núñez, Leanne P. Guy, N. Leclerc, E. Brugaletta, A. Yoldas, Harry Enke, Rosanna Sordo, Zoltan Balog, H. E. Huckle, L. Palaversa, Monica Rainer, T. A. Lister, F. A. Jansen, Ruth Carballo, Alessandro Spagna, J. M. Carrasco, Mikael Granvik, Derek W. Morris, F. Julbe, A. Hutton, J. Osinde, D. W. Evans, M. van Leeuwen, M. Weiler, F. Thévenin, F. Torra, Iain A. Steele, Lorenzo Rimoldini, Alessandro Sozzetti, Francesca Fragkoudi, K. Janßen, O. L. Creevey, J. González-Núñez, T. Pauwels, R. Buzzi, Miguel García-Torres, S. Liao, G. Tauran, Lennart Lindegren, C. Fouron, Pierre Fernique, Céline Reylé, P. Di Matteo, E. Szegedi-Elek, F. Pailler, Stefan Jordan, Roberto Molinaro, Elisabetta Caffau, Federica Spoto, Felix Franke, D. Barbato, Isabelle Lecoeur-Taïbi, Tristan Cantat-Gaudin, Alejandra Recio-Blanco, E. Livanou, W. Roux, X. Peñalosa Esteller, P. A. Palicio, J. H. J. de Bruijne, Sergi Blanco-Cuaresma, Deborah Busonero, F. Riclet, Conny Aerts, Georges Kordopatis, Guy Rixon, F. Solitro, Davide Massari, Mike Smith, D. Baines, Roberto Morbidelli, Gerry Gilmore, G. Plum, Alexey Mints, O. Marchal, Juan Zorec, Ángel Gómez, C. A. Stephenson, Michael Davidson, C. Fabricius, E. Licata, Sergio Messina, Laszlo Szabados, M. Biermann, A. Garofalo, G. Holland, F. De Angeli, Andreas Korn, E. Anglada Varela, Grigori Fedorets, S. Girona, E. Gerlach, Antonella Vallenari, M. Riello, Łukasz Wyrzykowski, Damien Ségransan, F. Taris, L. Bramante, Alberto Cellino, S. Regibo, Andrej Prsa, M. Sarasso, E. Poggio, W. Löffler, Paolo Giacobbe, Jordi Portell, Elisa Distefano, Eric Slezak, I. Bellas-Velidis, Nicolas Rambaux, E. Balbinot, J.-B. Delisle, Maroussia Roelens, E. Salguero, P. de Teodoro, E. van Dillen, Y. Lebreton, Francois Mignard, Sergei A. Klioner, Ulrich Bastian, N. Samaras, G. Orrù, R. E. de Souza, P. Esquej, Paul J. McMillan, A. C. Lanzafame, Sébastien Lambert, Beatrice Bucciarelli, Jose M Hernandez, M. Bernet, S. Ragaini, Gisella Clementini, A. F. Mulone, Ludovic Delchambre, C. Panem, Eric Gosset, P. David, M. Garcia-Reinaldos, Ana Ulla, F. Crifo, J. Guiraud, Mariateresa Crosta, L. Chaoul, C. Diener, Carlos Dafonte, Karri Muinonen, Alex Lobel, J.-L. Bassilana, Maria Süveges, Isabella Pagano, Dimitri Pourbaix, D. Eappachen, M. Haywood, R. Drimmel, Y. Viala, S. Voutsinas, D. Semeux, William Thuillot, N. A. Walton, Paolo Montegriffo, A. Abreu Aramburu, C. Fabre, H. Zhao, Alessandro Bressan, S. Bouquillon, Sanjeev Khanna, T. Lebzelter, N. Tonello, L. Siltala, M. G. Lattanzi, C. Crowley, P. Yvard, Carme Jordi, Elena Pancino, E. del Pozo, Jan Rybizki, Nami Mowlavi, C. Barache, Morgan Fouesneau, J. De Ridder, Ugo Becciani, Martin Altmann, F. van Leeuwen, P. M. Marrese, M. A. Álvarez, A. Jean-Antoine Piccolo, A. F. Lanza, Alberto Vecchiato, Thomas Wevers, Caroline Soubiran, C. P. Murphy, A. M. Piersimoni, Alessandra Mastrobuono-Battisti, Peter G. Jonker, A. Sagristà Sellés, T. Roegiers, S. Marinoni, Johannes Sahlmann, Rene Andrae, P. Sartoretti, G. Altavilla, Raphael Guerra, F. X. Pineau, M. Segol, T. Prusti, J. J. González-Vidal, J. J. Aguado, N. R. Millar, A. Baudesson-Stella, Andrea Chiavassa, Laurent Chemin, C. Turon, H. Steidelmüller, Douglas J. Marshall, A. G. Butkevich, Alberto Riva, P. de Laverny, Simchon Faigler, Laurent Galluccio, A. Mora, P. Re Fiorentin, C. Ordénovic, J. F. Le Campion, A. Delgado, V. Sanchez Gimenez, M. David, G. Sadowski, R. L. Smart, A. Masip, Laia Casamiquela, R. Messineo, R. Mor, J. Bakker, C. Dolding, J. M. Martín-Fleitas, S. Diakite, Coryn A. L. Bailer-Jones, D. Souami, P. Madrero Pardo, Martin A. Barstow, David Teyssier, Ummi Abbas, Jesus Salgado, Paolo Tanga, A. Burlacu, O. Vanel, Ulrike Heiter, Daniel Hestroffer, Sebastian L. Hidalgo, H. E. Delgado, Alberto Krone-Martins, C. Robin, Kevin Benson, Christos Siopis, S. Managau, P. Burgess, Tomaz Zwitter, M. M. S. Marcos Santos, S. Cowell, J. L. Halbwachs, Xavier Luri, Antti Penttilä, R. Geyer, Minia Manteiga, Yassine Damerdji, Nigel Hambly, S. Bartolomé, J. Álvarez Cid-Fuentes, P. Osborne, J. Juaristi Campillo, Mark Taylor, Richard I. Anderson, Y. Le Fustec, Thierry Morel, T. Cornez, Krzysztof A. Rybicki, L. Pulone, N. Bauchet, Pierre Kervella, C. Zurbach, Alfred Castro-Ginard, Frédéric Arenou, P. Ramos, Robert G. Mann, Annie C. Robin, J. C. Segovia, M. Barros, Hector Canovas, D. L. Harrison, Y. Lasne, L. Noval, David Hobbs, E. F. del Peloso, P. Castro Sampol, Yves Fremat, F. De Luise, Daniel Michalik, P. J. Richards, L. Karbevska, N. Hładczuk, K. Kruszyńska, T. Boch, Sofia Randich, A. G. A. Brown, C. Pagani, L. Martin Polo, M. Ramos-Lerate, Krzysztof Nienartowicz, Eduard Masana, E. Racero, E. Fraile, Marc Audard, N. Robichon, Luciana Bianchi, G. Gracia-Abril, R. Santoveña, R. Haigron, N. Unger, Jérôme Berthier, Despina Hatzidimitriou, R. Gutiérrez-Sánchez, M. Fabrizio, I. Gonzalez-Santamaria, A. Dapergolas, P. Panuzzo, Benoit Carry, Francesca Figueras, R. Blomme, Elmé Breedt, D. Munoz, Diego Bossini, G. Busso, D. Katz, Simon Hodgkin, Ennio Poretti, N. Brouillet, Marco Castellani, Nicholas Rowell, Arnaud Siebert, M. Romero-Gómez, Shay Zucker, W. van Reeven, A. Kochoska, G. Giuffrida, Eva Sciacca, T. Carlucci, L. M. Sarro, M. I. Carnerero, Amina Helmi, D. Garabato, B. Holl, Michele Bellazzini, L. Rohrbasser, Teresa Antoja, J. Torra, Thomas Hilger, Pedro García-Lario, Gérard Jasniewicz, Enrique Solano, S. G. Baker, W. J. Cooper, F. Royer, S. Accart, George M. Seabroke, João Alves, Emese Plachy, C. Nicolas, Silvio Leccia, N. Cheek, Uwe Lammers, Ramachrisna Teixeira, Techniche Universtât Desden, 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, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Lund Observatory, Lund University [Lund], Zentrum für astronomie, Universität Heidelberg [Heidelberg], Department of nuclear medicine, Haukeland University Hospital, University of Bergen (UiB)-University of Bergen (UiB), Merck Serono S.A [Geneva Research Center], Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), 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 de Paris (UP), Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), 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), Universität Heidelberg [Heidelberg] = Heidelberg University, Laboratoire d'études spatiales et d'instrumentation en astrophysique = Laboratory of Space Studies and Instrumentation in Astrophysics (LESIA), 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), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Planetary-system research, Department of Physics, Particle Physics and Astrophysics, Gaia Collaboration, Unidad de Excelencia Científica María de Maeztu Instituto de Ciencias del Cosmos Universidad de Barcelona, MDM-2014-0369, Centro de Excelencia Científica Severo Ochoa, Instituto de Ciencias del Cosmos de la Universidad de Barcelona, SEV2015-0493, Deliste, J. B. [0000-0001-5844-9888], Sozzeti, A. [0000-0002-7504-365X], Forderung der wissenschaftlichen Forschung (FWF), Belgian federal Science Policy Office (BELSPO), Hertha Firnberg Programme, Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Comite Francais d'Evaluation de la Cooperation Universitaire et Scientifique avec le Bresil (COFECUB), National Natural Science Foundation of China (NSFC), China Scholarship Council (CSC), European Commission (EC), European Research Council (ERC), Hungarian National Research, Development, and Innovation Office (NKFIH), Science Foundation Ireland (SFI), Israel Science Foundation (ISF), Agenzia Spaziale Italiana (ASI), Istituto Nazionale di Astrofisica (INAF), Netherlands Research School for Astronomy (NOVA), Fundacao para a Ciencia e a Tecnologia (FCT), Agencia Estatal de Investigación (AEI), European Space Agency (ESA), Centre National D'Etudes Spatiales (CNES), Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), Narodowe Centrum Nauki (NCN), Slovenian Research Agency, Swedish National Space Agency (SNSA), United Kingdom Science and Technology Facilities Council (STFC), Universitat de Barcelona (UB), Generalitat de Catalunya, Xunta de Galicia, Universidad de Cantabria, ITA, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), Astronomy, and Kapteyn Astronomical Institute
Subjects: Data Analysis, Solar System, Astronomy, kinematics and dynamics, virgo cluster, Astrophysics, 01 natural sciences, bar, Astronomi, astrofysik och kosmologi, large-magellanic-cloud, Methods, Astronomy, Astrophysics and Cosmology, 010303 astronomy & astrophysics, Physics, Astrophysics of Galaxies, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Astrophysics::Instrumentation and Methods for Astrophysics, Astrometry, VIRGO CLUSTER, Kinematics and Dynamics, Amplitude, kinematics, Physical Sciences, MILKY-WAY, astrometry, Galaxy: kinematics and dynamics, PROPER MOTION, Proper motion, perturbation, proper motions, reference systems, methods: data analysis, Astrophysics - Astrophysics of Galaxies, FOS: Physical sciences, Context (language use), proper motion, Astronomy & Astrophysics, MASS, Computer Science::Digital Libraries, Gravitational potential, Acceleration, Settore FIS/05 - Astronomia e Astrofisica, 0103 physical sciences, data analysis [methods], Vector spherical harmonics, KINEMATICS, distance, milky-way, Science & Technology, PERTURBATION, 010308 nuclear & particles physics, Astronomy and Astrophysics, kinematics and dynamics [Galaxy], 115 Astronomy, Space science, Physics::History of Physics, BAR, Galaxy, Space and Planetary Science, [SDU]Sciences of the Universe [physics], Astrophysics of Galaxies (astro-ph.GA), DISTANCE, mass, LARGE-MAGELLANIC-CLOUD
Abstract: Context. Gaia Early Data Release 3 (Gaia EDR3) provides accurate astrometry for about 1.6 million compact (QSO-like) extragalactic sources, 1.2 million of which have the best-quality five-parameter astrometric solutions., Aims. The proper motions of QSO-like sources are used to reveal a systematic pattern due to the acceleration of the solar systembarycentre with respect to the rest frame of the Universe. Apart from being an important scientific result by itself, the acceleration measured in this way is a good quality indicator of the Gaia astrometric solution., Methods. Theeffect of the acceleration was obtained as a part of the general expansion of the vector field of proper motions in vector spherical harmonics (VSH). Various versions of the VSH fit and various subsets of the sources were tried and compared to get the most consistent result and a realistic estimate of its uncertainty. Additional tests with the Gaia astrometric solution were used to get a better idea of the possible systematic errors in the estimate., Results. Our best estimate of the acceleration based on Gaia EDR3 is (2.32 +/- 0.16) x 10(-10) m s(-2) (or 7.33 +/- 0.51 km s(-1) Myr-1) towards alpha = 269.1 degrees +/- 5.4 degrees, delta = -31.6 degrees +/- 4.1 degrees, corresponding to a proper motion amplitude of 5.05 +/- 0.35 mu as yr(-1). This is in good agreement with the acceleration expected from current models of the Galactic gravitational potential. We expect that future Gaia data releases will provide estimates of the acceleration with uncertainties substantially below 0.1 mu as yr(-1).
Published: 2020
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256. Mechanically Interlocked Carbon Nanotubes as a Stable Electrocatalytic Platform for Oxygen Reduction

Author: Wielend D., Vera-Hidalgo M., Seelajaroen H., Sariciftci N.S., Pérez E.M., Whang D.R. and Funding from the European Union (ERC-Starting Grant: 307609 and Proof-of-Concept: 842606), MINECO (CTQ2017-86060-P), and the Comunidad de Madrid (Grant: MAD2D-CM program S2013/MIT-3007) is gratefully acknowledged. IMDEA Nanociencia acknowledges support from the 'Severo Ochoa' Programme for Centres of Excellence in R&D (MINECO, Grant: SEV-2016-0686). The authors gratefully acknowledge financial support from the Austrian Science Foundation (FWF) through the Wittgenstein Prize for Prof. N.S.S. (Z222-N19). The authors also thank Dr. Dogukan Hazar Apaydin for the initial help regarding the HO quantification method and evaporated AQ thin films. 2 2
Published: 2020

257. Genetic Tools to Study Cardiovascular Biology

Author: Rui Benedito, Irene Garcia-Gonzalez, Severin Mühleder, Macarena Fernández-Chacón, European Research Council, Ministerio de Ciencia e Innovación (España), Fundación ProCNIC, Fundación La Caixa, FWF Austrian Science Fund, and Austrian Scence Fund
Subjects: 0301 basic medicine, Physiology, media_common.quotation_subject, mosaics, ved/biology.organism_classification_rank.species, genetic tools, Computational biology, Review, Molecular resolution, Clonal analysis, lcsh:Physiology, 03 medical and health sciences, Genetic engineering, 0302 clinical medicine, Genetic resources, Physiology (medical), Model organism, Function (engineering), media_common, clonal analysis, lcsh:QP1-981, ved/biology, cardiovascular, transgenics, imaging, Cre, barcoding, 3. Good health, 030104 developmental biology, 030217 neurology & neurosurgery
Abstract: Progress in biomedical science is tightly associated with the improvement of methods and genetic tools to manipulate and analyze gene function in mice, the most widely used model organism in biomedical research. The joint effort of numerous individual laboratories and consortiums has contributed to the creation of a large genetic resource that enables scientists to image cells, probe signaling pathways activities, or modify a gene function in any desired cell type or time point, à la carte. However, as these tools significantly increase in number and become more sophisticated, it is more difficult to keep track of each tool's possibilities and understand their advantages and disadvantages. Knowing the best currently available genetic technology to answer a particular biological question is key to reach a higher standard in biomedical research. In this review, we list and discuss the main advantages and disadvantages of available mammalian genetic technology to analyze cardiovascular cell biology at higher cellular and molecular resolution. We start with the most simple and classical genetic approaches and end with the most advanced technology available to fluorescently label cells, conditionally target their genes, image their clonal expansion, and decode their lineages. RB is supported by the European Research Council (ERC-2014-StG-638028), the Centro Nacional de Investigaciones Cardiovasculares (CNIC), and the Ministerio de Ciencia y Innovación (MCIN: SAF2017-89299-P). The CNIC is supported by MCIN, the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (SEV-2015-0505). IG-G and MF-C were supported by PhD fellowships from Fundación La Caixa (CX-SO- 16-1 and CX_E-2015-01, respectively). SM was funded by the Austrian Science Fund (FWF) project J4358. Sí
Published: 2020

258. A fully human anti-BMP6 antibody reduces the need for erythropoietin in rodent models of the anemia of chronic disease

Author: Chiara Volani, Dominik Wolf, Verena Petzer, Stephanie Arndt, Sieghart Sopper, Markus Seifert, Sylvia Berger, Richard Hilbe, Christa Pfeifhofer-Obermair, Natascha Brigo, Alexander Hoffmann, Felix Böhm, Anja K. Bosserhoff, Jonathan Papworth, Lara Valente de Souza, Léon Kautz, Laura von Raffay, Volker Germaschewski, Matthew Wake, Igor Theurl, Luke Bayliss, Cecilia Deantonio, Malte Asshoff, Manfred Nairz, Egon Demetz, Piotr Tymoszuk, Prunelle Perrier, Philipp Grubwieser, Joana Carvalho, Stefanie Dichtl, Guenter Weiss, Department of Internal Medicine, Innsbruck Medical University, Innsbruck, Austria., Med Univ Innsbruck, Dept Internal Med 5, Hematol & Oncol, Innsbruck, Austria, Kymab Ltd, Cambridge, England, Med Univ Innsbruck, Christian Doppler Lab Iron Metab & Anemia Res, Innsbruck, Austria, Univ Med Ctr Regensburg, Dept Dermatol, Regensburg, Germany, Friedrich Alexander Univ Erlangen Nurnberg, Inst Biochem, Emil Fischer Ctr, Erlangen, Germany, Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ Clin Bonn, Internal Med 3, Oncol Oncol Immunooncol & Rheumatol, Bonn, Germany, doctoral college project (W1253 HOROS), Austrian Research Funds (FWF) Project (P 28302), Verein zur Forderung von Forschung und Weiterbildung in Infektiologie und Immunologie, Innsbruck, Christian Doppler Society, Austria, Krebshilfe Tirol project (15024), and Austrian Society of Hematology and Medical Oncology (OeGHO)
Subjects: Darbepoetin alfa, Bone Morphogenetic Protein 6, Ferroportin, Muscle Proteins, Pharmacology, Biochemistry, Mice, Random Allocation, 0302 clinical medicine, Bone Marrow, hemic and lymphatic diseases, Cation Transport Proteins, Erythroid Precursor Cells, 0303 health sciences, biology, Polysaccharides, Bacterial, Antibodies, Monoclonal, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Anemia, Drug Synergism, Hematology, Hep G2 Cells, Recombinant Proteins, 3. Good health, 030220 oncology & carcinogenesis, Erythropoiesis, Cytokines, medicine.drug, Anemia of chronic disease, Iron, Immunology, 03 medical and health sciences, Red Cells, Iron, and Erythropoiesis, Hepcidin, medicine, Animals, Humans, Renal Insufficiency, Chronic, Erythropoietin, 030304 developmental biology, Dose-Response Relationship, Drug, business.industry, Arthritis, Cell Biology, medicine.disease, biology.protein, business
Abstract: Recombinant erythropoietin (EPO) and iron substitution are a standard of care for treatment of anemias associated with chronic inflammation, including anemia of chronic kidney disease. A black box warning for EPO therapy and concerns about negative side effects related to high-dose iron supplementation as well as the significant proportion of patients becoming EPO resistant over time explains the medical need to define novel strategies to ameliorate anemia of chronic disease (ACD). As hepcidin is central to the iron-restrictive phenotype in ACD, therapeutic approaches targeting hepcidin were recently developed. We herein report the therapeutic effects of a fully human anti-BMP6 antibody (KY1070) either as monotherapy or in combination with Darbepoetin alfa on iron metabolism and anemia resolution in 2 different, well-established, and clinically relevant rodent models of ACD. In addition to counteracting hepcidin-driven iron limitation for erythropoiesis, we found that the combination of KY1070 and recombinant human EPO improved the erythroid response compared with either monotherapy in a qualitative and quantitative manner. Consequently, the combination of KY1070 and Darbepoetin alfa resulted in an EPO-sparing effect. Moreover, we found that suppression of hepcidin via KY1070 modulates ferroportin expression on erythroid precursor cells, thereby lowering potentially toxic-free intracellular iron levels and by accelerating erythroid output as reflected by increased maturation of erythrocyte progenitors. In summary, we conclude that treatment of ACD, as a highly complex disease, becomes more effective by a multifactorial therapeutic approach upon mobilization of endogenous iron deposits and stimulation of erythropoiesis.
Published: 2019
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259. Hot topics in the mechanisms of pulmonary arterial hypertension disease: cancer-like pathobiology, the role of the adventitia, systemic involvement, and right ventricular failure

