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101. Algebraic and Higher-Order Differential Cryptanalysis of Pyjamask-96

Author: Dobraunig, Rotella, Schoone, Laboratoire de Mathématiques de Versailles (LMV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund, FWF: J 4277-N38 Austrian Science Fund, FWF European Research Council, ERC: 788980, ERC-2017-ADG, and Christoph Dobraunig is supported by the Austrian Science Fund (FWF): J 4277-N38. Yann Rotella and Jan Schoone are supported by the European Research Council under the ERC advanced grant agreement under grant ERC-2017-ADG Nr. 788980 ESCADA.
Subjects: lcsh:Computer engineering. Computer hardware, algebraic cryptanalysis, higher-order differentials, Applied Mathematics, lcsh:TK7885-7895, Higher-order differential cryptanalysis, Computer Science Applications, Algebra, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], Computational Mathematics, cryptanalysis, symmetric cryptography, Pyjamask, Digital Security, Algebraic number, NIST call for lightweight cryptography, Software, Mathematics
Abstract: Cryptographic competitions, like the ongoing NIST call for lightweight cryptography, always provide a thriving research environment, where new interesting ideas are proposed and new cryptographic insights are made. One proposal for this NIST call that is accepted for the second round is Pyjamask. Pyjamask is an authenticated encryption scheme that builds upon two block ciphers, Pyjamask-96 and Pyjamask-128, that aim to minimize the number of AND operations at the cost of a very strong linear layer. A side-effect of this goal is a slow growth in the algebraic degree. In this paper, we focus on the block cipher Pyjamask-96 and are able to provide a theoretical key-recovery attack reaching 14 (out of 14) rounds as well as a practical attack on 8 rounds. We do this by combining higher-order differentials with an in-depth analysis of the system of equations gotten for 2.5 rounds of Pyjamask-96. The AEAD-scheme Pyjamask itself is not threatened by the work in this paper., IACR Transactions on Symmetric Cryptology, Volume 2020, Issue 1
Published: 2020
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102. Dogs fail to reciprocate the receipt of food from a human in a food-giving task

Author: Johannes Schullern-Schrattenhofen, Mayte Martínez, Lisa Poncet, Jim McGetrick, Marietta Amann, Friederike Range, Leona Fux, University of Veterinary Medicine [Vienna] (Vetmeduni), Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund (FWF) Austrian Science Fund (FWF) [W1262B29, P30704], DOC fellowship of the Austrian Academy of Sciences (OAW) at the Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, and Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Social Cognition, Male, medicine.medical_treatment, Social Sciences, 01 natural sciences, Task (project management), [SCCO]Cognitive science, Learning and Memory, Sociology, Medicine and Health Sciences, Psychology, Cooperative Behavior, Reciprocity (cultural anthropology), Receipt, Mammals, Multidisciplinary, Animal Behavior, Pets and Companion Animals, Statistical Models, 05 social sciences, Statistics, Eukaryota, Social Discrimination, Prosocial behavior, Vertebrates, Physical Sciences, Medicine, Female, Social psychology, Research Article, Social Psychology, Science, Animal-assisted therapy, 010603 evolutionary biology, Human Learning, Dogs, Human-Animal Interaction, Animal welfare, medicine, Animals, Learning, Humans, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Nutrition, Behavior, Organisms, Cognitive Psychology, Biology and Life Sciences, Helping Behavior, Diet, Prosocial Behavior, Food, Amniotes, HUBzero, Cognitive Science, Test phase, Zoology, Mathematics, Neuroscience
Abstract: International audience; Domestic dogs have been shown to reciprocate help received from conspecifics in food-giving tasks. However, it is not yet known whether dogs also reciprocate help received from humans. Here, we investigated whether dogs reciprocate the receipt of food from humans. In an experience phase, subjects encountered a helpful human who provided them with food by activating a food dispenser, and an unhelpful human who did not provide them with food. Subjects later had the opportunity to return food to each human type, in a test phase, via the same mechanism. In addition, a free interaction session was conducted in which the subject was free to interact with its owner and with whichever human partner it had encountered on that day. Two studies were carried out, which differed in the complexity of the experience phase and the time lag between the experience phase and test phase. Subjects did not reciprocate the receipt of food in either study. Furthermore, no difference was observed in the duration subjects spent in proximity to, or the latency to approach, the two human partners. Although our results suggest that dogs do not reciprocate help received from humans, they also suggest that the dogs did not recognize the cooperative or uncooperative act of the humans during the experience phase. It is plausible that aspects of the experimental design hindered the emergence of any potential reciprocity. However, it is also possible that dogs are simply not prosocial towards humans in food-giving contexts.
Published: 2021
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103. Visualisation of Chemical Shielding Tensors (VIST) to Elucidate Aromaticity and Antiaromaticity

Author: Plasser, Felix, Glöcklhofer, Florian, EPRSC, Engineering & Physical Science Research Council (EPSRC), and FWF Austrian Science Fund (FWF)
Subjects: Materials science, Full Paper, 0304 Medicinal and Biomolecular Chemistry, Aromaticity, Chemical shift, Organic Chemistry, π-Conjugated systems, Full Papers, 0305 Organic Chemistry, Hydrocarbons, Visualization, Theoretical physics, Chemical physics, Molecule, Physical and Theoretical Chemistry, Antiaromaticity, Chemical shielding
Abstract: Aromaticity is a central concept in chemistry, pervading areas from biochemistry to materials science. Recently, chemists also started to exploit intricate phenomena such as the interplay of local and global (anti)aromaticity or aromaticity in non‐planar systems and three dimensions. These phenomena pose new challenges in terms of our fundamental understanding and the practical visualisation of aromaticity. To overcome these challenges, a method for the visualisation of chemical shielding tensors (VIST) is developed here that allows for a 3D visualisation with quantitative information about the local variations and anisotropy of the chemical shielding. After exemplifying the method in different planar hydrocarbons, we study two non‐planar macrocycles to show the unique benefits of the VIST method for molecules with competing π‐conjugated systems and conclude with a norcorrole dimer showing clear evidence of through‐space aromaticity. We believe that the VIST method will be a highly valuable addition to the computational toolbox., A method for the visualisation of chemical shielding tensors (VIST) is developed, which provides a graphical representation of aromaticity and antiaromaticity, their local variations, and anisotropy. The method provides unique insight into fascinating phenomena such as the interplay of aromaticity and antiaromaticity in macrocycles with competing π‐conjugated systems.
Published: 2021
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104. Oligosilanylated Silocanes

Author: Meshgi, Mohammad Aghazadeh, Pocheim, Alexander, Baumgartner, Judith, Jouikov, Viatcheslav V., Marschner, Christoph, Technische Universität Graz (TU Graz), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Austrian Science Fund (Fonds zur Forderung der wissenschaftlichen Forschung) (FWF) Austrian Science Fund (FWF) [P 26417, P-30955], Austrian Exchange Service (OeAD) via the Scientific and Technological Cooperation project [FR 07/2018], French AMADEUS PHC program [39377YK], Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and 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)
Subjects: silanides, lcsh:QD241-441, Silicon, hypercoordination, lcsh:Organic chemistry, [CHIM]Chemical Sciences, Organosilicon Compounds, Silanes, DFT calculations, Article, cyclic voltammetry
Abstract: A number of mono- and dioligosilanylated silocanes were prepared. Compounds included silocanes with 1-methyl-1-tris(trimethylsilyl)silyl, 1,1-bis[tris(trimethylsilyl)silyl], and 1,1-bis[tris(trimethylsilyl)germyl] substitution pattern as well as two examples where the silocane silicon atom is part of a cyclosilane or oxacyclosilane ring. The mono-tris(trimethylsilyl)silylated compound could be converted to the respective silocanylbis(trimethylsilyl)silanides by reaction with KOtBu and in similar reactions the cyclosilanes were transformed to oligosilane-1,3-diides. However, the reaction of the 1,1-bis[tris(trimethylsilyl)silylated] silocane with two equivalents of KOtBu leads to the replacement of one tris(trimethylsilyl)silyl unit with a tert-butoxy substituent followed by silanide formation via KOtBu attack at one of the SiMe3 units of remaining tris(trimethylsilyl)silyl group. For none of the silylated silocanes, signs of hypercoordinative interaction between the nitrogen and silicon silocane atoms were detected either in the solid state. by single crystal XRD analysis, nor in solution by 29Si-NMR spectroscopy. This was further confirmed by cyclic voltammetry and a DFT study, which demonstrated that the N-Si distance in silocanes is not only dependent on the energy of a potential N-Si interaction, but also on steric factors and through-space interactions of the neighboring groups at Si and N, imposing the orientation of the pz(N) orbital relative to the N-Si-X axis.