Author: Marlene Rabinovitch, Wolfgang M. Kuebler, Brian B. Graham, Norbert F. Voelkel, Grazyna Kwapiszewska, Elena A. Goncharova, Soni Savai Pullamsetti, Christophe Guignabert, Kurt R. Stenmark, Edda Spiekerkoetter, Harm Jan Bogaard, Division of Pulmonary and Critical Care Medicine [Stanford, CA, USA] (Cardiovascular Institute), Stanford University-Stanford Cardiovascular Institute-Wall Center for Pulmonary Vascular Disease [Stanford, CA, USA], Division of Pulmonary, Allergy and Critical Care Medicine [Pittsburgh, PA, États-Unis], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Bioengineering [Pittsburgh, PA, USA], University of Pittsburgh (PITT), Université Paris-Saclay, Université Paris-Sud [Le Kremlin-Bicêtre] (Faculté de Médecine), Hypertension arterielle pulmonaire physiopathologie et innovation thérapeutique, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre chirurgical Marie Lannelongue, Department of Pediatrics [Denver, CO, USA] (School of Medicine), University of Colorado [Denver], Cardio Vascular Pulmonary Research Lab [Denver, CO, USA], Ludwig Boltzmann Institute for Lung Vascular Research [Graz], Stanford Cardiovascular Institute, Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU), VU University Medical Center [Amsterdam], Pulmonary Sciences and Critical Care [Denver, CO, USA] (School of Medicine), Max Planck Institute for Heart and Lung Research (MPI-HLR), Max-Planck-Gesellschaft, University of Giessen and Marburg Lung Center (UGMLC), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Keenan Research Centre for Biomedical Science [Toronto, ON, Canada], Li Ka Shing Knowledge Institute [Toronto, ON, Canada]-St. Michael’s Hopsital [Toronto, ON, Canada], Department of Surgery [Toronto, ON, Canada], University of Toronto, Department of Physiology [Toronto, ON, Canada], Université de Toronto [Canada]-Mount Sinai Hospital [Toronto, Canada] (MSH)-Lunenfeld-Tanenbaum Research Institute [Toronto, Canada], ES: NHLBI R01 HL128734, Department of Defense PR161256, Wall Center for Pulmonary Vascular Disease Stanford, Pulmonary Hypertension Association Career Development Grant. EAG: NIH/NHLBI R01HL130261, 2R01HL113178. CG: ANR-16-CE17-0014 (TAMIRAH), National Agency for Research (ANR), DEQ20150331712 (Equipe FRM 2015), Fondation de la Recherche Me´dicale (FRM), De´partement HospitaloUniversitaire Thorax Innovation (TORINO), Fonds de Dotation Recherche en Sante´ Respiratoire–(FRSR)–Fondation du Souffle (FdS), French Pulmonary Hypertension Association (HTAP France). KS: NIH/NHLBI: PPG P01 HL014985, 1R01HL125827, and DoD PR140977. GK: FWF P27848. MR: R01 HL074186, R01 HL087118, R01 HL122887, R01 HL138473, P01 HL108797, R24 HL123767, K12 HL120001. NV: none. HJB: Dutch Cardiovascular Alliance, PHAEDRA-IMPACT Consortium. BG: NHLBI P01HL014985, R03HL133306, and R01HL135872. SSP: The Max Planck Society, DFG, SFB 1213 (Project A01, A05), and the Excellence Cluster 147 CardioPulmonary System (ECCPS, EXC 147). WMK: HSFC G-16-00013171, DFG KU1218/9-1, DZHK, DZL, and ORF SCORR (RE07-086)., ANR-16-CE17-0014,TAMIRAH,Cibler l'activation anormale du récepteur des minéralocorticoïdes dans l'Hypertension Artérielle Pulmonaire : Une étude translationnelle vers un traitement(2016), Guignabert, Christophe, Cibler l'activation anormale du récepteur des minéralocorticoïdes dans l'Hypertension Artérielle Pulmonaire : Une étude translationnelle vers un traitement - - TAMIRAH2016 - ANR-16-CE17-0014 - AAPG2016 - VALID, Centre Chirurgical Marie Lannelongue (CCML)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Toronto-Mount Sinai Hospital [Toronto, Canada] (MSH)-Lunenfeld-Tanenbaum Research Institute [Toronto, Canada], Pulmonary medicine, and ACS - Pulmonary hypertension & thrombosis
Subjects: 0301 basic medicine, Pulmonary and Respiratory Medicine, Neointima, medicine.medical_specialty, Systemic disease, lcsh:Diseases of the circulatory (Cardiovascular) system, vascular remodeling, [SDV]Life Sciences [q-bio], Disease, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 030204 cardiovascular system & hematology, Cardiorespiratory Medicine and Haematology, Cardiovascular, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 03 medical and health sciences, 0302 clinical medicine, Rare Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Internal medicine, Adventitia, right ventricle function and dysfunction, Medicine, 2.1 Biological and endogenous factors, Aetiology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Lung, lcsh:RC705-779, business.industry, Cancer, lcsh:Diseases of the respiratory system, Leading Edge Science, medicine.disease, experimental pulmonary hypertension, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, medicine.anatomical_structure, Hot topics, Ventricle, lcsh:RC666-701, Cardiology, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Right ventricular failure, Pro-Con debate, business
Abstract: International audience; In order to intervene appropriately and develop disease-modifying therapeutics for pulmonary arterial hypertension, it is crucial to understand the mechanisms of disease pathogenesis and progression. We herein discuss four topics of disease mechanisms that are currently highly debated, yet still unsolved, in the field of pulmonary arterial hypertension. Is pulmonary arterial hypertension a cancer-like disease? Does the adventitia play an important role in the initiation of pulmonary vascular remodeling? Is pulmonary arterial hypertension a systemic disease? Does capillary loss drive right ventricular failure? While pulmonary arterial hypertension does not replicate all features of cancer, anti-proliferative cancer therapeutics might still be beneficial in pulmonary arterial hypertension if monitored for safety and tolerability. It was recognized that the adventitia as a cell-rich compartment is important in the disease pathogenesis of pulmonary arterial hypertension and should be a therapeutic target, albeit the data are inconclusive as to whether the adventitia is involved in the initiation of neointima formation. There was agreement that systemic diseases can lead to pulmonary arterial hypertension and that pulmonary arterial hypertension can have systemic effects related to the advanced lung pathology, yet there was less agreement on whether idiopathic pulmonary arterial hypertension is a systemic disease per se. Despite acknowledging the limitations of exactly assessing vascular density in the right ventricle, it was recognized that the failing right ventricle may show inadequate vascular adaptation resulting in inadequate delivery of oxygen and other metabolites. Although the debate was not meant to result in a definite resolution of the specific arguments, it sparked ideas about how we might resolve the discrepancies by improving our disease modeling (rodent models, large-animal studies, studies of human cells, tissues, and organs) as well as standardization of the models. Novel experimental approaches, such as lineage tracing and better three-dimensional imaging of experimental as well as human lung and heart tissues, might unravel how different cells contribute to the disease pathology.
Published: 2019
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260. The sum-of-digits function on arithmetic progressions

Author: Lukas Spiegelhofer, Thomas Stoll, Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and FWF project F5502-N26 (L. Spiegelhofer)
Subjects: arithmetic progression, 11A63, MathematicsofComputing_GENERAL, Binary number, 0102 computer and information sciences, 11B25, Digit sum, 01 natural sciences, Base (group theory), Integer, Subsequence, FOS: Mathematics, Discrete Mathematics and Combinatorics, sum-of-digits function, Number Theory (math.NT), 0101 mathematics, Arithmetic, 11A63, 11B25, ComputingMilieux_MISCELLANEOUS, Mathematics, Algebra and Number Theory, Mathematics::Combinatorics, Mathematics::Commutative Algebra, Mathematics - Number Theory, 010102 general mathematics, Function (mathematics), Cusick's conjecture, [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT], 010201 computation theory & mathematics, Arithmetic progression, Tuple
Abstract: Let $s_2$ be the sum-of-digits function in base $2$, which returns the number of non-zero binary digits of a nonnegative integer $n$. We study $s_2$ alon g arithmetic subsequences and show that --- up to a shift --- the set of $m$-tuples of integers that appear as an arithmetic subsequence of $s_2$ has full complexity., 6 pages
Published: 2019
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261. Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure

Author: Sebastian Will, Maria Waldl, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler, Institute for Theoretical Chemistry [Vienna] (ITC), University of Vienna [Vienna], Algorithms and Models for Integrative BIOlogy (AMIBIO), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Department of Computer Science [Leipzig], Universität Leipzig [Leipzig], Bioinformatics Group, University of Freiburg [Freiburg], and Partial financial support by the German Federal Ministry of Education and Research (BMBF, project no. 031A538A, de.NBI-RBC and 031L0164C, RNAproNET) and the Austrian science fund (FWF project I 2874 'Prediction of RNA-RNA interactions' and doctoral college W 1207 'RNA Biology') is gratefully acknowledged.
Subjects: 0301 basic medicine, Physics, Base pair, 0206 medical engineering, RNA, incongruent evolution, Rfam, RNA alignment, 02 engineering and technology, Computational biology, RNA secondary structure, 4-way alignment, Conserved sequence, Nucleic acid secondary structure, 03 medical and health sciences, 030104 developmental biology, RNA Sequence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Protein secondary structure, 020602 bioinformatics, Sequence (medicine)
Abstract: International audience; RNA molecules may be subject to independent selection pressures on sequence and structure. This can, in principle, lead to the preservation of structural features without maintaining the exact position on the conserved sequence. Consequently, structurally analogous base pairs are no longer formed by homologous bases, and homologous nucleotides do not preserve their structural context. In other words, the evolution of sequence and structure is incongruent. We model this phenomenon by introducing bi-alignments, defined as a pair of alignments, one modeling sequence homology; the other, structural homology, together with an alignment of the two alignments that models the relative shifts between conserved sequence and conserved structure. Bialignments therefore form a special class of four-way alignments. A preliminary survey of the Rfam database suggests that incongruent evolution is not a very rare phenomenon among structured ncRNAs and RNA elements.
Published: 2019
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262. Biocompatible Glyconanoparticles by Grafting of Sophorolipid Monolayers on Monodisperse Iron Oxide Nanoparticles

Author: Viviana Cristiglio, Niki Baccile, Isabelle Grillo, Andrea Scheberl, Krishna Chaithanya Batchu, Erik Reimhult, Andrea Lassenberger, Daniel Hermida-Merino, Department of Nanobiotechnology [Vienna], Department of Nanobiotechnology, University of Natural Resources and Life Sciences (BOKU)-University of Natural Resources and Life Sciences (BOKU), Institut Laue-Langevin (ILL), ILL, European Synchrotron Radiation Facility (ESRF), Spectroscopie, Modélisation, Interfaces pour L'Environnement et la Santé (LCMCP-SMiLES), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Laue-Langevin (ILL), Grenoble, France, under the experiment number 9-12-481 (D33, D16 beamlines), European Synchrotron Radiation Facility (ESRF), Grenoble, France, under the experiment number SC-4419., and Austrian Science Fund (FWF) project I 3064
Subjects: Thermogravimetric analysis, Dispersity, small angle X-ray scattering, Biomedical Engineering, core-shell nanoparticle, 02 engineering and technology, small angle neutron scattering, 010402 general chemistry, 01 natural sciences, Biomaterials, Metal, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Amphiphile, Monolayer, iron oxide nanoparticle, colloidal stability, glyconanoparticle, Ligand, Sophorolipid, nanoparticle surface functionalization, Biochemistry (medical), General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, sophorolipid, chemistry, Chemical engineering, visual_art, visual_art.visual_art_medium, lipid shell, 0210 nano-technology, Iron oxide nanoparticles
Abstract: International audience; This work presents synthesis and characterization of sophorolipid-coated monodisperse iron oxide nanoparticles. Sophorolipids are biological glycosylated amphiphiles produced by the yeast S. bombicola. In their open acidic form, sophorolipids have been used as surface stabilizing agent for metal and metal oxide nanoparticles but with poor control over size and structural properties. In this work, the COOH function of sophorolipids (SL) was modified with nitrodopamine (NDA), a catechol known for its high affinity to iron ions. The resulting new form of sophorolipid-nitrodopamide (SL-NDA) was used as surface ligand for monodisperse iron oxide nanoparticles. We show, by a combination of thermogravimetric analysis and small angle X-ray and neutron scattering, that iron oxide nanoparticles (IONP) are stabilized by a single, high-density SL-NDA layer, which results in excellent colloidal stability under biologically relevant conditions such as high protein and salt concentration. The IONP grafted with SL-NDA showed negligible uptake and no cytotoxicity tested on two representative cell lines. Thus, they reveal the potential of sophorolipids as stable and non-toxic surface coatings for IONP-based biomedical and biotechnological applications.
Published: 2019
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263. The Involution Tool for Accurate Digital Timingand Power Analysis

Author: Jürgen Maier, Ulrich Schmid, Matthias Függer, Daniel Öhlinger, Institute of Computer Engineering [Vienna], Vienna University of Technology (TU Wien), Centre National de la Recherche Scientifique (CNRS), Laboratoire Spécification et Vérification [Cachan] (LSV), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Université Paris-Saclay, Modeling and Exploitation of Interaction and Concurrency (MEXICO), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), This research was partially funded by the Austrian Science Fund (FWF) projects SIC (P26436) and RiSE (S11405), projects FREDDA (ANR-17-CE40-0013) and DEPEC MODE (Departement STIC), and by DigiCosme(working group HicDiesMeus), and ANR-17-CE40-0013,FREDDA,Méthodes formelles pour la conception d'algorithmes distribués(2017)
Subjects: [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Computer science, Glitch propagation, NAND gate, 02 engineering and technology, Integrated circuit, 01 natural sciences, law.invention, Computer Science::Hardware Architecture, law, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, Involution (philosophy), Digital timing simulation, 010302 applied physics, Combinational logic, Pulse degradation, Design tools, Static timing analysis, NAND logic, 020202 computer hardware & architecture, Tree (data structure), [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Delay models, Inverter, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Algorithm
Abstract: International audience; We introduce the prototype of a digital timing simulation and power analysis tool for integrated circuit (Involution Tool) which employs the involution delay model introduced by Függer et al. at DATE'15. Unlike the pure and inertial delay models typically used in digital timing analysis tools, the involu-tion model faithfully captures pulse propagation. The presented tool is able to quantify for the first time the accuracy of the latter by facilitating comparisons of its timing and power predictions with both SPICE-generated results and results achieved by standard timing analysis tools. It is easily customizable, both w.r.t. different instances of the involution model and different circuits, and supports automatic test case generation, including parameter sweeping. We demonstrate its capabilities by providing timing and power analysis results for three circuits in varying technologies: an inverter tree, the clock tree of an open-source processor, and a combinational circuit that involves multi-input NAND gates. It turns out that the timing and power predictions of two natural types of involution models are significantly better than the predictions obtained by standard digital simulations for the inverter tree and the clock tree. For the NAND circuit, the performance is comparable but not significantly better. Our simulations thus confirm the benefits of the involution model, but also demonstrate shortcomings for multi-input gates.
Published: 2019
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264. Hopf dreams

Author: Bergeron, Nantel, Ceballos, Cesar, Pilaud, Vincent, Department of Mathematics and Statistics [Toronto], York University [Toronto], University of Vienna [Vienna], Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Nantel Bergeron was supported by NSERC and a York Research Chair.Cesar Ceballos was supported by the Austrian Science Foundation FWF, grant F 5008-N15, in the framework of the Special Research Program Algorithmic and Enumerative Combinatorics.Vincent Pilaud was supported by ANR SC3A 15 CE40 0004 01 and CAPPS 17 CE40 0018.Project partially supported by the project 'Austria/France Scientific & Technological Cooperation' (Austrian BMWFW Project No. FR 10/2018 and French PHC Amadeus 2018 Project No. 39444WJ)., ANR-15-CE40-0004,SC3A,Surfaces, Catégorification et Combinatoire des Algèbres Amassées(2015), ANR-17-CE40-0018,CAPPS,Analyse Combinatoire de Polytopes et de Subdivisions Polyédrales(2017), Pilaud, Vincent, Surfaces, Catégorification et Combinatoire des Algèbres Amassées - - SC3A2015 - ANR-15-CE40-0004 - AAPG2015 - VALID, and Analyse Combinatoire de Polytopes et de Subdivisions Polyédrales - - CAPPS2017 - ANR-17-CE40-0018 - AAPG2017 - VALID
Subjects: [MATH.MATH-CO] Mathematics [math]/Combinatorics [math.CO], [INFO.INFO-DM] Computer Science [cs]/Discrete Mathematics [cs.DM], Pipe dream, Multivariate diagonal harmonics, Tamari lattice, Mathematics::Quantum Algebra, Mathematics::Rings and Algebras, [MATH.MATH-CO]Mathematics [math]/Combinatorics [math.CO], [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Hopf algebra
Abstract: We introduce a Hopf algebra structure on a family of reduced pipe dreams with a natural surjection onto a commutative Hopf algebra of permutations. We then study three Hopf subalgebras of permutations whose preimages by the surjection yield three relevant Hopf subalgebras of pipe dreams. The first is the Loday-Ronco Hopf algebra on binary trees, the second is related to a special family of lattice walks on the quarter plane, and the third is a Hopf algebra on ν-trees related to ν-Tamari lattices. The latter motivates a new notion of Hopf chains in the Tamari lattice with applications in the theory of multivariate diagonal harmonics., Nous introduisons une structure d’algèbre de Hopf sur une famille d’arrangements de tuyaux, avec une surjection naturelle sur une algèbre de Hopf commutative de permutations. Nous étudions ensuite trois sous-algèbres de Hopf de permutations dont les préimages par la surjection donnent trois sous-algèbres de Hopf d’arrangements de tuyaux intéressantes. La première est l’algèbre de Hopf de Loday-Ronco sur les arbres binaires, la seconde est reliée à une famille spéciale de chemins dans le quart de plan, et la troisième est une algèbre de Hopf sur des ν-arbres reliée aux treillis de ν-Tamari. Cette dernière motive une nouvelle notion de chaînes de Hopf dans le treillis de Tamari, avec des applications à la théorie des harmoniques diagonaux multivariés.
Published: 2019