Published: 2021
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105. Shrub growth in the Alps diverges from air temperature since the 1990s

Author: Francon, Loïc, Corona, Christophe, Till-Bottraud, Irène, Choler, Philippe, Roussel, Erwan, Carlson, Bradley, Morin, Samuel, Girard, Brigitte, Stoffel, Markus, Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Université Clermont Auvergne (UCA)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève (UNIGE), 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 (UGA), Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur les Ecosystèmes d'Altitude (CREA Mont-Blanc), Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Climate Change Impacts and Risks in the Anthropocene (C-CIA), Institute for Environmental Sciences, University of Geneva, program ProXyCliM - CNRS (Mission interdisciplinarite-RNMSH)Austrian Science Fund (FWF)FWF I 4918, ANR-20-CE91-0008,ACOUFOLLOW,ANALYSES DU DYSFONCTIONNEMENT ET DE LA REPARATION DU XYLÈME INDUIT PAR LE GEL CHEZ LES ARBUSTES, LES CONIFÈRES ET LES ARBRES À FEUILLES CADUQUES :(2020), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Université de Genève = University of Geneva (UNIGE), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and 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 -Centre National de la Recherche Scientifique (CNRS)
Subjects: ddc:333.7-333.9, dendroecology, Rhododendron ferrugineum, shrubs, climate change, topography, alpine, ddc:550, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, divergence
Abstract: In the European Alps, air temperature has increased almost twice as much as the global average over the last century and, as a corollary, snow cover duration has decreased substantially. In the Arctic, dendroecological studies have evidenced that shrub growth is highly sensitive to temperature—this phenomenon has often been linked to shrub expansion and ecosystem greening. Yet, the impacts of climate change on mountain shrub radial growth have not been studied with a comparable level of detail so far. Moreover, dendroecological studies performed in mountain environments did not account for the potential modulation and/or buffering of global warming impacts by topography, despite its possible crucial role in complex alpine environments. To fill this gap, we analyzed a network of eight sites dominated by the dwarf shrub Rhododendron ferrugineum. The sites selected for analysis represent the diversity of continentality, elevation and slope aspect that can be found across the French Alps. We quantified annual radial increment growth for 119 individuals, assembled meteorological reanalyzes specifically accounting for topographic effects (elevation, slope and aspect) and assessed climate-growth relations using a mixed modeling approach. In agreement with a vast majority of dendroecological work conducted in alpine and arctic environments, we find that the number of growing degree days during the snow-free period snow-free growing degree days (SFGDDs) is a strong and consistent driver of R. ferrugineum growth across all sites since 1960 until the late 1980s. We also document a marked loss of sensitivity of radial growth to increasing SFGDD since the 1990s, with this decoupling being more pronounced at the driest sites. Our observations of the spatial and temporal variability of shrub sensitivity to limiting factors can be compared to the ‘divergence' problem observed in tree-ring series from circumpolar and alpine regions and, accordingly, sheds light on possible future trajectories of alpine shrub growth in response to ongoing climate change.