265. First Order Error Correction for Trimmed Quadrature in Isogeometric Analysis

Author: Felix Scholz, Bert Jüttler, Angelos Mantzaflaris, Institute of Applied Geometry [Linz], Johannes Kepler Universität Linz (JKU), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), AlgebRe, geOmetrie, Modelisation et AlgoriTHmes (AROMATH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-National and Kapodistrian University of Athens (NKUA), and The authors gratefully acknowledge the support provided by the Austrian Science Fund (FWF) through project NFN S11708 and by the European Research Council (ERC), project GA 694515.
Subjects: [INFO.INFO-SC]Computer Science [cs]/Symbolic Computation [cs.SC], Computer science, Line integral, MathematicsofComputing_NUMERICALANALYSIS, 010103 numerical & computational mathematics, Isogeometric analysis, 01 natural sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Quadrature (mathematics), 010101 applied mathematics, symbols.namesake, Taylor series, symbols, Gaussian quadrature, Trimming, Linear approximation, 0101 mathematics, Error detection and correction, Algorithm, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract: International audience; In this work, we develop a specialized quadrature rule for trimmed domains , where the trimming curve is given implicitly by a real-valued function on the whole domain. We follow an error correction approach: In a first step, we obtain an adaptive subdivision of the domain in such a way that each cell falls in a pre-defined base case. We then extend the classical approach of linear approximation of the trimming curve by adding an error correction term based on a Taylor expansion of the blending between the linearized implicit trimming curve and the original one. This approach leads to an accurate method which improves the convergence of the quadrature error by one order compared to piecewise linear approximation of the trimming curve. It is at the same time efficient, since essentially the computation of one extra one-dimensional integral on each trimmed cell is required. Finally, the method is easy to implement, since it only involves one additional line integral and refrains from any point inversion or optimization operations. The convergence is analyzed theoretically and numerical experiments confirm that the accuracy is improved without compromising the computational complexity.
Published: 2019
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266. Cold acclimation triggers lipidomic and metabolic adjustments in the spotted wing drosophila Drosophila suzukii (Matsumara)

Author: Hervé Colinet, Thomas Enriquez, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), This work has been funded by the SUZUKILL project (The French National Research Agency: ANR-15-CE21-0017 and the Austrian Science Fund, FWF:I 2604-B25)., ANR-15-CE21-0017,Suzukill,Gestion de la tolérance au froid et de la qualité des mouches, Drosophila suzukii, produites en masse pour faciliter la mise en place d'un contrôle biologique par les méthodes de lâchers d'insectes stériles et incompatibles(2015), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, 0301 basic medicine, Wing, biology, Physiology, Cold tolerance, Cold exposure, homeoviscous adaptation, Homeoviscous adaptation, cold tolerance, 15. Life on land, biology.organism_classification, 01 natural sciences, Cell biology, lipids, 010602 entomology, 03 medical and health sciences, 030104 developmental biology, Physiology (medical), Cold acclimation, metabolic profiles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Drosophila suzukii, Drosophila, thermal plasticity
Abstract: International audience; Chronic cold exposure is detrimental to chill susceptible insects that may accumulate chill injuries. To cope with deleterious effects of cold temperature, insects employ a variety of physiological strategies and metabolic adjustments, such as production of cryoprotectants, or remodeling of cellular membranes. Cold tolerance is a key element determining the fundamental niche of species. Because Drosophila suzukii is an invasive fruit pest, originating from East Asia, knowledge about its thermal biology is urgently needed. Physiological mechanisms underlying cold tolerance plasticity remain poorly understood in this species. Here, we explored metabolic and lipidomic modifications associated with the acquisition of cold tolerance in D. suzukii using Omics technologies (LC- and GC-MS/MS). In both cold-acclimated males and females, we observed physiological changes consistent with homeoviscous/homeophasic adaptation of membranes: reshuffling of phospholipid headgroups and increasing unsaturation rate of fatty acids. Modification of fatty acids unsaturation were also observed in triacylglycerides, whichwould likely increase accessibility of lipid reserves. At the metabolic level, we observed clear-cut differentiation of metabolic profiles withcold-acclimated metabotypes showing accumulation of several potential cryoprotectants (sugars and amino acids). Metabolic pathwayanalyses indicated a remodeling of various processes, including purine metabolism and aminoacyl tRNA biosynthesis. These data provide alarge-scale characterization of lipid rearrangements and metabolic pathway modifications in D. suzukii in response to cold acclimationand contribute to characterizing the strategies used by this species to modulate cold tolerance.
Published: 2019
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267. Cold acclimation triggers major transcriptional changes in Drosophila suzukii

Author: Thomas Enriquez, Hervé Colinet, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), ANR-15-CE21-0017, Agence Nationale de la Recherche, FWF I 2604-B25, Austrian Science Fund, ANR-15-CE21-0017,Suzukill,Gestion de la tolérance au froid et de la qualité des mouches, Drosophila suzukii, produites en masse pour faciliter la mise en place d'un contrôle biologique par les méthodes de lâchers d'insectes stériles et incompatibles(2015), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Unité d'Ecologie et de Biogéographie (UEB), Université Catholique de Louvain = Catholic University of Louvain (UCL), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Briand, Valerie
Subjects: 0106 biological sciences, Thermotolerance, Thermal plasticity, lcsh:QH426-470, Acclimatization, lcsh:Biotechnology, Carbohydrate metabolism, Biology, Cold tolerance, 01 natural sciences, Transcriptome, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene expression, Genetics, Cold acclimation, Animals, Drosophila Proteins, Homeostasis, Genes expression, Drosophila suzukii, Transcriptomics, Gene, Drosophila, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, fungi, Spotted wing drosophila, biology.organism_classification, Cell biology, Cold Temperature, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, lcsh:Genetics, Gene Expression Regulation, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, Biotechnology, Research Article
Abstract: Background Insects have the capacity to adjust their physiological mechanisms during their lifetime to promote cold tolerance and cope with sublethal thermal conditions, a phenomenon referred to as thermal acclimation. The spotted wing drosophila, Drosophila suzukii, is an invasive fruit pest that, like many other species, enhances its thermotolerance in response to thermal acclimation. However, little is known about the underlying mechanisms of this plastic response. Here, we promoted flies’ cold tolerance by gradually increasing acclimation duration (i.e. pre-exposure from 2 h to 9 days at 10 °C), and then compared transcriptomic responses of cold hardy versus cold susceptible phenotypes using RNA sequencing. Results Cold tolerance of D. suzukii increased with acclimation duration; the longer the acclimation, the higher the cold tolerance. Cold-tolerant flies that were acclimated for 9 days were selected for transcriptomic analyses. RNA sequencing revealed a total of 2908 differentially expressed genes: 1583 were up- and 1325 were downregulated in cold acclimated flies. Functional annotation revealed many enriched GO-terms among which ionic transport across membranes and signaling were highly represented in acclimated flies. Neuronal activity and carbohydrate metabolism were also enriched GO-terms in acclimated flies. Results also revealed many GO-terms related to oogenesis which were underrepresented in acclimated flies. Conclusions Involvement of a large cluster of genes related to ion transport in cold acclimated flies suggests adjustments in the capacity to maintain ion and water homeostasis. These processes are key mechanisms underlying cold tolerance in insects. Down regulation of genes related to oogenesis in cold acclimated females likely reflects that females were conditioned at 10 °C, a temperature that prevents oogenesis. Overall, these results help to understand the molecular underpinnings of cold tolerance acquisition in D. suzukii. These data are of importance considering that the invasive success of D. suzukii in diverse climatic regions relates to its high thermal plasticity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5745-7) contains supplementary material, which is available to authorized users.
Published: 2019
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268. Detecting the macroevolutionary signal of species interactions

Author: Marjorie G. Weber, Scott L. Nuismer, Carlos J. Melián, Daniele Silvestro, Cecilia S. Andreazzi, Ole Seehausen, Blake Matthews, Emma E. Goldberg, Florence Débarre, Seth M. Rudman, Ayana B. Martins, Jonathan P. Drury, Luke J. Harmon, Anita Narwani, Matthew W. Pennell, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), University of Idaho [Moscow, USA], Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Durham University, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Universidade Estadual de Campinas (UNICAMP), University of British Columbia (UBC), University of Pennsylvania [Philadelphia], University of Bern, University of Gothenburg (GU), Michigan State University System, National Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO)12089121450653, Swedish Research Council2015-04748, Knut & Alice Wallenberg Foundation, Austrian Science Fund (FWF)31003A_15346431003A_163338Z32Z0_166422, ANR-14-ACHN-0003,MOLA,Modélisation mathématique de l'adaptation locale.(2014), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Department of Fish Ecology and Evolution, Center of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Institute of Zoology, University of Bern, Université de Bern, Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), and Universidade Estadual de Campinas = University of Campinas (UNICAMP)
Subjects: 0106 biological sciences, 0301 basic medicine, Competitive Behavior, trait evolution, Genetic Speciation, [SDV]Life Sciences [q-bio], Diversification (marketing strategy), Macroevolution, Biology, phylogeny, Models, Biological, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Adaptive radiation, Genetic algorithm, Animals, Ecosystem, Ecology, Evolution, Behavior and Systematics, Coevolution, ComputingMilieux_MISCELLANEOUS, macroevolution, species interactions, Extinction, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], extinction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 15. Life on land, Complex dynamics, 030104 developmental biology, speciation, Evolutionary biology, coevolution, network, Trait, 570 Life sciences, biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad-scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, although the evidence for species interactions shaping macroevolution is strong, further work using integrative and model-based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space.
Published: 2019
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269. Intermicrobial interaction: Aspergillus fumigatus siderophores protect against competition by Pseudomonas aeruginosa

Author: Shajia R Ansari, Eric Déziel, David A. Stevens, Hubertus Haas, Anna-Maria Dietl, Gabriele Sass, California Institute for Medical Research (CIMR), Innsbruck Medical University [Austria] (IMU), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, This research was funded by John Flatley (CIMR no. 3770) to D.A.S., Child Health Research Institute, Stanford Transdisciplinary Initiatives Program (CIMR no. 3777) to D.A.S., Austrian Science Fund/Infect-ERA program (FWF grant I1616/Infect-ERA project AspMetNet) to H.H., and HOROS program (W1253) to A.-M.D., and The authors thank Marife Martinez for excellent technical support. The A. fumigatus mutant strain AfΔsidA was kindly provided by M. M. Moore, Department of Biological Sciences, Simon Fraser University, Burnaby, Canada.
Subjects: 0301 basic medicine, Siderophore, Siderophores, Pathology and Laboratory Medicine, medicine.disease_cause, Aspergillus fumigatus, chemistry.chemical_compound, Drug Metabolism, Microbial Physiology, Medicine and Health Sciences, skin and connective tissue diseases, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Fungal Pathogens, Multidisciplinary, Pyoverdine, biology, Chemistry, Microbial Growth and Development, Eukaryota, Pseudomonas Aeruginosa, Bacterial Pathogens, Aspergillus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fungal Molds, Medical Microbiology, Celastrol, Engineering and Technology, Medicine, Pathogens, Oligopeptides, Research Article, Heat Treatment, Science, 030106 microbiology, Mycology, Fungus, Microbiology, 03 medical and health sciences, Pseudomonas, Antibiosis, medicine, Pharmacokinetics, Microbial Pathogens, Pharmacology, Bacteria, Pseudomonas aeruginosa, Bacterial Growth, Organisms, Fungi, Wild type, Biofilm, Biology and Life Sciences, Bacteriology, biology.organism_classification, bacterial infections and mycoses, 030104 developmental biology, Manufacturing Processes, Biofilms, Bacterial Biofilms, Developmental Biology
Abstract: International audience; Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens frequently co-inhabiting immunocompromised patient airways, particularly in people with cystic fibrosis. Both microbes depend on the availability of iron, and compete for iron in their microenvironment. We showed previously that the P. aeruginosa siderophore pyoverdine is the main instrument in battling A. fumigatus biofilms, by iron chelation and denial of iron to the fungus. Here we show that A. fumigatus siderophores defend against anti-fungal P. aeruginosa effects. P. aeruginosa supernatants produced in the presence of wildtype A. fumigatus planktonic supernatants (Afsup) showed less activity against A. fumigatus biofilms than P. aeruginosa supernatants without Afsup, despite higher production of pyoverdine by P. aeruginosa. Supernatants of A. fumigatus cultures lacking the sidA gene (AfΔsidA), unable to produce hydroxamate siderophores, were less capable of protecting A. fumigatus biofilms from P. aeruginosa supernatants and pyoverdine. AfΔsidA biofilm was more sensitive towards inhibitory effects of pyoverdine, the iron chelator deferiprone (DFP), or amphothericin B than wildtype A. fumigatus biofilm. Supplementation of sidA-deficient A. fumigatus biofilm with A. fumigatus siderophores restored resistance to pyoverdine. The A. fumigatus siderophore production inhibitor celastrol sensitized wildtype A. fumigatus biofilms towards the anti-fungal activity of DFP. In conclusion, A. fumigatus hydroxamate siderophores play a pivotal role in A. fumigatus competition for iron against P. aeruginosa.
Published: 2019
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270. International external quality assurance of JAK2 V617F quantification

Author: Julia Asp, Marta Vorland, Anni Aggerholm, Lasse Kjær, Karl Haslam, Elisabeth Oppliger Leibundgut, Rajko Kusec, Karolina Matiakowska, Robert Kralovics, Frank Dicker, Alessandro Pancrazzi, Morten Andersen, Lars Palmqvist, Sylvie Hermouet, Margarida Coucelo, Bruno Cassinat, Filippo Navaglia, Andrey Sudarikov, Aleksandar Eftimov, Vibe Skov, Thomas Kielsgaard Kristensen, François Girodon, Laurence Lodé, Niels Pallisgaard, Eric Lippert, Jiri Schwarz, Marzena Wojtaszewska, Hajnalka Andrikovics, Guy Wayne Novotny, Dorota Link-Lenczowska, Susanna Akiki, Melanie J. Percy, Dina Naguib, Beatriz Bellosillo, Department of Clinical Chemistry and Transfusion Medicine [Gothenburg, Sweden] (Institute of Biomedicine), University of Gothenburg (GU)-Sahlgrenska Academy at University of Gothenburg [Göteborg], Department of Hematology [Roskilde, Denmark], Zealand University Hospital [Roskilde, Denmark], Department of Pathology [Barcelona, Spain], Hospital del Mar [Barcelona, Spain], Department of Pathology [Odense, Denmark], Odense University Hospital [Odense, Denmark], Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Munich Leukemia Laboratory [Munich, Germany], Institute of Hematology and Blood Transfusion [Prague, Czech Republic], Department of Hematology and Bone Marrow Transplantation [Poznan, Poland], Poznan University of Medical Sciences [Poznan, Poland], Department of Laboratory Medicine and Pathology [Doha, Qatar], Qatar Rehabilitation Institute (QRI)-Hamad Bin Khalifa Medical City (HBKM), Aarhus University Hospital, Rigshospitalet [Copenhagen], Copenhagen University Hospital, Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Bern [Bern, Switzerland] (University Hospital Bern ), Centro di Ricerca e Innovazione per le Malattie Mieloproliferative - CRIMM [ Florence, Italy], Haukeland University Hospital, University of Bergen (UiB), Central Hospital of Southern Pest [Budapest, Hungary], CeMM Research Center for Molecular Medicine [Vienna, Austria], Austrian Academy of Sciences (OeAW), Department of Internal Medicine I [Vienna, Austria], Medizinische Universität Wien = Medical University of Vienna, Service de Biologie Cellulaire [AP-HP, Hôpital Saint-Louis], Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Clinical Hematology Unit, Hospital Pediátrico [Coimbra, Portugal], Centro Hospitalar e Universitário [Coimbra], Center for Biomolecular Pharmaceutical Analyses [Skopje, Republic of Macedonia] (Faculty of Pharmacy), University of Ss. Cyril and Methodius in Skopje, Macedonia (UKIM), St James’s Hospital [Dublin, Ireland], Zagreb School of Medicine [Zagreb, Croatia] (Dubrava University Hospital), University of Zagreb, Molecular Diagnostics Laboratory [Krakow, Poland] (Hematology Diagnostics Department), Jagiellonian University Hospital [Krakow, Poland], Hématologie Biologique [CHU de Montpellier], Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Faculty of Medicine [Bydgoszcz, Poland], Nicolaus Copernicus University [Toruń], CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Department of Laboratory Medicine [Padova, Italy], University - Hospital of Padova [Italy], Department of Hematology & Department of Pathology [Herlev, Denmark] (Molecular Unit), Herlev and Gentofte Hospital-University of Copenhagen = Københavns Universitet (KU), Belfast City Hospital [Belfast, UK], National Research Center for Hematology [Moscow, Russia], Molecular Mechanisms of Chronic Inflammation in Hematological Diseases (CRCINA-ÉQUIPE 16), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Laboratoire d'Hematologie [CHU Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), RK acknowledges the support received by the Austrian Science Fund (FWF): F4702-B20 and P29018-B30., Bernardo, Elizabeth, Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Service de Biologie Cellulaire [Saint-Louis], Ss. Cyril and Methodius University in Skopje (UKIM), Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), Herlev and Gentofte Hospital-University of Copenhagen = Københavns Universitet (UCPH), and Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)
Subjects: Male, medicine.medical_specialty, Standardization, Quality Assurance, Health Care, Computer science, media_common.quotation_subject, Mutation, Missense, [SDV.CAN]Life Sciences [q-bio]/Cancer, 610 Medicine & health, Real-Time Polymerase Chain Reaction, Real-Time Polymerase Chain Reaction/standards, Myeloproliferative neoplasms, 03 medical and health sciences, External quality assurance, JAK2 V617F, Quantitative PCR, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, hemic and lymphatic diseases, medicine, Humans, Medical physics, Quality (business), Instrumentation (computer programming), Pathology, Molecular, media_common, Janus Kinase 2/genetics, business.industry, Amino acid substitution, Hematology, General Medicine, Janus Kinase 2, Amino Acid Substitution, Pathology, Molecular/standards, 030220 oncology & carcinogenesis, Female, business, Quality assurance, 030215 immunology
Abstract: IF 2.845; International audience; External quality assurance (EQA) programs are vital to ensure high quality and standardized results in molecular diagnostics. It is important that EQA for quantitative analysis takes into account the variation in methodology. Results cannot be expected to be more accurate than limits of the technology used, and it is essential to recognize factors causing substantial outlier results. The present study aimed to identify parameters of specific importance for JAK2 V617F quantification by quantitative PCR, using different starting materials, assays, and technical platforms. Sixteen samples were issued to participating laboratories in two EQA rounds. In the first round, 19 laboratories from 11 European countries analyzing JAK2 V617F as part of their routine diagnostics returned results from in-house assays. In the second round, 25 laboratories from 17 countries participated. Despite variations in starting material, assay setup and instrumentation the laboratories were generally well aligned in the EQA program. However, EQA based on a single technology appears to be a valuable tool to achieve standardization of the quantification of JAK2 V617F allelic burden.
Published: 2019
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271. Verification of Randomized Distributed Algorithms under Round-Rigid Adversaries

Author: Bertrand, Nathalie, Konnov, Igor, Lazic, Marijana, Widder, Josef, SUpervision of large MOdular and distributed systems (SUMO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Modeling and Verification of Distributed Algorithms and Systems (VERIDIS), Max-Planck-Institut für Informatik (MPII), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-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 Formal Methods (LORIA - FM), 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), Proof-oriented development of computer-based systems (MOSEL), Department of Formal Methods (LORIA - FM), 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), Vienna University of Technology (TU Wien), Supported by: the Austrian Science Fund (FWF) through the National Research Network RiSE (S11403 and S11405), project PRAVDA (P27722), and Doctoral College LogiCS (W1255-N23), and by the Vienna Science and Technology Fund (WWTF) through project APALACHE (ICT15-103).Part of this work was done while some authors were visiting the Simons Institute for the Theory of Computing., GRID5000, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), 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)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Max-Planck-Institut für Informatik (MPII), and Max-Planck-Gesellschaft-Max-Planck-Gesellschaft
Subjects: [INFO]Computer Science [cs]
Abstract: Experiments presented in this paper were carried out using the Grid5000 testbed, supported by a scientific interest group hosted by Inria and including CNRS, RENATER and several Universities as well as other organizations, see grid5000.fr; Randomized fault-tolerant distributed algorithms pose a number of challenges for automated verification: (i) parameterization in the number of processes and faults, (ii) randomized choices and probabilistic properties, and (iii) an unbounded number of asynchronous rounds. The combination of these challenges makes verification hard. Challenge (i) was recently addressed in the framework of threshold automata. We extend threshold automata to model randomized algorithms that perform an unbounded number of asynchronous rounds. For non-probabilistic properties, we show that it is necessary and sufficient to verify these properties under round-rigid schedules, that is, schedules where no process enters round r before all other processes finished round r −1. For almost-sure termination, we analyze these algorithms under round-rigid adversaries , that is, fair adversaries that only generate round-rigid schedules. This allows us to do compositional and inductive reasoning that reduces verification of the asynchronous multi-round algorithms to model checking of a one-round threshold automaton. We apply this framework to classic algorithms: Ben-Or's and Bracha's seminal consensus algorithms for crashes and Byzantine faults, 2-set agreement for crash faults, and RS-Bosco for the Byzantine case.
Published: 2019

272. Direct and indirect effects of flood regime on macroinvertebrate assemblages in a floodplain riverscape

Author: Christopher T. Robinson, Pierre C. M. Chanut, Chrystelle Gabbud, Thibault Datry, Department of Aquatic Ecology, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Institute of Integrative Biology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institute of Earth Surface Dynamics, Université de Lausanne (UNIL), Austrian Science Fund (FWF)407040_153942Swiss National Science Foundation (SNSF)407040_153942, Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)
Subjects: 0106 biological sciences, Hydrology, floodplain, geography, geography.geographical_feature_category, Ecology, Flood myth, Floodplain, Ecological succession, Flood regime, Stream invertebrates, 010604 marine biology & hydrobiology, flood regime, ecological succession, 15. Life on land, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, stream invertebrates, 13. Climate action, [SDE]Environmental Sciences, Ecology, Evolution, Behavior and Systematics, Earth-Surface Processes
Abstract: Floods are necessary for the functioning of floodplain ecosystems. Ultimately, flood effects on biota are spatially complex and unfold at various time scales. Yet, biodiversity conservation in regulated floodplains requires a sound quantification of the main pathways how floods affect riverine ecosystems. Here, we investigated the relative effects of flood frequency, magnitude, and time elapsed since the last flood on macroinvertebrate communities of 24 parafluvial habitats in the Maggia river floodplain, Switzerland. Parafluvial habitats were sampled seasonally over 1 year, and a combination of 2D hydrodynamic modelling and piecewise structural equation modelling was used to quantify the direct and indirect effects of local hydrological metrics on macroinvertebrate communities. We found that high flood frequency favoured rheophilic species (EPT taxa) over other groups (Coleoptera, Diptera) and prevented strong competitive interactions and competitive exclusion by maintaining low food resource levels. Importantly, we found that parafluvial habitats exhibited more lentic-like characteristics as time passed after a flood, which caused EPT taxa to be relatively more abundant and taxa richness higher immediately after flood disturbance. Lastly, overall taxa richness increased over time after a flood and even more so after larger floods. Our results suggest that variation in flood magnitude, frequency, and return period maximizes beta diversity within floodplain riverscapes due to the independent and spatially interactive responses of parafluvial habitats.
Published: 2019
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273. Cre mRNA Is Not Transferred by EVs from Endothelial and Adipose-Derived Stromal/Stem Cells during Vascular Network Formation

Author: Madhusudhan Reddy Bobbili, Wolfgang Holnthoner, Heinz Redl, Severin Mühleder, Johannes Oesterreicher, Jaana Schneider, Johannes Grillari, Andreas Spittler, Marianne Pultar, Eleni Priglinger, Austrian Research Promotion Agency, and FWF Austrian Science Fund
Subjects: 0301 basic medicine, Cell type, Cell signaling, Stromal cell, Adipose tissue, Cre recombinase, Cell Communication, Biology, Article, Catalysis, lcsh:Chemistry, Inorganic Chemistry, Extracellular Vesicles, 03 medical and health sciences, microRNA, Humans, RNA, Messenger, Physical and Theoretical Chemistry, lcsh:QH301-705.5, Molecular Biology, Spectroscopy, Cre-loxP system, Integrases, 030102 biochemistry & molecular biology, Organic Chemistry, Mesenchymal stem cell, Endothelial Cells, Mesenchymal Stem Cells, General Medicine, Coculture Techniques, endothelial cells, cell–cell communication, Computer Science Applications, Cell biology, MicroRNAs, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, Blood Vessels, Stem cell, extracellular vesicles, coculture
Abstract: Coculture systems employing adipose tissue-derived mesenchymal stromal/stem cells (ASC) and endothelial cells (EC) represent a widely used technique to model vascularization. Within this system, cell-cell communication is crucial for the achievement of functional vascular network formation. Extracellular vesicles (EVs) have recently emerged as key players in cell communication by transferring bioactive molecules between cells. In this study we aimed to address the role of EVs in ASC/EC cocultures by discriminating between cells, which have received functional EV cargo from cells that have not. Therefore, we employed the Cre-loxP system, which is based on donor cells expressing the Cre recombinase, whose mRNA was previously shown to be packaged into EVs and reporter cells containing a construct of floxed dsRed upstream of the eGFP coding sequence. The evaluation of Cre induced color switch in the reporter system via EVs indicated that there is no EV-mediated RNA transmission either between EC themselves or EC and ASC. However, since Cre mRNA was not found present in EVs, it remains unclear if Cre mRNA is generally not packaged into EVs or if EVs are not taken up by the utilized cell types. Our data indicate that this technique may not be applicable to evaluate EV-mediated cell-to-cell communication in an in vitro setting using EC and ASC. Further investigations will require a functional system showing efficient and specific loading of Cre mRNA or protein into EVs. This research was partially funded by the Austrian Research promotion agency. Severin Mühleder was funded by the Austrian Science Fund (FWF). Sí
Published: 2021
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274. KymoRod: a method for automated kinematic analysis of rod-shaped plant organs

Author: Herman Höfte, Renaud Bastien, Marjolaine Martin, David Legland, Alexis Peaucelle, Bruno Moulia, Stéphane Douady, Lucien Fregosi, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Matière et Systèmes Complexes (MSC (UMR_7057)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), ANR/FWF grant 'Pectosign', Laboratoire d'Excellence 'Saclay Plant Science', European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Matière et Systèmes Complexes (MSC)
Subjects: hypocotyle, 0106 biological sciences, 0301 basic medicine, Scale (ratio), Arabidopsis, Context (language use), Plant Science, Kinematics, analyse d'image, Curvature, Plant Roots, 01 natural sciences, mechano-sensing, 03 medical and health sciences, image analysis, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Growth rate, hypocotyl, Plant system, cellulose synthesis inhibitor, biology, Arabidopsis Proteins, arabidopsis thaliana, Cell Biology, root, biology.organism_classification, elongation growth, cellulose, cinématique, racine, 030104 developmental biology, kinematics, Biological system, mechanoreceptor, mécanorécepteur, technical advance, 010606 plant biology & botany
Abstract: A major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well-documented molecular scale and the organ scale by providing quantitative methods to study within-organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod-shaped organs that does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio-temporal information on curvature, growth anisotropy and relative elemental growth rate and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth-inhibiting drug or in a mechano-sensing mutant. The method is freely available as an intuitive and user-friendly Matlab application called KymoRod.
Published: 2016
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275. Elevated CO 2 maintains grassland net carbon uptake under a future heat and drought extreme

Author: Sébastien Devidal, Christophe Escape, Jean-François Soussana, Lionel Thiery, Nathalie Fromin, Jacques Roy, Catherine Picon-Cochard, Clément Piel, Marc Defossez, Angela Augusti, Alexandru Milcu, Olivier Darsonville, Marie-Lise Benot, Florence Volaire, Damien Landais, Michael Bahn, Olivier Ravel, Écotron Européen de Montpellier - UPS 3248, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universität Innsbruck [Innsbruck], Collège de Direction, Écotron Européen de Montpellier, Unité de recherche sur l'Ecosystème Prairial (UREP), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Collège de Direction (CODIR), ANR VALIDATE project, ECOTRONS Research Infrastructure ('Investissement d'Avenir' AnaEE-France ANR-11-INBS-0001), European FP7 ExpeER Transnational Access program, OAD WTZ-programme Austria-France, FWF Project P28572-B22., ANR-07-VULN-0011,VALIDATE,Vulnérabilité des prairies et des élevages au changement climatique et aux événements extrêmes.(2007), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), European Project: 266018,EC:FP7:KBBE,FP7-KBBE-2010-4,ANIMALCHANGE(2011), European Project: 262060,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,EXPEER(2010), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, Hot Temperature, 010504 meteorology & atmospheric sciences, Atmospheric sciences, 01 natural sciences, Grassland, Soil, chemistry.chemical_compound, Climate change, Milieux et Changements globaux, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, changement climatique, Multidisciplinary, geography.geographical_feature_category, écotron, Biological Sciences, Droughts, Carbon dioxide, élevation du gaz carbonique, [SDE.MCG]Environmental Sciences/Global Changes, chemistry.chemical_element, [object Object], Carbon Cycle, Carbon cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, climat extrème, Carbon fluxes, Grassland ecosystem, Ecosystem, 0105 earth and related environmental sciences, Hydrology, geography, flux de carbone, Carbon Dioxide, Extreme events, 15. Life on land, écosystème prairial, Carbon, Plant Leaves, croissance racinaire, chemistry, 13. Climate action, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Plant nutrition, Intensity (heat transfer), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, 010606 plant biology & botany
Abstract: International audience; Extreme climatic events (ECEs) such as droughts and heat waves are predicted to increase in intensity and frequency and impact the terrestrial carbon balance. However, we lack direct experimental evidence of how the net carbon uptake of ecosystems is affected by ECEs under future elevated atmospheric CO2 concentrations (eCO2). Taking advantage of an advanced controlled environment facility for ecosystem research (Ecotron), we simulated eCO2 and extreme cooccurring heat and drought events as projected for the 2050s and analyzed their effects on the ecosystem-level carbon and water fluxes in a C3 grassland. Our results indicate that eCO2 not only slows down the decline of ecosystem carbon uptake during the ECE but also enhances its recovery after the ECE, as mediated by increases of root growth and plant nitrogen uptake induced by the ECE. These findings indicate that, in the predicted near future climate, eCO2 could mitigate the effects of extreme droughts and heat waves on ecosystem net carbon uptake.
Published: 2016
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276. Spermine and Spermidine Priming against Botrytis cinerea Modulates ROS Dynamics and Metabolism in Arabidopsis

Author: Anis M. Limami, Wim Van den Ende, Henry Christopher Janse van Rensburg, KU Leuven (Laboratory of Molecular Plant Biology), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Agency project Fonds voor Wetenschappelijk Onderzoek (FWO) Vlaanderen (grant number G0F1517N)—Fonds zur Förderung der wissenschaftlichen Forschung (FWF) Austria (grant number I 3231-B25).
Subjects: 0106 biological sciences, 0301 basic medicine, Sucrose, Antifungal Agents, spermine, lcsh:QR1-502, Arabidopsis, Spermine, Nitrate Reductase, 01 natural sciences, Biochemistry, lcsh:Microbiology, chemistry.chemical_compound, Ascorbate Peroxidases, Plant Growth Regulators, Gene Expression Regulation, Plant, Plant Immunity, gamma-Aminobutyric Acid, Disease Resistance, Botrytis cinerea, reactive oxygen species, biology, Chemistry, Catalase, Botrytis, Asparagine, Life Sciences & Biomedicine, Peroxidase, Biochemistry & Molecular Biology, Phenylalanine, polyamines, Fructose, B. cinerea, Nitrate reductase, Article, 03 medical and health sciences, spermidine, mental disorders, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, priming, Molecular Biology, Plant Diseases, amino acids, Science & Technology, fungi, Hydrogen Peroxide, biology.organism_classification, Plant Leaves, Spermidine, Glucose, 030104 developmental biology, sugars, biology.protein, 010606 plant biology & botany
Abstract: Polyamines (PAs) are ubiquitous small aliphatic polycations important for growth, development, and environmental stress responses in plants. Here, we demonstrate that exogenous application of spermine (Spm) and spermidine (Spd) induced cell death at high concentrations, but primed resistance against the necrotrophic fungus Botrytis cinerea in Arabidopsis. At low concentrations, Spm was more effective than Spd. Treatments with higher exogenous Spd and Spm concentrations resulted in a biphasic endogenous PA accumulation. Exogenous Spm induced the accumulation of H2O2 after treatment but also after infection with B. cinerea. Both Spm and Spd induced the activities of catalase, ascorbate peroxidase, and guaiacol peroxidase after treatment but also after infection with B. cinerea. The soluble sugars glucose, fructose, and sucrose accumulated after treatment with high concentrations of PAs, whereas only Spm induced sugar accumulation after infection. Total and active nitrate reductase (NR) activities were inhibited by Spm treatment, whereas Spd inhibited active NR at low concentrations but promoted active NR at high concentrations. Finally, γaminobutyric acid accumulated after treatment and infection in plants treated with high concentrations of Spm. Phenylalanine and asparagine also accumulated after infection in plants treated with a high concentration of Spm. Our data illustrate that Spm and Spd are effective in priming resistance against B. cinerea, opening the door for the development of sustainable alternatives for chemical pesticides. ispartof: BIOMOLECULES vol:11 issue:2 ispartof: location:Switzerland status: published
Published: 2021
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277. Fluorescence-Based Nanoparticle Tracking Analysis and Flow Cytometry for Characterization of Endothelial Extracellular Vesicle Release

Author: Jaana Schneider, Wolfgang Holnthoner, Johannes Zipperle, Marianne Pultar, Johannes Grillari, Severin Mühleder, Johannes Oesterreicher, Austrian Research Promotion Agency, FWF Austrian Science Fund, Particle Metrix, Austrian Research Promotion Agency FFG, and Austrian Science Fund
Subjects: 0301 basic medicine, Nanoparticle tracking analysis, Cell Fractionation, Article, nano particle tracking, Fluorescence, Catalysis, Umbilical vein, Flow cytometry, lcsh:Chemistry, Inorganic Chemistry, Extracellular Vesicles, 03 medical and health sciences, 0302 clinical medicine, Cell-Derived Microparticles, Human Umbilical Vein Endothelial Cells, medicine, Humans, Secretion, Particle Size, Physical and Theoretical Chemistry, lcsh:QH301-705.5, Molecular Biology, Cells, Cultured, Spectroscopy, medicine.diagnostic_test, Chemistry, Cell Cycle, Organic Chemistry, Endothelial Cells, General Medicine, Extracellular vesicle, Flow Cytometry, Microvesicles, Computer Science Applications, Characterization (materials science), fluorescence triggering flow cytometry, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, Cell Tracking, 030220 oncology & carcinogenesis, Biophysics, Nanoparticles, Biomarkers
Abstract: As extracellular vesicles (EVs) have become a prominent topic in life sciences, a growing number of studies are published on a regular basis addressing their biological relevance and possible applications. Nevertheless, the fundamental question of the true vesicular nature as well as possible influences on the EV secretion behavior have often been not adequately addressed. Furthermore, research regarding endothelial cell-derived EVs (EndoEVs) often focused on the large vesicular fractions comprising of microvesicles (MV) and apoptotic bodies. In this study we aimed to further extend the current knowledge of the influence of pre-isolation conditions, such as cell density and conditioning time, on EndoEV release from human umbilical vein endothelial cells (HUVECs). We combined fluorescence nanoparticle tracking analysis (NTA) and the established fluorescence-triggered flow cytometry (FT-FC) protocol to allow vesicle-specific detection and characterization of size and surface markers. We found significant effects of cell density and conditioning time on both abundance and size distribution of EndoEVs. Additionally, we present detailed information regarding the surface marker display on EVs from different fractions and size ranges. Our data provide crucial relevance for future projects aiming to elucidate EV secretion behavior of endothelial cells. Moreover, we show that the influence of different conditioning parameters on the nature of EndoEVs has to be considered. This research was funded by the Austrian Research promotion agency and Particle Metrix. Severin Mühleder was funded by the Austrian Science Fund (FWF) project J4358. Sí
Published: 2020
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278. Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana

Author: Mathieu Erhardt, Christophe Ritzenthaler, Hélène Scheer, Denise Altenbach, Marco Incarbone, Lauriane Kuhn, Patrice Dunoyer, Jean-Michel Hily, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Centre National de la Recherche Scientifique (CNRS)European CommissionEuropean Regional Development Fund (ERDF) in the framework of the INTERREG V Upper Rhine programs VITIFUTUR projectsAustrian Science Fund (FWF)M 2921-B
Subjects: 0106 biological sciences, 0301 basic medicine, Small RNA, Tombusvirus, Arabidopsis, lcsh:QR1-502, 01 natural sciences, lcsh:Microbiology, 03 medical and health sciences, Pathosystem, Tomato bushy stunt virus, Virology, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, ComputingMilieux_MISCELLANEOUS, Genetics, biology, fungi, food and beverages, biology.organism_classification, 3. Good health, Tombusviridae, 030104 developmental biology, Infectious Diseases, 010606 plant biology & botany
Abstract: Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant&ndash, microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant&ndash, virus interactions in complement to Saccharomyces cerevisiae.
Published: 2020
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279. Optimal Decoding of Cellular Identities in a Genetic Network

Author: Eric Wieschaus, William Bialek, Thomas Gregor, Mariela D. Petkova, Gašper Tkačik, Harvard University, Department of Physics, Princeton University (DPPU), Princeton University, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported, in part, by U.S. NIH grants (P50GM071508, R01GM077599, and R01GM097275), U.S. NSF grants (PHY-1607612, CCF-0939370, Center for the Science of Information, PHY–1734030, Center for the Physics of Biological Function), an Austrian Science Fund grant (FWF P28844 to G.T.), and an Howard Hughes Medical Institute International Student Research Fellowship (to M.D.P.)., Harvard University [Cambridge], Institute of Science and Technology [Austria] (IST Austria), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Embryo, Nonmammalian, MESH: GTPase-Activating Proteins, 0302 clinical medicine, MESH: Gene Expression Regulation, Developmental, Drosophila Proteins, MESH: Embryonic Development, Gene Regulatory Networks, MESH: Animals, MESH: Models, Genetic, [SDV.BDD]Life Sciences [q-bio]/Development Biology, MESH: Gene Regulatory Networks, 0303 health sciences, cell fate, GTPase-Activating Proteins, Gene Expression Regulation, Developmental, Cell Differentiation, MESH: Transcription Factors, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Drosophila melanogaster, Drosophila, developmental precision, Algorithm, Decoding methods, MESH: Body Patterning, MESH: Cell Differentiation, MESH: Drosophila Proteins, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Genetic network, Embryonic Development, Cell fate determination, Biology, General Biochemistry, Genetics and Molecular Biology, Article, MESH: Drosophila melanogaster, 03 medical and health sciences, Position (vector), genetic networks, Animals, Enhancer, Gap gene, 030304 developmental biology, Body Patterning, Models, Genetic, embryonic patterning, fungi, MESH: Embryo, Nonmammalian, cell specification, Expression (mathematics), optimality, quantitative imaging, 030217 neurology & neurosurgery, Free parameter, Transcription Factors
Abstract: In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. Using the gap gene network in the early fly embryo as an example, we use such a framework to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.
Published: 2019
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280. Combinatorics of nondeterministic walks of the Dyck and Motzkin type

Author: De Panafieu, Elie, Lamali, Mohamed Lamine, Wallner, Michael, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Vienna University of Technology (TU Wien), and Projet ANR JCJC HERA (ANR-18-CE25-0002)Exzellenzstipendium of the Austrian Federal Ministry of Education, Science and Research and the Erwin Schrödinger Fellowshipof the Austrian Science Fund (FWF):~J~4162-N35.
Subjects: [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], generating functions, [MATH.MATH-CO]Mathematics [math]/Combinatorics [math.CO], networking, analytic combinatorics, encapsulation, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Random walks, Computer Science::Formal Languages and Automata Theory
Abstract: International audience; This paper introduces nondeterministic walks, a new variant of one-dimensional discrete walks. At each step, a nondeterministic walk draws a random set of steps from a predefined set of sets and explores all possible extensions in parallel. We introduce our new model on Dyck steps with the nondeterministic step set {{−1}, {1}, {−1, 1}} and Motzkin steps with the nondeterministic step set {{−1}, {0}, {1}, {−1, 0}, {−1, 1}, {0, 1}, {−1, 0, 1}}. For general lists of step sets and a given length, we express the generating function of nondeterministic walks where at least one of the walks explored in parallel is a bridge (ends at the origin). In the particular cases of Dyck and Motzkin steps, we also compute the asymptotic probability that at least one of those parallel walks is a meander (stays nonnegative) or an excursion (stays nonnegative and ends at the origin). This research is motivated by the study of networks involving encapsulations and decapsulations of protocols. Our results are obtained using generating functions and analytic combinatorics.
Published: 2019

281. A characterization of Krull monoids for which sets of lengths are (almost) arithmetical progressions

Author: Alfred Geroldinger, Wolfgang A. Schmid, Institut für Mathematik [Graz] (IM), Karl-Franzens-Universität [Graz, Autriche], Laboratoire Analyse, Géométrie et Applications (LAGA), Université Paris 8 Vincennes-Saint-Denis (UP8)-Centre National de la Recherche Scientifique (CNRS)-Institut Galilée-Université Paris 13 (UP13), and This work was supported by the Austrian Science Fund FWF, Project Number P28864-N35.
Subjects: Monoid, Class (set theory), [MATH.MATH-AC]Mathematics [math]/Commutative Algebra [math.AC], General Mathematics, Structure (category theory), transfer Krull monoids, Characterization (mathematics), Krull monoids, Commutative Algebra (math.AC), 01 natural sciences, Combinatorics, Prime factor, FOS: Mathematics, Arithmetic function, Number Theory (math.NT), 0101 mathematics, MSC 11B30, 13A05, 13F05, 20M13, Mathematics, Mathematics - Number Theory, Group (mathematics), 010102 general mathematics, Mathematics - Commutative Algebra, 16. Peace & justice, [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT], zero-sum sequences, sets of lengths
Abstract: Let H be a Krull monoid with finite class group G and suppose that every class contains a prime divisor. Then sets of lengths in H have a well-defined structure which just depends on the class group G. With methods from additive combinatorics we establish a characterization of those class groups G guaranteeing that all sets of lengths are (almost) arithmetical progressions., Comment: To appear in Rev. Mat. Iberoamericana. The content of this preprint was initially disseminated as part (mostly Chapter 4) of an early version of the manuscript ''A characterization of class groups via sets of lengths'' (hal-01131955, version 1 and arXiv:1503.04679v1) by the same authors
Published: 2019
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282. Lipidomics Reveals Seasonal Shifts in a Large-Bodied Hibernator, the Brown Bear

Author: Giroud, Sylvain, Chery, Isabelle, Bertile, Fabrice, Bertrand-Michel, Justine, Tascher, Georg, Gauquelin-Koch, Guillemette, Arnemo, Jon, Swenson, Jon, Singh, Navinder, Lefai, Etienne, Evans, Alina, Simon, Chantal, Blanc, Stéphane, Gaillard, Brigitte, Research Institute of Wildlife Ecology, University of Veterinary Medicine, University of Veterinary Medicine, Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Plateau MetaToul-LIPIDOMIQUE = MetaToul-Lipidomics, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National d'Études Spatiales [Toulouse] (CNES), Department of Forestry and Wildlife Management, Hedmark University College, Norwegian Institute for Nature Research (NINA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Norwegian Environmental Agency, Swedish Environmental Protection Agency, Polish-Norwegian Research Program [POL-NOR/198352/85/2013], Austrian Science Fund (FWF) [P27267-B25], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-MetaToul-MetaboHUB, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), MetaToul-Lipidomic Core Facility, MetaboHUB, Institut National de la Santé et de la Recherche Médicale (INSERM), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL)
Subjects: glycerophospholipids, [SDE] Environmental Sciences, Physiology, Physiology (medical), [SDE]Environmental Sciences, lipids (amino acids, peptides, and proteins), ceramide, hibernation, body temperature, metabolism, fatty acids, Original Research, sphingomyelin
Abstract: International audience; Prior to winter, heterotherms retain polyunsaturated fatty acids ("PUFA"), resulting in enhanced energy savings during hibernation, through deeper and longer torpor bouts. Hibernating bears exhibit a less dramatic reduction (2-5 degrees C) in body temperature, but lower their metabolism to a degree close to that of small hibernators. We determined the lipid composition, via lipidomics, in skeletal muscle and white adipose tissues ("WAT"), to assess lipid retention, and in blood plasma, to reflect lipid trafficking, of winter hibernating and summer active wild Scandinavian brown bears (Ursus arctos). We found that the proportion of monounsaturated fatty acids in muscle of bears was significantly higher during winter. During hibernation, omega-3 PUFAs were retained in WAT and short-length fatty acids were released into the plasma. The analysis of individual lipid moieties indicated significant changes of specific fatty acids, which are in line with the observed seasonal shift in the major lipid categories and can be involved in specific regulations of metabolisms. These results strongly suggest that the shift in lipid composition is well conserved among hibernators, independent of body mass and of the animals' body temperature.
Published: 2019
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283. Sediment Respiration Pulses in Intermittent Rivers and Ephemeral Streams

Author: Robert J. Rolls, Chelsea J. Little, Simone Guareschi, Annamaria Zoppini, R. Vander Vorste, Eduardo J. Martín, Arnaud Foulquier, Núria Cid, Kate S. Boersma, Michael T. Bogan, Björn Gücker, Cleo Woelfle-Erskine, Amina Taleb, V. D. Diaz-Villanueva, Manuela Morais, J. Marshall, Arturo Elosegi, Vladimir Pešić, Lluís Gómez-Gener, S. Kubheka, Marko Miliša, Clara Mendoza-Lera, Florian Altermatt, Rachel Stubbington, Iola G. Boëchat, Ryan M. Burrows, Arnaud Dehedin, Damien Banas, Iñaki Odriozola, Núria Bonada, Roland Corti, Marcos Moleón, R. Gómez, Ricardo J. Albariño, Erin E. Beller, Alex Laini, Pablo Rodríguez-Lozano, Andreas Bruder, Melanie L. Blanchette, Felicitas Hoppeler, Shai Arnon, B. de Freitas Terra, A. Papatheodoulou, Nathan J. Waltham, Christophe Piscart, Rafael Marcé, Catherine M. Febria, A. Uzan, Peter M. Negus, Dev K. Niyogi, Dominik Zak, Sophie Cauvy-Fraunié, Ana Savić, Catherine Leigh, R. Figueroa, Sarig Gafny, Alisha L. Steward, Emile Faye, Elisabeth I. Meyer, Petr Pařil, Daniel C. Allen, Klement Tockner, D. von Schiller, Mark O. Gessner, K. Brintrup, Jason L. Hwan, Fiona Dyer, C. P. Duerdoth, Gonzalo García-Baquero, Michael Danger, Isabel Pardo, Musa C. Mlambo, R. del Campo, Tommaso Cancellario, Brian Four, A. M. De Girolamo, Thibault Datry, Oleksandra Shumilova, María Isabel Arce, M. M. Sánchez-Montoya, Marek Polášek, Nick Bond, Juan F. Blanco-Libreros, Simone D. Langhans, Stephanie M. Carlson, Andy Banegas-Medina, Manuel A. S. Graça, Joanna Blessing, Biel Obrador, Stefan Lorenz, Christiane Zarfl, Angus R. McIntosh, European Commission, Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Leibniz Association, Department of Plant Biology and Ecology, University of the Basque Country, Department of Advanced Materials, Cranfield University, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Purdue University [West Lafayette], Centro de investigaciones biológicas, Spanish National Research Council (CSIC), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Electronique Quantique, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB)-Faculté de Physique, 748625, Horizon 2020 Framework Programme, 603629, European Commission, CGL2017‐86788‐C3‐3‐P, Ministerio de Economía y Competitividad, PP00P3_179089, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, IT‐951‐16, Eusko Jaurlaritza, CA15113, European Cooperation in Science and Technology, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Universitat de Barcelona (UB), RiverLy (UR Riverly), Laboratoire d'Ecologie Alpine (LECA ), 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]), Austrian Science Fund (FWF), Instituto Catalán de Investigación del Agua - ICRA (SPAIN) (ICRA), Laboratory of Molecular Structure Characterization [Prague] (MBU / CAS), Institute of Microbiology of the Czech Academy of Sciences (MBU / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Barcelona, Technische Universität Berlin (TU), Nottingham Trent University, Instituto Nacional de Investigaciones en Biodiversidad y Medioambiente [Bariloche] (INIBIOMA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), University of Oklahoma (OU), Universität Zürich [Zürich] = University of Zurich (UZH), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), The Jacob Blaustein Institutes for Desert Research (BIDR), Ben-Gurion University of the Negev (BGU), Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universidad de Concepción - University of Concepcion [Chile], Department of Geography [Berkeley], University of California [Berkeley], University of California-University of California, Edith Cowan University (ECU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Planning and Transport Research Centre (PATREC), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Queensland Government, Universidade Federal de São João del-Rei (UFSJ), University of San Diego, University of Arizona, La Trobe University, Scuola universitaria professionale della Svizzera italiana [Manno] (SUPSI), Australian Rivers Institute, Griffith University [Brisbane], Universidad de Navarra [Pamplona] (UNAV), Department of Environmental Science, Policy, and Management [Berkeley] (ESPM), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual Vale do Acarau, Asconit Consultants, National Research Council, Water Research Institute, Universidad de Murcia, Queen Mary University of London (QMUL), University of Canberra, Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), School of biological Sciences [Christchurch], University of Canterbury [Christchurch], University of Windsor [Ca], Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Institut National de la Recherche Agronomique (INRA), Ruppin Academic Center, Department of Ecology and Environmental Science [Umeå], Umeå University, Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], Loughborough University, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Ezemvelo KZN Wildlife, University of Parma = Università degli studi di Parma [Parme, Italie], University of Otago [Dunedin, Nouvelle-Zélande], Basque Centre for Climate Change (BC3), Queensland University of Technology [Brisbane] (QUT), Julius Kühn-Institut (JKI), Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), University of Zagreb, Rhodes University, Grahamstown, Universidad de Granada (UGR), Universidade de Évora, Missouri University of Science and Technology (Missouri S&T), University of Missouri System, Terra Cypria - Cyprus Conservation Foundation, Universidade de Vigo, Masaryk University [Brno] (MUNI), University of Montenegro (UCG), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), School of Environmental and Rural Science, University of New England (UNE), University of Niš, Freie Universität Berlin, University of Trento [Trento], Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], Israel Nature and Parks Authority, Partenaires INRAE, Centre for TropicalWater and Aquatic Ecosystem Research (TropWATER), School of Earth and Environmental Sciences [Australia], James Cook University (JCU)-James Cook University (JCU), University of Washington [Seattle], Universität Rostock, Aarhus University [Aarhus], Center for Applied Geoscience [Tübingen] (ZAG), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Short-Term Scientific Mission of the COST Action : CA15113, European Cooperation in Science and Technology (COST), European Commission : 603629 , 748625, Grant for Research Groups of the Basque University System - Basque Government : IT-951-16, Spanish Ministry of Science, Innovation and Universities through project CHYDROCHANGE : CGL2017-86788C3-2-P , CGL2017-86788-C3-3-P, Swiss National Science Foundation (SNSF) - European Commission : PP00P3_150698, PP00P3_179089, EU project LIFE+ TRivers : LIFE13 ENV/ES/000341, INTER-COST project : LTC17017, CONICYT/FONDAT/15130015, European Project: 748625,H2020-MSCA-IF-2016,SABER CULTURAL, European Project: 0934954(2009), Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic] (MBU / CAS), Technical University of Berlin / Technische Universität Berlin (TU), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), University of San Diego (USD), Scuola universitaria professionale della Svizzera italiana = University of Applied Sciences and Arts of Southern Switzerland [Manno] (SUPSI), Università degli studi di Parma = University of Parma (UNIPR), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Universidad de Granada = University of Granada (UGR), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Carbon sequestration, 0106 biological sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, river, CO, 2, intermittent, respiration, stream, temporary, STREAMS, Atmospheric sciences, 01 natural sciences, River sediments, chemistry.chemical_compound, Rivers, Respiration, Environmental Chemistry, Ecosystem, Captura i emmagatzematge de diòxid de carboni, ComputingMilieux_MISCELLANEOUS, Cursos d'aigua, 0105 earth and related environmental sciences, General Environmental Science, Riparian zone, Global and Planetary Change, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Sediments fluvials, fungi, River, Stream, Intermittent, Temporary, CO2, CO2 emissions, C cycling, stream respiration, Sediment, Vegetation, 15. Life on land, 6. Clean water, chemistry, 13. Climate action, CO 2, [SDE]Environmental Sciences, Carbon dioxide, Plant cover, Environmental science
Abstract: The dataset (Data File S1; DOI: 10.6084/m9.figshare.8863721) and the R code used to generate the results (Code S1; DOI: 10.6084/m9.figshare.8863655), including step by step explanations of the statistical tests, have been deposited in Figshare Digital Repository (https://figshare.com/projects/Sediment_Respiration_Pulses_in_Intermittent_Rivers_and_Ephemeral_Streams/66104)., Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO2) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO2. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32–66-fold upon sediment rewetting. Structural equation modelling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting-drying cycles on respiration and CO2 emissions in stream networks., We thank Y. Etxeberria, L. Sánchez, C. Gutiérrez, G. LeGoff and B. Launay for laboratory support. DvS was supported by a Short-Term Scientific Mission of the COST Action CA15113 (SMIRES, Science and Management of Intermittent Rivers and Ephemeral Streams, www.smires.eu), supported by COST (European Cooperation in Science and Technology) and received additional funding from the EU’s 7th Framework Programme for research, technological development and demonstration under grant agreement No. 603629 (GLOBAQUA) and a Grant for Research Groups of the Basque University System (IT-951-16) funded by the Basque Government. RM and BO were supported by the Spanish Ministry of Science, Innovation and Universities through project C-HYDROCHANGE (CGL2017-86788-C3-2-P and CGL2017-86788-C3-3-P). FA was funded by the Swiss National Science Foundation grants No. PP00P3_150698 and PP00P3_179089. NC was supported by the EU project LIFE+ TRivers (LIFE13 ENV/ES/000341). SDL received funding from the EU’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 748625. PP and MP were supported by INTER-COST project LTC17017. The authors declare that they have no competing interests.
Published: 2019
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284. Evolution and comparative genomics of the most common Trichoderma species