Published: 2021
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106. Shortcomings of meta-GGA functionals when describing magnetism

Author: Fabien Tran, Georg K. H. Madsen, Peter Blaha, Guillaume Baudesson, Jesús Carrete, Karlheinz Schwarz, David J. Singh, Vienna University of Technology (TU Wien), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), University of Missouri System, Austrian Science Fund (FWF)Austrian Science Fund (FWF) [W1243], US Department of Energy, Basic Energy SciencesUnited States Department of Energy (DOE) [DE-SC0019114], Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and 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)
Subjects: Physics, Condensed Matter - Materials Science, Magnetic moment, Magnetism, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Ferromagnetism, 0103 physical sciences, [CHIM]Chemical Sciences, Antiferromagnetism, Condensed Matter::Strongly Correlated Electrons, Statistical physics, 010306 general physics, 0210 nano-technology
Abstract: International audience; Several recent studies have shown that SCAN, a functional belonging to the meta-generalized gradient approximation (MGGA) family, leads to significantly overestimated magnetic moments in itinerant ferromagnetic metals. However, this behavior is not inherent to the MGGA level of approximation since TPSS, for instance, does not lead to such severe overestimations. In order to provide a broader view of the accuracy of MGGA functionals for magnetism, we extend the assessment to more functionals but also to antiferromagnetic solids. The results show that to describe magnetism there is overall no real advantage in using a MGGA functional compared to GGAs. For both types of approximation, an improvement in ferromagnetic metals is necessarily accompanied by a deterioration (underestimation) in antiferromagnetic insulators, and vice versa. We also provide some analysis in order to understand in more detail the relation between the mathematical form of the functionals and the results.
Published: 2020
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107. RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes

Author: Gregor Entzian, Ronny Lorenz, Yann Ponty, Ivo L. Hofacker, Andrea Tanzer, 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), ANR-14-CE34-0011,RNALands,Fast and Efficient Sampling of Structures in RNA Folding Landscapes(2014), and This work has been supported by the Austrian/French project RNALands (ANR-14-CE34-0011 & FWF I 1804 N28), the FWF Elise-Richter project ’RNAmod’ (FWF V 762) and the Austrian science fund FWF project SFP F43 Regulation of the RNA transcriptome.
Subjects: Statistics and Probability, Adaptive sampling, AcademicSubjects/SCI01060, Computer science, 0206 medical engineering, 02 engineering and technology, Biochemistry, 03 medical and health sciences, symbols.namesake, State space, Molecular Biology, 030304 developmental biology, 0303 health sciences, Sampling (statistics), Folding (DSP implementation), Original Papers, Structural Bioinformatics, Computer Science Applications, Dynamic programming, Computational Mathematics, Computational Theory and Mathematics, symbols, Benchmark (computing), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithm, 020602 bioinformatics, Combinatorial explosion, Gibbs sampling
Abstract: Motivation Predicting the folding dynamics of RNAs is a computationally difficult problem, first and foremost due to the combinatorial explosion of alternative structures in the folding space. Abstractions are therefore needed to simplify downstream analyses, and thus make them computationally tractable. This can be achieved by various structure sampling algorithms. However, current sampling methods are still time consuming and frequently fail to represent key elements of the folding space. Method We introduce RNAxplorer, a novel adaptive sampling method to efficiently explore the structure space of RNAs. RNAxplorer uses dynamic programming to perform an efficient Boltzmann sampling in the presence of guiding potentials, which are accumulated into pseudo-energy terms and reflect similarity to already well-sampled structures. This way, we effectively steer sampling toward underrepresented or unexplored regions of the structure space. Results We developed and applied different measures to benchmark our sampling methods against its competitors. Most of the measures show that RNAxplorer produces more diverse structure samples, yields rare conformations that may be inaccessible to other sampling methods and is better at finding the most relevant kinetic traps in the landscape. Thus, it produces a more representative coarse graining of the landscape, which is well suited to subsequently compute better approximations of RNA folding kinetics. Availabilityand implementation https://github.com/ViennaRNA/RNAxplorer/. Supplementary information Supplementary data are available at Bioinformatics online.