Author: Sabrina Sarrocco, Eva M. Kubicek, Andrei Stecca Steindorff, Igor V. Grigoriev, Bernard Henrissat, Qirong Shen, Alan Kuo, Alexey G. Kopchinskiy, Feng Cai, Giovanni Vannacci, Eliane Ferreira Noronha, Gelsomina Manganiello, Christian P. Kubicek, Jian Zhang, Komal Chenthamara, Irina S. Druzhinina, Riccardo Baroncelli, Vienna University of Technology, United States Department of Energy, Universidade de Brasília (UnB), Seconda Università degli Studi di Napoli = Second University of Naples, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Nanjing Agricultural University (NAU), Universidad de Salamanca, Department of Agriculture, Food and Environment, University of California [Berkeley] (UC Berkeley), University of California (UC), 2017YFD 0200806, Austrian Science Foundation (FWF) 25613-B20 I-1249, CAPES foundation 99999.001745/2014-00, CNPq 482697/2011-3, 141180/2012-9, Office of Science of the U.S. Department of Energy DE-AC02-05CH11231, Seconda Università degli studi di Napoli, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Nanjing Agricultural University, University of California [Berkeley], University of California, Kubicek, C. P., Steindorff, A. S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A. G., Kubicek, E. M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E. F., Vannacci, G., Shen, Q., Grigoriev, I. V., Druzhinina, I. S., Kubicek C.P., Steindorff A.S., Chenthamara K., Manganiello G., Henrissat B., Zhang J., Cai F., Kopchinskiy A.G., Kubicek E.M., Kuo A., Baroncelli R., Sarrocco S., Noronha E.F., Vannacci G., Shen Q., Grigoriev I.V., and Druzhinina I.S.
Subjects: hypocréales, 0106 biological sciences, enzyme cellulolytique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene loss, Medical and Health Sciences, 01 natural sciences, Genome, Orphan, Biopolymers, Clade, Gene gain, Environmental opportunism, 2. Zero hunger, Trichoderma, 0303 health sciences, biology, Ascomycota, Orphans, Hydrolysis, Reproduction, Gene lo, food and beverages, Genomics, Biological Sciences, Ankyrin domains, CAZymes, Core genome, SSCPs, Fungal, CAZyme, Biotechnology, Research Article, Genome evolution, lcsh:QH426-470, Evolution, Bioinformatics, lcsh:Biotechnology, Hypocreales, Genes, Fungal, Biotechnologies, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Genetics, analyse génomique, Gene, 030304 developmental biology, Comparative genomics, Human Genome, Molecular, diversité fongique, biology.organism_classification, Carbon, lcsh:Genetics, Genes, Evolutionary biology, Ankyrin domain, Extracellular Space, 010606 plant biology & botany
Abstract: Background The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist. Electronic supplementary material The online version of this article (10.1186/s12864-019-5680-7) contains supplementary material, which is available to authorized users.
Published: 2019
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285. Scanning Tunneling Microscopy of the Ordered Water Monolayer on MgO(001)/Ag(001) Ultrathin Films

Author: Hollerer M., Prochinig D., Puschnig P., Carrasco E., Freund H.-J., Sterrer M. and Financial support from the Austrian Science Fund (FWF) project I3731 is acknowledged. The computational results presented have been achieved using the computing facilities of the University of Graz and the Vienna Scientific Cluster (VSC3).
Published: 2019

286. Biodiversity and ecosystem service in Transylvania - New approach to sustainable vineyards

Author: Popescu, Daniela, Comsa, M., Hoble, Adela, Bunea, Claudiu Ioan, Gaman, T., Tamas, A. S., Guernion, Muriel, Kratschmer, Sophie, Zaller, Johann G., Winter, Silvia, Technical University of Cluj-Napoca, Université 1 Decembrie 1918 [Alba Iulia], Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Natural Resources and Life Sciences (BOKU), 2013-2014 BiodivERsA/FACCE JPI joint call, Bundesministerium fur Bildung und Forschung (BMBF, Germany) Federal Ministry of Education and Research (BMBF), Agence National de la Recherche (ANR, France) French National Research Agency (ANR), Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFIS-CDI, Romania) [6/2015], Ministerio des economia y competitividad (MINECO, Spain), FWF-Der Wissenschaftsfonds (Austria), ANR-16-EBI3-0016,SoilMan,Ecosystem services driven by the diversity of soil biota – understanding and management -(2016), Jonchère, Laurent, Ecosystem services driven by the diversity of soil biota – understanding and management - - - SoilMan2016 - ANR-16-EBI3-0016 - BiodivERsA - VALID, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU)
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, agroecosystems, Vitis vinifera L, biota richness, landscape, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, soil management
Abstract: International audience; In the last decades intensification and mechanisation of vineyard management caused a separation of production and conservation areas in the vineyards. However, there is limited field evaluation of its impact on commercial vineyard level. Our study evaluates the (i) effects of two soil management (permanent and alternative vegetation cover and bare soil) in vineyard inter-rows and (ii) effects of surrounding landscape complexity on biota richness (bees, earthworms, plants) and production parameters in sixteen commercial vineyards in Central Romania. Biota richness (bees, earthworms, plants) and abundance are influenced by vineyard management intensity. Biodiversity is higher in low intensity vineyards (alternative or permanent cover crop) than in high intensity (bare soil). In this study, management practices seem to have more influence on vineyard inter-row biodiversity and on quality parameters of grapes than surrounding landscape.
Published: 2019

287. BIODIVERSITY AND ECOSYSTEM SERVICE IN TRANSYLVANIA - NEW APPROACH TO A SUSTAINABLE VINEYARDS

Author: Popescu, D., Comsa, M., Hoble, A., Bunea, C. I., Gaman, T., Tamas, A. S., Guernion, M., Kratschmer, S., Zaller, J. G., Silvia Winter, Universitatea Tehnica din Cluj-Napoca (UTCN), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), 2013-2014 BiodivERsA/FACCE JPI joint call, Bundesministerium fur Bildung und Forschung (BMBF, Germany)Federal Ministry of Education and Research (BMBF), Agence National de la Recherche (ANR, France)French National Research Agency (ANR), Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFIS-CDI, Romania) [6/2015], Ministerio des economia y competitividad (MINECO, Spain), FWF-Der Wissenschaftsfonds (Austria), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Natural Resources and Life Sciences (BOKU), and Jonchère, Laurent
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, agroecosystems, Vitis vinifera L, biota richness, landscape, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, soil management
Abstract: International audience; In the last decades intensification and mechanisation of vineyard management caused a separation of production and conservation areas in the vineyards. However, there is limited field evaluation of its impact on commercial vineyard level. Our study evaluates the (i) effects of two soil management (permanent and alternative vegetation cover and bare soil) in vineyard inter-rows and (ii) effects of surrounding landscape complexity on biota richness (bees, earthworms, plants) and production parameters in sixteen commercial vineyards in Central Romania. Biota richness (bees, earthworms, plants) and abundance are influenced by vineyard management intensity. Biodiversity is higher in low intensity vineyards (alternative or permanent cover crop) than in high intensity (bare soil). In this study, management practices seem to have more influence on vineyard inter-row biodiversity and on quality parameters of grapes than surrounding landscape.
Published: 2019

288. Simulating rewetting events in intermittent rivers and ephemeral streams: a global analysis of leached nutrients and organic matter

Author: Arnaud Foulquier, Michael T. Bogan, Björn Gücker, Roland Corti, Daniel von Schiller, Pablo Rodríguez-Lozano, Fiona Dyer, Vladimir Pešić, Stefan Lorenz, Klement Tockner, Jonathan C. Marshall, Lluís Gómez-Gener, Ana Savić, Thibault Datry, Dominik Zak, Rubén del Campo, Marcos Moleón, Clara Mendoza-Lera, Elisabeth I. Meyer, Chelsea J. Little, Simone Guareschi, Ross Vander Vorste, Richardo Figueroa, Florian Altermatt, Michael Danger, Oleksandra Shumilova, Musa C. Mlambo, Rosa Gómez Cerezo, Annamaria Zoppini, Joanna Blessing, Kate S. Boersma, Petr Paril, Núria Bonada, Alisha L. Steward, Christiane Zarfl, Amina Taleb, Manuel A. S. Graça, Juan F. Blanco-Libreros, Peter M. Negus, Isabel Pardo, Iola G. Boëchat, Ryan M. Burrows, Stephanie M. Carlson, Angus R. McIntosh, Mark O. Gessner, Andy Banegas-Medina, Simone D. Langhans, María Isabel Arce, Kate Brintrup, Rachel Stubbington, Pierre Gnohossou, Biel Obrador, Athina Papatheodoulou, Erin E. Beller, Nick Bond, Shai Arnon, Robert J. Rolls, Brian Four, Catherine M. Febria, Sophie Cauvy-Fraunié, Bianca de Freitas Terra, Catherine Leigh, Emile Faye, Andreas Bruder, Daniel C. Allan, Jason L. Hwan, Núria Cid, Skhumbuzo Kubheka, Damien Banas, Nathan J. Waltham, M. M. Sánchez-Montoya, Arturo Elosegi, Marko Miliša, Dev K. Niyogi, Anna Maria De Girolamo, Tommaso Cancellario, Melanie L. Blanchette, European Commission, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Freie Universität Berlin, University of Trento, Universität Rostock, Aarhus University, Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), University of the Basque Country (University of the Basque Country), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), University of Barcelona, Austrian Science Fund (FWF), University of Oklahoma (OU), University of Zurich, Centro de Edafologia y Biologia Aplicada del Segura, Ben-Gurion University of the Negev (BGU), Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universidad de Concepción, University of California [Berkeley], University of California, Edith Cowan University, University of Antioquia, Queensland Government, Universidade Federal de São João del-Rei (UFSJ), University of California [San Diego] (UC San Diego), University of Arizona, Universitat Autònoma de Barcelona [Barcelona] (UAB), La Trobe University, University of Applied Sciences and Arts Switzerland, Griffith University [Brisbane], University of Navarra, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL), Universidade Estadual Vale do Acarau, National Council of Research, Water Research Institute, Universidad de Murcia, University of Canberra, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Canterbury, University of Windsor, Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Institut National de la Recherche Agronomique (INRA), Berlin Institute of Technology, Université de Parakou, Umea University, University of Coimbra, Ezemvelo KZN Wildlife, University of Otago [Dunedin, Nouvelle-Zélande], Basque Centre for Climate Change (BC3), Queensland University of Technology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Julius Kühn-Institut (JKI), Brandenburg University of Technology, University of Münster, University of Zagreb, Rhodes University, Universidad de Granada (UGR), Missouri University of Science and Technology (Missouri S&T), University of Missouri System, Terra Cypria - Cyprus Conservation Foundation, Universidate de Vigo, Masaryk University, University of Montenegro (UCG), University of New England (UNE), University of Niš, Nottingham Trent University, Université de Tlemcen, James Cook University (JCU), University of Tübingen, Aarhus University [Aarhus], Laboratoire d'Ecologie Alpine (LECA ), 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]), Universitat Autònoma de Barcelona (UAB), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Canterbury [Christchurch], University of Windsor [Ca], Université de Parakou (UP), Department of Ecology and Environmental Science [Umeå], Umeå University, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Rhodes University, Grahamstown, Universidade de Vigo, and Masaryk University [Brno] (MUNI)
Subjects: 0106 biological sciences, Geologic Sediments, sédiment, 010504 meteorology & atmospheric sciences, Climate, rehumectation, 01 natural sciences, Substance nutritive, Klimatforskning, chemistry.chemical_compound, zone humide temporaire, Nutrient, Nitrate, matière organique dissoute, Dissolved organic carbon, Canvi climàtic, Primary Research Article, Organic Chemicals, General Environmental Science, chemistry.chemical_classification, Global and Planetary Change, leaf litter, cycle des nutriments, Ecology, zone climatique, Litière végétale, Sediments fluvials, sediments, Lessivage du sol, 6. Clean water, Lixiviació, biofilms, leaching, rewetting, temporary rivers, climatic region, climate change, Environmental chemistry, Leaching (pedology), Biogeochemical cycle, Climate Research, P40 - Météorologie et climatologie, [SDE.MCG]Environmental Sciences/Global Changes, Cours d'eau, Climate change, Biological Availability, 010603 evolutionary biology, River sediments, Sécheresse, biodisponibilité, Rivers, Environmental Chemistry, Organic matter, litière du sol, Matière organique, P10 - Ressources en eau et leur gestion, variation géographique, 0105 earth and related environmental sciences, Changement climatique, Nitrates, entraînement par lessivage, P35 - Fertilité du sol, Nutrients, 15. Life on land, Primary Research Articles, Arid, Climatic change, Plant Leaves, chemistry, 13. Climate action, Environmental science, bioavailability
Abstract: Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico‐chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%–98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events., In this study we experimentally simulated under laboratory conditions rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase from intermittent rivers and ephemeral streams covering global spatial scale. We determined the amounts and quality of the leached nutrients and dissolved organic matter, assessed their inter‐substrate and cross‐climate differences, and estimated areal fluxes from 1 m2 of riverbeds. In addition, we evaluated the variance in leachate characteristics related to selected environmental variables and substrate characteristics.
Published: 2019
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289. Arrival angles of teleseismic fundamental mode Rayleigh waves across the AlpArray

Author: Kolinsky, Petr, Bokelmann, Götz, Hetenyi, Gyorgy, Abreu, Rafael, Allegretti, Ivo, Apoloner, Maria-Theresia, Aubert, Coralie, Besancon, Simon, Bes De Berc, Maxime, Bokelmann, Goetz, Brunel, Didier, Capello, Marco, Carman, Martina, Cavaliere, Adriano, Cheze, Jerome, Chiarabba, Claudio, Clinton, John, Cougoulat, Glenn, Grawford, Wayne C., Cristiano, Luigia, Czifra, Tibor, D'Alema, Ezio, Danesi, Stefania, Daniel, Romuald, Dannowski, Anke, Dasovic, Iva, Deschamps, Anne, Dessa, Jean-Xavier, Doubre, Cecile, Egdorf, Sven, Fiket, Tomislav, Fischer, Kasper, Friederich, Wolfgang, Fuchs, Florian, Funke, Sigward, Giardini, Domenico, Govoni, Aladino, Graczer, Zoltan, Groeschl, Gidera, Heimers, Stefan, Heit, Ben, Herak, Davorka, Herak, Marijan, Huber, Johann, Jaric, Dejan, Jedlicka, Petr, Jia, Yan, Jund, Helene, Kissling, Edi, Klingen, Stefan, Klotz, Bernhard, Kopp, Heidrun, Korn, Michael, Kotek, Josef, Kuhne, Lothar, Kuk, Kreso, Lange, Dietrich, Loos, Jürgen, Lovati, Sara, Malengros, Deny, Margheriti, Lucia, Maron, Christophe, Martin, Xavier, Massa, Marco, Mazzarini, Francesco, Meier, Thomas, Metral, Laurent, Molinari, Irene, Moretti, Milena, Nardi, Anna, Pahor, Jurij, Paul, Anne, Pequegnat, Catherine, Petersen, Daniel, Pesaresi, Damiano, Piccinini, Davide, Piromallo, Claudia, Plenefisch, Thomas, Plomerova, Jaroslava, Pondrelli, Silvia, Prevolnik, Snjezan, Racine, Roman, Regnier, Marc, Reiss, Miriam, Ritter, Joachim, Rumpker, Georg, Salimbeni, Simone, Santulin, Marco, Scherer, Werner, Schippkus, Sven, Schulte-Kortnack, Detlef, Sipka, Vesna, Solarino, Stefano, Spallarossa, Daniele, Spieker, Kathrin, Stipcevic, Josip, Strollo, Angelo, Sule, Balint, Szanyi, Gyongyver, Szucs, Eszter, Thomas, Christine, Thorwart, Martin, Tilmann, Frederik, Ueding, Stefan, Vallocchia, Massimiliano, Vecsey, Ludek, Voigt, Rene, Wassermann, Joachim, Weber, Zoltan, Weidle, Christian, Wesztergom, Viktor, Weyland, Gauthier, Wiemer, Stefan, Wolf, Felix, Wolyniec, David, Zieke, Thomas, Zivcic, Mladen, Zlebcikova, Helena, Institut für Meteorologie und Geophysik [Wien] (IMGW), Universität Wien, Austrian Science Fund (FWF)through project P 26391–AlpArray Austria and P 30707–AlpArrayAustria 2. The Python Toolbox ObsPy by Beyreuther et al. (2010)was used for data pre-processing. Maps were plotted using GenericMapping Tools by Wessel et al. (2013)., and University of Vienna [Vienna]
Subjects: Beamforming, Wave propagation, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Earth structure, engineering.material, 010502 geochemistry & geophysics, 01 natural sciences, symbols.namesake, Geochemistry and Petrology, Time-series analysis, Wave scattering and diffraction, Rayleigh wave, 0105 earth and related environmental sciences, Anomaly (natural sciences), Geodesy, Europe, Geophysics, Phase correlation, symbols, engineering, Structure of the Earth, Surface waves and free oscillations, Geology, Earthquake location, Gaussian beam
Abstract: International audience; The dense AlpArray network allows studying seismic wave propagation with high spatial resolution. Here we introduce an array approach to measure arrival angles of teleseismic Rayleigh waves. The approach combines the advantages of phase correlation as in the two-station method with array beamforming to obtain the phase-velocity vector. 20 earthquakes from the first two years of the AlpArray project are selected, and spatial patterns of arrival-angle deviations across the AlpArray are shown in maps, depending on period and earthquake location. The cause of these intriguing spatial patterns is discussed. A simple wave-propagation modelling example using an isolated anomaly and a Gaussian beam solution suggests that much of the complexity can be explained as a result of wave interference after passing a structural anomaly along the wave paths. This indicates that arrival-angle information constitutes useful additional information on the Earth structure, beyond what is currently used in inversions.
Published: 2019
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290. Nonlocal van der Waals functionals for solids: Choosing an appropriate one

Author: Peter Blaha, Leila Kalantari, Fabien Tran, Boubacar Traore, Xavier Rocquefelte, Vienna University of Technology (TU Wien), Institut des Fonctions Optiques pour les Technologies de l'informatiON (Institut FOTON), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund (FWF) [F41, P27738-N28], TU-D doctoral college (TU Wien), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: Work (thermodynamics), Condensed Matter - Materials Science, Materials science, Physics and Astronomy (miscellaneous), Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, symbols.namesake, Molecular solid, Quantum mechanics, 0103 physical sciences, symbols, [CHIM]Chemical Sciences, Order (group theory), General Materials Science, van der Waals force, 010306 general physics, 0210 nano-technology
Abstract: International audience; The nonlocal van der Waals (NL-vdW) functionals [M. Dion et al., Phys. Rev. Lett. 92, 246401 (2004)] are being applied more and more frequently in solid-state physics, since they have shown to be much more reliable than the traditional semilocal functionals for systems in which weak interactions play a major role. However, a certain number of NL-vdW functionals have been proposed during the last few years, such that it is not always clear which one should be used. In this work, an assessment of NL-vdW functionals is presented. Our test set consists of weakly bound solids, namely rare gases, layered systems such as graphite, and molecular solids, but also strongly bound solids in order to provide a more general conclusion about the accuracy of NL-vdW functionals for extended systems. We found that among the tested functionals, rev-vdW-DF2 [I. Hamada, Phys. Rev. 13 89, 121103(R) (2014)] is very accurate for weakly bound solids, but also quite reliable for strongly bound solids.
Published: 2019
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291. Convergence of the Chern-Moser-Beloshapka normal forms

Author: Bernhard Lamel, Laurent Stolovitch, Fakultät für Mathematik [Wien], Universität Wien, Laboratoire Jean Alexandre Dieudonné (JAD), 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)-Centre National de la Recherche Scientifique (CNRS), Qatar Science Foundation, NPRP 7-511-1-098, FWF (Austrian Science Foundation) grant I1776 for the international cooperation project 'Dynamics and CR geometry', and ANR-14-CE34-0002,Dynamics and CR Geometry,Dynamics and CR Geometry(2014)
Subjects: Mathematics - Differential Geometry, Pure mathematics, General Mathematics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Holomorphic function, Dynamical Systems (math.DS), 01 natural sciences, 0103 physical sciences, Convergence (routing), FOS: Mathematics, Order (group theory), Direct proof, Mathematics - Dynamical Systems, Complex Variables (math.CV), 0101 mathematics, Mathematics, Mathematics - Complex Variables, Mathematics::Complex Variables, Applied Mathematics, 010102 general mathematics, [MATH.MATH-CV]Mathematics [math]/Complex Variables [math.CV], Codimension, Action (physics), Transformation (function), Differential Geometry (math.DG), [MATH.MATH-DG]Mathematics [math]/Differential Geometry [math.DG], A-normal form, CR geometry, normal forms, 010307 mathematical physics
Abstract: In this article, we give a normal form for real-analytic, Levi-nondegenerate submanifolds of ℂ N {\mathbb{C}^{N}} of codimension d ≥ 1 {d\geq 1} under the action of formal biholomorphisms. We find a very general sufficient condition on the formal normal form that ensures that the normalizing transformation to this normal form is holomorphic. In the case d = 1 {d=1} our methods in particular allow us to obtain a new and direct proof of the convergence of the Chern–Moser normal form.
Published: 2019
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292. MicroRNAs facilitate skeletal muscle maintenance and metabolic suppression in hibernating brown bears

Author: Kenneth B. Storey, Blandine Chazarin, Sylvain Giroud, Guillemette Gauquelin-Koch, Bryan E. Luu, Jon M. Arnemo, Fabrice Bertile, Etienne Lefai, Jon E. Swenson, Alina L. Evans, Biology, SAMS, MCGill University, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management (NMBU), Norvegian Institute for Nature Research, Centre National d’Études Spatiales [Paris] (CNES), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Forestry & Wildlife Management, Inland Norway University of Applied Sciences - Høgskolen i Innlandet, Wildlife Fish and Environment Studies, Swedish University of Agricultural Sciences (SLU), McGill University = Université McGill [Montréal, Canada], Unité de Nutrition Humaine (UNH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Wildlife, Fish and Environmental Studies, Centre National D'etudes Spatiales874Natural Sciences and Engineering Research Council of Canada6793Universite de Strasbourg Center National de la Recherche Scientifique Miljodirektoratet Naturvardsverket Svenska Jagareforbundet Austrian Science Fund (FWF) Centre National D'etudes Spatiales, and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-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 Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Hibernation, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Physiology, Glucose uptake, Clinical Biochemistry, Inflammation, ubiquitin ligase, noncoding RNA, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Downregulation and upregulation, atrophy, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, RNA, Messenger, Muscle, Skeletal, biology, Skeletal muscle, myomiR, Cell Biology, medicine.disease, Muscle atrophy, Mef2a, Cell biology, Ubiquitin ligase, Ursus arctos, MicroRNAs, Muscular Atrophy, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, biology.protein, medicine.symptom, Ursidae, Signal Transduction
Abstract: Early ViewOnline Version of Record before inclusion in an issue; Hibernating brown bears, Ursus arctos, undergo extended periods of inactivity and yet these large hibernators are resilient to muscle disuse atrophy. Physiological characteristics associated with atrophy resistance in bear muscle have been examined (e.g., muscle mechanics, neural activity) but roles for molecular signaling/regulatory mechanisms in the resistance to muscle wasting in bears still require investigation. Using quantitative reverse transcription PCR (RT-qPCR), the present study characterized the responses of 36 microRNAs linked with development, metabolism, and regeneration of skeletal muscle, in the vastus lateralis of brown bears comparing winter hibernating and summer active animals. Relative levels of mRNA of selected genes (mef2a, pax7, id2, prkaa1, and mstn) implicated upstream and downstream of the microRNAs were examined. Results indicated that hibernation elicited a myogenic microRNA, or "myomiR", response via MEF2A-mediated signaling. Upregulation of MEF2A-controlled miR-1 and miR-206 and respective downregulation of pax7 and id2 mRNA are suggestive of responses that promote skeletal muscle maintenance. Increased levels of metabolic microRNAs, such as miR-27, miR-29, and miR-33, may facilitate metabolic suppression during hibernation via mechanisms that decrease glucose uptake and fatty acid oxidation. This study identified myomiR-mediated mechanisms for the promotion of muscle regeneration, suppression of ubiquitin ligases, and resistance to muscle atrophy during hibernation mediated by observed increases in miR-206, miR-221, miR-31, miR-23a, and miR-29b. This was further supported by the downregulation of myomiRs associated with a muscle injury and inflammation (miR-199a and miR-223) during hibernation. The present study provides evidence of myomiR-mediated signaling pathways that are activated during hibernation to maintain skeletal muscle functionality in brown bears.
Published: 2019
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293. Distributed Optimal Control Models in Environmental Economics: A Review

Author: Emmanuelle Augeraud-Véron, Raouf Boucekkine, Vladimir M. Veliov, Groupe de Recherche en Economie Théorique et Appliquée (GREThA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institute for Advanced Studies - Aix-Marseille University (IMéRA), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ORCOS, Vienna University of Technology, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), The third author is supported by the Austrian Science Foundation (FWF) under grant No P31400-N32., ANR-16-CE03-0005,GREEN-Econ,Vers une économie plus verte : politiques environnementales et adaptation sociétale(2016), and Lai Tong, Charles
Subjects: 0209 industrial biotechnology, Computer science, 02 engineering and technology, 01 natural sciences, Mathematical research, optimal control, 020901 industrial engineering & automation, JEL: C - Mathematical and Quantitative Methods/C.C6 - Mathematical Methods • Programming Models • Mathematical and Simulation Modeling/C.C6.C61 - Optimization Techniques • Programming Models • Dynamic Analysis, partial differential equations, JEL: C - Mathematical and Quantitative Methods/C.C6 - Mathematical Methods • Programming Models • Mathematical and Simulation Modeling/C.C6.C60 - General, 0101 mathematics, [MATH]Mathematics [math], [SHS.ECO] Humanities and Social Sciences/Economics and Finance, distributed systems, Partial differential equation, Applied Mathematics, 010102 general mathematics, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q5 - Environmental Economics/Q.Q5.Q50 - General, Environmental economics, Optimal control, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q5 - Environmental Economics/Q.Q5.Q57 - Ecological Economics: Ecosystem Services • Biodiversity Conservation • Bioeconomics • Industrial Ecology, Variety (cybernetics), Modeling and Simulation, environmental economics, State (computer science), Mathematical structure
Abstract: International audience; We review the most recent advances in distributed optimal control applied to Environmental Economics, covering in particular problems where the state dynamics are governed by partial differential equations (PDEs). This is a quite fresh application area of distributed optimal control, which has already suggested several new mathematical research lines due to the specificities of the Environmental Economics problems involved. We enhance the latter through a survey of the variety of themes and associated mathematical structures beared by this literature. We also provide a quick tour of the existing tools in the theory of distributed optimal control that have been applied so far in Environmental Economics.
Published: 2019
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294. A weak solution theory for stochastic Volterra equations of convolution type

Author: Jaber, Eduardo Abi, Cuchiero, Christa, Larsson, Martin, Pulido, Sergio, Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Vienna University of Economics and Business, Wirtschaftsuniversität Wien [Austria] (WU), Department of Mathematics - ETH, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), The work of Eduardo Abi Jaber was supported by grants from Région Ile-de-France. Christa Cuchierogratefully acknowledges financial support by the Vienna Science and Technology Fund (WWTF) under grantMA16-021. The research of Sergio Pulido benefited from the support of the Chair Markets in Transition(Fédération Bancaire Française), the project ANR 11-LABX-0019, and the MATH AmSud project SaSMoTiDep 18-MATH-17., ANR-11-LABX-0019/11-LABX-0019,LABEX FCD,LABEX Finance & Croissance Durable(2011), Université Paris 1 Panthéon-Sorbonne (UP1), Centre d'économie de la Sorbonne (CES), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), University of Vienna [Vienna], Department of Mathematical Sciences (Carnegie Mellon), Carnegie Mellon University [Pittsburgh] (CMU), The work of Eduardo Abi Jaber was supported by grants from Région Île-de-France. Christa Cuchiero gratefully acknowledges financial support by the Vienna Science and Technology Fund (WWTF) under grant MA16-021 and the Austrian Science Fund (FWF) under grant Y1235 of the START-program. The research of Sergio Pulido benefited from the support of the Chair Markets in Transition (Fédération Bancaire Française) and the project ANR 11-LABX-0019. Sergio Pulido acknowledges support by the Europlace Institute of Finance (EIF) and the Labex Louis Bachelier, research project: 'The impact of information on financial markets'., ANR-11-LABX-0019,LABEX FCD,LABEX Finance & Croissance Durable(2011), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and ENSIIE-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Statistics and Probability, 010102 general mathematics, Probability (math.PR), 01 natural sciences, nonlinear Hawkes processes, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 010104 statistics & probability, stochastic convolution equations, stochastic Volterra equations, FOS: Mathematics, 0101 mathematics, Statistics, Probability and Uncertainty, MSC 2010 subject classifications: Primary 60H20, secondary 60H05, 60G22, 60G17, MSC 2010 subject classications: Primary 60H20, Mathematics - Probability, martingale problem
Abstract: International audience; We obtain general weak existence and stability results for stochastic convolution equations with jumps under mild regularity assumptions, allowing for non-Lipschitz coefficients and singular kernels. Our approach relies on weak convergence in $L^p$ spaces. The main tools are new a priori estimates on Sobolev--Slobodeckij norms of the solution, as well as a novel martingale problem that is equivalent to the original equation. This leads to generic approximation and stability theorems in the spirit of classical martingale problem theory. We also prove uniqueness and path regularity of solutions under additional hypotheses. To illustrate the applicability of our results, we consider scaling limits of nonlinear Hawkes processes and approximations of stochastic Volterra processes by Markovian semimartingales.
Published: 2019
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295. French [Chapitre 5]

Author: Hummel, M., Wissner, Inka, Edition, Littératures, Langages, Informatique, Arts, Didactique, Discours - UFC (UR 4661) (ELLIADD), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), and Austrian Science Fund (FWF), project number P 30751-G30
Subjects: Latin-Romance transition, standardization, Latin, adverbials, prepositional adverbials, analyticization, ComputingMilieux_MISCELLANEOUS, Romance, adverb, adverbial locutions, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2019
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296. Twenty-three unsolved problems in hydrology (UPH) – a community perspective