Published: 2020
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108. Eigenvector models for solving the seismic inverse problem for the Helmholtz equation

Author: Otmar Scherzer, Florian Faucher, Hélène Barucq, Faculty of Mathematics [Vienna], University of Vienna [Vienna], Advanced 3D Numerical Modeling in Geophysics (Magique 3D), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Florian Faucher is funded by the Austrian Science Fund (FWF) under the Lise Meitnerfellowship M 2791-N. The research of Florian Faucher is also supported by the Inria–TOTAL strategic action DIP. Otmar Scherzer is supported by the FWF, with SFBF68, project F6807-N36 (Tomography with Uncertainties).Otmar Scherzer also acknowledges support from the FWF via the project I3661-N27 (Novel Error Measures and Source Conditions of Regularization Methods for Inverse Problems). Hélène Barucq acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement Number 777778 (Rise action Mathrocks) and with the E2S–UPPA CHICkPEA project.
Subjects: Waveform inversion, Diffusion equation, Partial differential equation, Seismic tomography, Wave propagation, Helmholtz equation, Basis (linear algebra), Computer science, Inverse transform sampling, Inverse problem, 010502 geochemistry & geophysics, 01 natural sciences, 010101 applied mathematics, Seismic tomog-raphy, Geophysics, Image processing, Geochemistry and Petrology, Numerical modelling, Applied mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], 0101 mathematics, Representation (mathematics), [SDU.STU.AG]Sciences of the Universe [physics]/Earth Sciences/Applied geology, Eigenvalues and eigenvectors, 0105 earth and related environmental sciences
Abstract: SUMMARY We study the seismic inverse problem for the recovery of subsurface properties in acoustic media. In order to reduce the ill-posedness of the problem, the heterogeneous wave speed parameter is represented using a limited number of coefficients associated with a basis of eigenvectors of a diffusion equation, following the regularization by discretization approach. We compare several choices for the diffusion coefficient in the partial differential equations, which are extracted from the field of image processing. We first investigate their efficiency for image decomposition (accuracy of the representation with respect to the number of variables). Next, we implement the method in the quantitative reconstruction procedure for seismic imaging, following the full waveform inversion method, where the difficulty resides in that the basis is defined from an initial model where none of the actual structures is known. In particular, we demonstrate that the method may be relevant for the reconstruction of media with salt-domes. We use the method in 2-D and 3-D experiments, and show that the eigenvector representation compensates for the lack of low-frequency information, it eventually serves us to extract guidelines for the implementation of the method.
Published: 2020
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109. Evaluation of soil erosion risk and identification of soil cover and management factor (C) for RUSLE in European vineyards with different soil management

Author: Giorgio Capello, Daniela Popescu, Marcella Biddoccu, Daniel Cluzeau, Peter Strauss, José A. Gómez, Eugenio Cavallo, Gema Guzmán, Silvia Winter, Annegret Nicolai, Adela Hoble, Claudiu Bunea, Johann G. Zaller, T. Thielke, Spanish National Research Council (CSIC), Institute for land and water management research, University of Natural Resources and Life Sciences (BOKU), University of Natural Resources and Life Sciences, Department of Integrated Biology and Biodiversity Research, Institute of Zoology (BOKU), 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), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), University of Agricultural Sciences and Veterinary Medicine Cluj Napoca, European BiodivERsA project VineDivers through the BiodivERsA/FACCE JPI (2013-2014 joint call) for research proposals, Austrian Science Fund Austrian Science Fund (FWF) [I 2044-/I 2043-/I 2042-B25 FWF], Spanish Ministry of Economy and Competitiveness [PCIN2014-098], Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI), European Commissio nEuropean Commission European Commission Joint Research Centre [773903], Federal Ministry of Education and Research (BMBF/Germany) Federal Ministry of Education and Research (BMBF), French National Research Agency (ANR) French National Research Agency (ANR), CNR Short Term Mobility Program 2016, ANR-14-EBID-0006,VineDivers,Biodiversity-based ecosystem services in vineyards: analysing interlinkages between plants, pollinators, soil biota and soil erosion across Europe(2014), European Commission, Austrian Science Fund, Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), Ministry of Education and Research (Romania), Federal Ministry of Education and Research (Germany), Consiglio Nazionale delle Ricerche, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), 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), Université de Rennes (UR), and University of Agricultural Sciences and Veterinary Medicine Cluj Napoca = Universitatea de Științe Agricole și Medicină Veterinară Cluj-Napoca
Subjects: Soil management, 0208 environmental biotechnology, Soil Science, 02 engineering and technology, Vineyard, RUSLE, Cover crop, Water content, Nature and Landscape Conservation, Water Science and Technology, 2. Zero hunger, Land use, 04 agricultural and veterinary sciences, 15. Life on land, 020801 environmental engineering, Water resources, Europe, Universal Soil Loss Equation, lcsh:TA1-2040, Erosion, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Spatial variability, Water resource management, lcsh:Engineering (General). Civil engineering (General), Agronomy and Crop Science
Abstract: Vineyards show some of the largest erosion rates reported in agricultural areas in Europe. Reported rates vary considerably under the same land use, since erosion processes are highly affected by climate, soil, topography and by the adopted soil management practices. Literature also shows differences in the effect of same conservation practices on reducing soil erosion from conventional, bare soil based, management. The Revised Universal Soil Loss Equation (RUSLE) is commonly adopted to estimate rates of water erosion on cropland under different forms of land use and management, but it requires proper value of soil cover and management (C) factors in order to obtain a reliable evaluation of local soil erosion rates. In this study the ORUSCAL (Orchard RUSle CALibration) is used to identify the best calibration strategy against long-term experimental data. Afterwards, ORUSCAL is used in order to apply the RUSLE technology from farm based information across different European wine-growing regions. The results suggest that the best strategy for calibration should incorporate the soil moisture sub-factor (Sm) to provide better soil loss predictions. The C factor, whose average values ranged from 0.012 to 0.597, presented a large spatial variability due to coupling with local climate and specific local management. The comparison across the five wine-growing regions indicates that for the soil protection management, permanent cover crop is the best measure for accomplishing sustainable erosion rates across the studied areas. Alternate and temporary cover crops, that are used in areas of limited water resources to prevent competition with vines, failed to achieve sustainable erosion rates, that still need to be addressed. This raises the need for a careful use of C values developed under different environmental conditions., This study was funded by the European BiodivERsA project VineDivers (https://short.boku.ac.at/vinedivers) through the BiodivERsA/FACCE JPI (2013–2014 joint call) for research proposals, with the national funders: Austrian Science Fund (grant numbers I 2044-/I 2043-/I 2042-B25 FWF), French National Research Agency (ANR), Spanish Ministry of Economy and Competitiveness (PCIN-2014-098), Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) and Federal Ministry of Education and Research (BMBF/Germany). Also to the CNR Short Term Mobility Program 2016 for funding a stay at IAS-CSIC during which M.Biddoccu contributed to this study and the SHui project funded by the European Commission (GA 773903), which supported the final steps of the analysis presented in this manuscript.
Published: 2020
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110. Loss and fractionation of noble gas isotopes and moderately volatile elements from planetary embryos and early Venus, Earth and Mars