Author: Alena Gonzalez Bevacqua, Murugesu Sivapalan, Rui Tong, Ruud van der Ent, Holger Lange, Krzysztof Kochanek, Kate Heal, Moussa Sidibe, Ida Westerberg, Scott T. Allen, Pablo Borges de Amorim, Eric Lindquist, Georgia Destouni, Maria-Helena Ramos, Bruce Misstear, Andrew J. Wade, Keith Beven, Luca Brocca, Mike Kirkby, Sina Khatami, David K. Kreamer, Pieter R. van Oel, Zahra Kalantari, Shreedhar Maskey, Sergiy Vorogushyn, Shamshagul Mashtayeva, James W. Kirchner, Andis Kalvans, Hubert H. G. Savenije, Sebastian H. Mernild, Gerrit H. de Rooij, Santosh K. Aryal, Ennio Ferrari, Julien Malard, Alberto Montanari, Ladislav Holko, Sonu Khanal, Silvia Kohnová, Camyla Innocente, Mel Sandells, Josie Geris, Tom Gleeson, Felipe P. J. de Barros, Ben Jarihani, Anne Van Loon, Stefan Krause, Maria Mavrova-Guirguinova, Marlies Barendrecht, María José Polo, Flavia Tauro, Zongxue Xu, B. I. Gartsman, Elena Ridolfi, Charles Perrin, Miriam Glendell, Yuanfang Chen, Ilja van Meerveld, Theresa Blume, Harald Kunstmann, Gemma Carr, Alireza Nabizadeh, Ebru Eris, Christopher J. White, Heidi Kreibich, Hannes Müller-Thomy, Ashish Sharma, Laura Foglia, Josep Mas-Pla, Subhabrata Panda, Shervan Gharari, Renzo Rosso, J. E. Reynolds, Stefano Ferraris, Saket Pande, Markus Hrachowitz, Laurent Pfister, David E. Robertson, Thomas Skaugen, Roy C. Sidle, Rafael Pimentel, Ross Woods, Alena Bartosova, Erkan Istanbulluoglu, Grant Ferguson, Anam Amin, Chris Hopkinson, Korbinian Breinl, David A. Post, Mathew Herrnegger, Aldo Fiori, Ingelin Steinsland, Dawei Han, Lina Stein, Alberto Viglione, Akhilendra Bhushan Gupta, Bakhram Nurtaev, Maurizio Mazzoleni, Charles H. Luce, Martine van der Ploeg, Ronald van Nooijen, Jean-Philippe Vidal, Tirthankar Roy, Borbála Széles, Jens Kiesel, Cristina Prieto Sierra, Junguo Liu, Hafzullah Aksoy, Andreas Schumann, Pierluigi Claps, Berit Arheimer, Georgia Papacharalampous, Wouter Buytaert, Keirnan Fowler, Ulrich Strasser, David C. Finger, Elena Volpi, Matthew R. Hipsey, Paula Cunha David, Margarida L. R. Liberato, Alexander Gelfan, Barry Croke, V.O. Odongo, David M. Hannah, Günter Blöschl, Hristos Tyralis, Olga Makarieva, Nataliia Nesterova, Bettina Schaefli, Kamshat Tussupova, Guillaume Thirel, Kay Helfricht, Timothy E. Link, Earl Bardsley, Wouter J. M. Knoben, Vazken Andréassian, Ján Szolgay, Mojtaba Shafiei, Jose Luis Salinas, Jan Seibert, Benjamin Fersch, Doris Duethmann, Azhar Inam, Yongqiang Zhang, Giuliano Di Baldassarre, Simon Gascoin, Hugh Smith, Martyn P. Clark, Xiaohong Chen, Maik Renner, Tissa H. Illangasekare, Remko Uijlenhoet, Victor R. Baker, Ravindra Dwivedi, Eric Servat, Christophe Cudennec, Jeffrey J. McDonnell, Sabine M. Spiessl, Yangbo Chen, Thom Bogaard, Wouter R. Berghuijs, María P. González-Dugo, Gilles Boulet, Fernando Nardi, Eric Gaume, Jana von Freyberg, Gil Mahé, Peter Chifflard, Mitja Brilly, William H. Farmer, Monica Riva, James Feiccabrino, Claire Lupton, Anna Scolobig, João H.M. Sá, Przemysław Wachniew, Daniel P. Loucks, Jessica M. Driscoll, Bob Su, Elena Toth, Okke Batelaan, Eric F. Wood, Annette Dathe, David G. Tarboton, Attilio Castellarin, Alla Kolechkina, Björn Guse, Christopher M. U. Neale, Salvatore Grimaldi, Zhonghe Pang, Fuqiang Tian, Marc F. P. Bierkens, Christine Stumpp, Philip J. Ward, Stefan Haun, António Chambel, Riccardo Rigon, Andrea Castelletti, Michael E. Böttcher, Rens van Beek, Gianfausto Salvadori, Adrian A. Harpold, Adrian L. Collins, Hana Hlaváčiková, Clara Hohmann, Koray K. Yilmaz, Technical University of Vienna [Vienna] (TU WIEN), Utrecht University [Utrecht], University of Évora [Portugal], Sol Agro et hydrosystème Spatialisation (SAS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Stockholm University, Roma Tre University, Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), Institut Fédéral de Recherches [Suisse], University of Saskatchewan [Saskatoon] (U of S), Delft University of Technology (TU Delft), Department of Civil and Environmental Engineering [Urbana], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Civil Chemical Environmental and Materials Engineering [Bologna] (DICAM), University of Bologna, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Politecnico di Torino [Torino] (Polito), Istanbul Technical University, Department of Land, Environment, Agriculture and Forestry (TeSAF), Universita degli Studi di Padova, Hydrosystèmes continentaux anthropisés : ressources, risques, restauration (UR HYCAR), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Swedish Meteorological and Hydrological Institute (SMHI), Water Resources Section, Centre d'études spatiales de la biosphère (CESBIO), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Imperial College London, Sun Yat-Sen University (SYSU), Hohai University, Research Applications Laboratory [Boulder] (RAL), National Center for Atmospheric Research [Boulder] (NCAR), Department of Earth Sciences [ Uppsala], Uppsala University, University of Reykjavik [Islande], Structure et fonctionnement des systèmes hydriques continentaux (SISYPHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-MINES ParisTech - École nationale supérieure des mines de Paris-Centre National de la Recherche Scientifique (CNRS), Département Géotechnique, Eau et Risques (IFSTTAR/GER), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-PRES Université Nantes Angers Le Mans (UNAM), Water Problems Institute of the Russian Academy of Sciences, Russian Academy of Sciences [Moscow] (RAS), The James Hutton Institute, School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Center for Experimental Study of Subsurface Environmental Processes (CESEP), Colorado School of Mines, Slovak University of Technology in Bratislava, Hydrology Section, German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ), South University of Science and Technology of China, School of Environmental Science and Engineering, Sun Yat-Sen University (SYSU)-Sun Yat-Sen University (SYSU), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Water Science and Engineering, Institute for Water Education (UNESCO–IHE), Università di Bologna [Bologna] (UNIBO), Luxembourg Institute of Science and Technology (LIST), Andalusian Institute of Earth Sciences (IACT), Spanish National Research Council [Madrid] (CSIC), University of Pennsylvania [Philadelphia], Dipartimento di Ingegneria Idraulica, Ambientale, Infrastrutture Viarie, Rilevamento, ICT Institute of Politecnico di Milano, University of Edinburgh, Boise State University, Coventry University, University of the Sunshine Coast (USC), Department of Civil and Environmental Engineering, Utah State University (USU), Department of Hydraulic Engineering, State Key Laboratory of Hydroscience and Engineering, Tsinghua University [Beijing], Wagenigen University, Utrecht Centre for Geosciences, Météo-France [Paris], Météo France, Department of Mathematical Sciences, Durham University, Princeton University, Ege Üniversitesi, Water and Climate Risk, Bloschl G., Bierkens M.F.P., Chambel A., Cudennec C., Destouni G., Fiori A., Kirchner J.W., McDonnell J.J., Savenije H.H.G., Sivapalan M., Stumpp C., Toth E., Volpi E., Carr G., Lupton C., Salinas J., Szeles B., Viglione A., Aksoy H., Allen S.T., Amin A., Andreassian V., Arheimer B., Aryal S.K., Baker V., Bardsley E., Barendrecht M.H., Bartosova A., Batelaan O., Berghuijs W.R., Beven K., Blume T., Bogaard T., Borges de Amorim P., Bottcher M.E., Boulet G., Breinl K., Brilly M., Brocca L., Buytaert W., Castellarin A., Castelletti A., Chen X., Chen Y., Chifflard P., Claps P., Clark M.P., Collins A.L., Croke B., Dathe A., David P.C., de Barros F.P.J., de Rooij G., Di Baldassarre G., Driscoll J.M., Duethmann D., Dwivedi R., Eris E., Farmer W.H., Feiccabrino J., Ferguson G., Ferrari E., Ferraris S., Fersch B., Finger D., Foglia L., Fowler K., Gartsman B., Gascoin S., Gaume E., Gelfan A., Geris J., Gharari S., Gleeson T., Glendell M., Gonzalez Bevacqua A., Gonzalez-Dugo M.P., Grimaldi S., Gupta A.B., Guse B., Han D., Hannah D., Harpold A., Haun S., Heal K., Helfricht K., Herrnegger M., Hipsey M., Hlavacikova H., Hohmann C., Holko L., Hopkinson C., Hrachowitz M., Illangasekare T.H., Inam A., Innocente C., Istanbulluoglu E., Jarihani B., Kalantari Z., Kalvans A., Khanal S., Khatami S., Kiesel J., Kirkby M., Knoben W., Kochanek K., Kohnova S., Kolechkina A., Krause S., Kreamer D., Kreibich H., Kunstmann H., Lange H., Liberato M.L.R., Lindquist E., Link T., Liu J., Loucks D.P., Luce C., Mahe G., Makarieva O., Malard J., Mashtayeva S., Maskey S., Mas-Pla J., Mavrova-Guirguinova M., Mazzoleni M., Mernild S., Misstear B.D., Montanari A., Muller-Thomy H., Nabizadeh A., Nardi F., Neale C., Nesterova N., Nurtaev B., Odongo V.O., Panda S., Pande S., Pang Z., Papacharalampous G., Perrin C., Pfister L., Pimentel R., Polo M.J., Post D., Prieto Sierra C., Ramos M.-H., Renner M., Reynolds J.E., Ridolfi E., Rigon R., Riva M., Robertson D.E., Rosso R., Roy T., Sa J.H.M., Salvadori G., Sandells M., Schaefli B., Schumann A., Scolobig A., Seibert J., Servat E., Shafiei M., Sharma A., Sidibe M., Sidle R.C., Skaugen T., Smith H., Spiessl S.M., Stein L., Steinsland I., Strasser U., Su B., Szolgay J., Tarboton D., Tauro F., Thirel G., Tian F., Tong R., Tussupova K., Tyralis H., Uijlenhoet R., van Beek R., van der Ent R.J., van der Ploeg M., Van Loon A.F., van Meerveld I., van Nooijen R., van Oel P.R., Vidal J.-P., von Freyberg J., Vorogushyn S., Wachniew P., Wade A.J., Ward P., Westerberg I.K., White C., Wood E.F., Woods R., Xu Z., Yilmaz K.K., Zhang Y., Vienna University of Technology (TU Wien), 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), Politecnico di Torino = Polytechnic of Turin (Polito), Istanbul Technical University (ITÜ), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), Department of Earth Sciences [Uppsala], Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Southern University of Science and Technology of China (SUSTech), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Tsinghua University [Beijing] (THU), Austrian Science Fund (FWF) : DK W1219-N28, Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi Roma Tre = Roma Tre University (ROMA TRE), University of Bologna/Università di Bologna, Università degli Studi di Padova = University of Padua (Unipd), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), 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 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Southern University of Science and Technology (SUSTech), University of Pennsylvania, Météo-France, Castellarin, A, Tækni- og verkfræðideild (HR), School of Science and Engineering (RU), Háskólinn í Reykjavík, Reykjavik University, Department of Water Resources, UT-I-ITC-WCC, Faculty of Geo-Information Science and Earth Observation, Bloschl, G., Bierkens, M. F. P., Chambel, A., Cudennec, C., Destouni, G., Fiori, A., Kirchner, J. W., Mcdonnell, J. J., Savenije, H. H. G., Sivapalan, M., Stumpp, C., Toth, E., Volpi, E., Carr, G., Lupton, C., Salinas, J., Szeles, B., Viglione, A., Aksoy, H., Allen, S. T., Amin, A., Andreassian, V., Arheimer, B., Aryal, S. K., Baker, V., Bardsley, E., Barendrecht, M. H., Bartosova, A., Batelaan, O., Berghuijs, W. R., Beven, K., Blume, T., Bogaard, T., Borges de Amorim, P., Bottcher, M. E., Boulet, G., Breinl, K., Brilly, M., Brocca, L., Buytaert, W., Castellarin, A., Castelletti, A., Chen, X., Chen, Y., Chifflard, P., Claps, P., Clark, M. P., Collins, A. L., Croke, B., Dathe, A., David, P. C., de Barros, F. P. J., de Rooij, G., Di Baldassarre, G., Driscoll, J. M., Duethmann, D., Dwivedi, R., Eris, E., Farmer, W. H., Feiccabrino, J., Ferguson, G., Ferrari, E., Ferraris, S., Fersch, B., Finger, D., Foglia, L., Fowler, K., Gartsman, B., Gascoin, S., Gaume, E., Gelfan, A., Geris, J., Gharari, S., Gleeson, T., Glendell, M., Gonzalez Bevacqua, A., Gonzalez-Dugo, M. P., Grimaldi, S., Gupta, A. B., Guse, B., Han, D., Hannah, D., Harpold, A., Haun, S., Heal, K., Helfricht, K., Herrnegger, M., Hipsey, M., Hlavacikova, H., Hohmann, C., Holko, L., Hopkinson, C., Hrachowitz, M., Illangasekare, T. H., Inam, A., Innocente, C., Istanbulluoglu, E., Jarihani, B., Kalantari, Z., Kalvans, A., Khanal, S., Khatami, S., Kiesel, J., Kirkby, M., Knoben, W., Kochanek, K., Kohnova, S., Kolechkina, A., Krause, S., Kreamer, D., Kreibich, H., Kunstmann, H., Lange, H., Liberato, M. L. R., Lindquist, E., Link, T., Liu, J., Loucks, D. P., Luce, C., Mahe, G., Makarieva, O., Malard, J., Mashtayeva, S., Maskey, S., Mas-Pla, J., Mavrova-Guirguinova, M., Mazzoleni, M., Mernild, S., Misstear, B. D., Montanari, A., Muller-Thomy, H., Nabizadeh, A., Nardi, F., Neale, C., Nesterova, N., Nurtaev, B., Odongo, V. O., Panda, S., Pande, S., Pang, Z., Papacharalampous, G., Perrin, C., Pfister, L., Pimentel, R., Polo, M. J., Post, D., Prieto Sierra, C., Ramos, M. -H., Renner, M., Reynolds, J. E., Ridolfi, E., Rigon, R., Riva, M., Robertson, D. E., Rosso, R., Roy, T., Sa, J. H. M., Salvadori, G., Sandells, M., Schaefli, B., Schumann, A., Scolobig, A., Seibert, J., Servat, E., Shafiei, M., Sharma, A., Sidibe, M., Sidle, R. C., Skaugen, T., Smith, H., Spiessl, S. M., Stein, L., Steinsland, I., Strasser, U., Su, B., Szolgay, J., Tarboton, D., Tauro, F., Thirel, G., Tian, F., Tong, R., Tussupova, K., Tyralis, H., Uijlenhoet, R., van Beek, R., van der Ent, R. J., van der Ploeg, M., Van Loon, A. F., van Meerveld, I., van Nooijen, R., van Oel, P. R., Vidal, J. -P., von Freyberg, J., Vorogushyn, S., Wachniew, P., Wade, A. J., Ward, P., Westerberg, I. K., White, C., Wood, E. F., Woods, R., Xu, Z., Yilmaz, K. K., Zhang, Y., Hydrologie, and Landscape functioning, Geocomputation and Hydrology
Subjects: hydrology, science questions, research agenda, interdisciplinary, knowledge gaps, 0208 environmental biotechnology, UT-Hybrid-D, WASS, hydrology, 02 engineering and technology, Oceanografi, hydrologi och vattenresurser, Hydrology and Quantitative Water Management, Oceanography, Hydrology and Water Resources, QE, Þekking, 910 Geography & travel, VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Hydrologi: 454, ComputingMilieux_MISCELLANEOUS, media_common, Water Science and Technology, knowledge gap, [SHS.SOCIO]Humanities and Social Sciences/Sociology, VDP::Landbruks- og Fiskerifag: 900, Hydroglogy, 6. Clean water, Justice and Strong Institutions, TA, Spite, science questions, Discipline, Hydrologie en Kwantitatief Waterbeheer, research agenda, knowledge gaps, interdisciplinary, SDG 16 - Peace, Process (engineering), media_common.quotation_subject, Hidrologia, Vatnafræði, Context (language use), Digital media, ITC-HYBRID, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Hydrology, WIMEK, business.industry, SDG 16 - Peace, Justice and Strong Institutions, Public consultation, Rannsóknir, 500 Science, Bodemfysica en Landbeheer, [SDE.ES]Environmental Sciences/Environmental and Society, Water Resources Management, 020801 environmental engineering, Soil Physics and Land Management, Socio-hydrology, ITC-ISI-JOURNAL-ARTICLE, Aðferðafræði, business, Diversity (politics)
Abstract: Publisher's version (útgefin grein), This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come., We would like to thank the members of the IAHS, EGU, AGU and IAH for supporting this initiative. The LinkedIn group and overall secretariat was hosted by the IAHS, the Splinter meeting by EGU and the Vienna Catchment Science Symposium by the Vienna Doctoral Programme on Water Resource Systems (DK W1219-N28) funded by the Austrian Science Funds (FWF)., "Peer Reviewed"
Published: 2019
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297. On irregularities of distribution of binary sequences Rrelative to arithmetic progressions, II (constructive bounds)

Author: András Sárközy, Katalin Gyarmati, Cécile Dartyge, Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Algebra and Number Theory [Budapest], Eötvös Loránd University (ELTE), Research partially supported by Hungarian National Foundation for Scientific Research, Grants No. K100291, K119528 and NK104183 and the ANR-FWF bilateral project MuDeRa Multiplicativity: Determinism and Randomness (France-Austria), and ANR-14-CE34-0009,MuDeRa,Multiplicativity, determinism, and Randomness(2014)
Subjects: Discrete mathematics, binary sequences, Distribution (number theory), 010102 general mathematics, 2010 Mathematics subject classification : primary 11K38, secondary 11B25, Binary number, Probability and statistics, 010103 numerical & computational mathematics, General Medicine, 01 natural sciences, Constructive, [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT], arithmetic progressions, 0101 mathematics, irregularities of distribution, Mathematics
Abstract: In Part I of this paper we studied the irregularities of distribution of binary sequences relative to short arithmetic progressions. First we introduced a quantitative measure for this property. Then we studied the typical and minimal values of this measure for binary sequences of a given length. In this paper our goal is to give constructive bounds for these minimal values.
Published: 2018
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298. EGFR is required for FOS-dependent bone tumor development via RSK2/CREB signaling

Author: Linder, Markus, Glitzner, Elisabeth, Srivatsa, Sriram, Bakiri, Latifa, Matsuoka, Kazuhiko, Shahrouzi, Parastoo, Dumanic, Monika, Novoszel, Philipp, Mohr, Thomas, Langer, Oliver, Wanek, Thomas, Mitterhauser, Markus, Wagner, Erwin Friedrich, Sibilia, Maria, FWF Austrian Science Fund, and European Research Council
Subjects: c‐Fos, Osteosarcoma, CREB, Epidermal growth factor receptor, RSK2
Abstract: Osteosarcoma (OS) is a rare tumor of the bone occurring mainly in young adults accounting for 5% of all childhood cancers. Because of the limited therapeutic options, there has been no survival improvement for OS patients in the past 40 years. The epidermal growth factor receptor (EGFR) is highly expressed in OS; however, its clinical relevance is unclear. Here, we employed an autochthonous c-Fos-dependent OS mouse model (H2-c-fosLTR) and human OS tumor biopsies for preclinical studies aimed at identifying novel biomarkers and therapeutic benefits of anti-EGFR therapies. We show that EGFR deletion/inhibition results in reduced tumor formation in H2-c-fosLTR mice by directly inhibiting the proliferation of cancer-initiating osteoblastic cells by a mechanism involving RSK2/CREB-dependent c-Fos expression. Furthermore, OS patients with co-expression of EGFR and c-Fos exhibit reduced overall survival. Preclinical studies using human OS xenografts revealed that only tumors expressing both EGFR and c-Fos responded to anti-EGFR therapy demonstrating that c-Fos can be considered as a novel biomarker predicting response to anti-EGFR treatment in OS patients. We thank Martina Hammer for maintaining mouse colonies, Malgorzata Tryniecki for genotyping, Bilge Vasfiye Göcen for technical assistance, and Andrea Nolz for help with X‐ray imaging. We are grateful to Marlon R. Schneider for providing the ColAREG transgenic mice and to Eugenie S. Kleinerman for providing the LM7 OS cell line. This work was supported by the Austrian Science Fund (FWF) (DK W1212). M.S. is supported by an ERC‐Advanced grant (ERC‐2015‐AdG TNT‐Tumors 694883). The [11C]erlotinib PET imaging part of this work was supported by the FWF project “Transmembrane Transporters in Health and Disease” (SFB F35). Sí
Published: 2018

299. Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms

Author: Esmaeel, Qassim, Miotto, Lidiane, Rondeau, Marine, Leclère, Valérie, Clément, Christophe, Jacquard, Cédric, Sanchez, Lisa, Barka, Essaid, Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), University of Lille, Université du Littoral Côte d'Opale (ULCO), Université de Reims Champagne-Ardenne (URCA), Institut Charles Viollette (ICV) - EA 7394 (ICV), Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de la Recherche Agronomique (INRA)-Université d'Artois (UA)-Institut Supérieur d'Agriculture, University of Reims Champagne-Ardenne, European Union funding through the INTERREG V FWF (France Wallonie Flandre) a SmartBioControl project (BioScreen project), Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), and Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille
Subjects: [SDV]Life Sciences [q-bio], fungi, lcsh:QR1-502, food and beverages, Review, Paraburkholderia phytofirmans PsJN, perception, Microbiology, biotic and abiotic stress, lcsh:Microbiology, PGPR, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, endophyte, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The use of plant-associated bacteria has received many scientific and economic attention as an effective and alternative method to reduce the chemical pesticides use in agriculture. The genus Burkholderia includes at least 90 species including pathogenic strains, plant pathogens, as well as plant beneficial species as those related to Paraburkholderia, which has been reported to be associated with plants and exerts a positive effect on plant growth and fitness. Paraburkholderia phytofirmans PsJN, a beneficial endophyte able to colonize a wide range of plants, is an established model for plant-associated endophytic bacteria. Indeed, in addition to its plant growth promoting ability, it can also induce plant resistance against biotic as well as abiotic stresses. Here, we summarized an inventory of knowledge on PsJN-plant interaction, from the perception to the resistance mechanisms induced in the plant by a way of the atypical colonization mode of this endophyte. We also have carried out an extensive genome analysis to identify all gene clusters which contribute to the adaptive mechanisms under different environments and partly explaining the high ecological competence of P. phytofirmans PsJN.
Published: 2018
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300. The Chemistry and Topography of Stabilized and Functionalized Graphene Oxide Coatings

Author: Manoj Tripathi, Giorgio Speranza, Tsz-ting Wong, Timothy O'Brien, Firas Awaja, Science Foundation Ireland, European Regional Development Fund, Horizon 2020, and FWF
Subjects: Polymers and Plastics, Diamond-like carbon, Oxide, coatings, 02 engineering and technology, engineering.material, 010402 general chemistry, 01 natural sciences, molecular structures, law.invention, chemistry.chemical_compound, Coating, X-ray photoelectron spectroscopy, law, XPS, Peek, Thin film, Graphene oxide, Graphene, graphene, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 0104 chemical sciences, thin films, chemistry, Chemical engineering, engineering, 0210 nano-technology, Layer (electronics)
Abstract: Graphene oxide (GO) thin films and coatings are regarded as superior in quality to other materials especially for biomedical applications. However, the lack of stability and understanding of their structure and defects hinder their use in value added applications. Here, we describe our successful attempt at stabilizing, reducing and functionalizing GO through multiple plasma treatments with polymerizing (to deposit a crosslinking and compressing layer of diamond like carbon, DLC) and non‐polymerizing precursors (H2, O2, and N2). The hybrid GO and DLC coatings on semi crystalline PEEK were evaluated using AFM, SEM, and XPS. The GO deposited layer showed roughness around 70 nm and, despite care, resulted in several wrinkles and particle aggregations. The hybrid coatings conformed to the roughness and crystalline features of PEEK. XPS showed that the DLC layer cross‐linked the GO nano‐flakes while not completely masking which enable the partial exposure of GO. The GO‐DLC hybrid interface is higher in thickness than the PEEK‐GO and is dominating the overall thickness of the hybrid structure ≈13 ± 1 μm. XPS measurements showed that the often unstable CO functional groups on the surface of the hybrid coating can be reduced by effective plasma treatment. Plasma treatments also generated CO functional groups that probably originated from the decomposed carboxyl groups. The plasma treatment also contributed to the reduction of GO. Treatment with H2 was more effective in oxygen reduction than with the N2, however, treatment with N2 increased the reactants on GO as N2 is heavier tending to deposit more on a surface. Plasma treatment with O2 increased the surface oxygen content further and hence more defects on the hybrid surface. This publication has emanated from research conducted with the financial support of Science Foundation Ireland (SFI) and is co-funded under the European Regional Development Fund under Grant Number 13/RC/2073. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 713690. FA would also acknowledge funding from the FWF under the Lise Meitner program (M-1777). peer-reviewed 2019-08-01
Published: 2018

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