Author: Colin P. Johnstone, Bernard Marty, Martin Leizinger, Hiroyuki Kurokawa, Yuichiro Ueno, Manuel Scherf, Helmut Lammer, Thomas I. Maindl, Bruce Fegley, Luca Fossati, Kristina G. Kislyakova, Christoph Burger, Petra Odert, Markus Benedikt, Guillaume Avice, Space Research Institute of Austrian Academy of Sciences (IWF), Austrian Academy of Sciences (OeAW), Earth-Life Science Institute [Tokyo] (ELSI), Tokyo Institute of Technology [Tokyo] (TITECH), Institut für Astrophysik [Wien], Universität Wien, Institute for Geophysics, Astrophysics and Meteorology [Graz] (IGAM), Karl-Franzens-Universität Graz, Centre de Recherches Pétrographiques et Géochimiques (CRPG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Washington Univ, Dept Earth & Planetary Sci, St Louis, MO 63130 USA, McDonnell Center for Space Sciences, Washington University in St Louis, and Austrian Science Fund (FWF)S116-N16S11604-N16S11606-N16S11607-N16S11608-N16S11603-N16Austrian Science Fund (FWF)P27256-N27P30949-N36Austrian Forschungsforderungsgesellschaft (FFG) project RASEN Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of ScienceGrants-in-Aid for Scientific Research (KAKENHI)17H0117517H0645718K1360219H0196019H05072FFG project 'TAPAS4CHEOPS' P853993
Subjects: 010504 meteorology & atmospheric sciences, FOS: Physical sciences, Magma oceans, 01 natural sciences, Rock-forming elements, Astrobiology, Physics::Geophysics, Protoplanetary disk, Isotopes, Planet, 0103 physical sciences, 010303 astronomy & astrophysics, Volatiles, Physics::Atmospheric and Oceanic Physics, 0105 earth and related environmental sciences, Hydrodynamic escape, Earth and Planetary Astrophysics (astro-ph.EP), Atmospheric escape, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], Primordial atmospheres, Steam atmospheres, Noble gas, Astronomy and Astrophysics, Crust, Mars Exploration Program, Noble gases, Planetary science, 13. Climate action, Space and Planetary Science, [SDU]Sciences of the Universe [physics], Physics::Space Physics, Environmental science, Astrophysics::Earth and Planetary Astrophysics, Planetary evolution, Astrophysics - Earth and Planetary Astrophysics
Abstract: Here we discuss the current state of knowledge on how atmospheric escape processes can fractionate noble gas isotopes and moderately volatile rock-forming elements that populate primordial atmospheres, magma ocean related environments, and catastrophically outgassed steam atmospheres. Variations of isotopes and volatile elements in different planetary reservoirs keep information about atmospheric escape, composition and even the source of accreting material. We summarize our knowledge on atmospheric isotope ratios and discuss the latest evidence that proto-Venus and Earth captured small H$_2$-dominated primordial atmospheres that were lost by EUV-driven hydrodynamic escape after the disk dispersed. All relevant thermal and non-thermal atmospheric escape processes that can fractionate various isotopes and volatile elements are discussed. Erosion of early atmospheres, crust and mantle by large planetary impactors are also addressed. Further, we discuss how moderately volatile elements such as the radioactive heat producing element $^{40}$K and other rock-forming elements such as Mg can also be outgassed and lost from magma oceans that originate on large planetary embryos and accreting planets. Outgassed elements escape from planetary embryos with masses that are $\geq$\,M$_{\rm Moon}$ directly, or due to hydrodynamic drag of escaping H atoms originating from primordial- or steam atmospheres at more massive embryos. We discuss how these processes affect the final elemental composition and ratios such as K/U, Fe/Mg of early planets and their building blocks. Finally, we review modeling efforts that constrain the early evolution of Venus, Earth and Mars by reproducing their measured present day atmospheric $^{36}$Ar/$^{38}$Ar, $^{20}$Ne/$^{22}$Ne noble gas isotope ratios and the role of isotopes on the loss of water and its connection to the redox state on early Mars., Comment: 65 pages, 17 figures. This is a preprint of an article published in Space Science Reviews. The final authenticated version can be found online at: https://doi.org/10.1007/s11214-020-00701-x
Published: 2020
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111. Podoplanin Gene Disruption in Mice Promotes in vivo Neural Progenitor Cells Proliferation, Selectively Impairs Dentate Gyrus Synaptic Depression and Induces Anxiety-Like Behaviors

Author: Cicvaric, Ana, Sachernegg, Hannah M., Stojanovic, Tamara, Symmank, Dörte, Smani Hajami, Tarik, Moeslinger, Thomas, Monje, Francisco J., Universidad de Sevilla. Departamento de Fisiología Médica y Biofísica, CTS-200: Transplante Corazón, Conservación Corazón Donante, and Austrian Science Fund [FWF]Austrian Science Fund (FWF) [P_27551].
Subjects: NGF, Podoplanin, Neurogenesis, LTD, Anxiety-like behavior, Hippocampus, Cell proliferation
Abstract: Podoplanin (Pdpn), a brain-tumor-related glycoprotein identified in humans and animals, is endogenously expressed in several organs critical for life support such as kidney, lung, heart and brain. In the brain, Pdpn has been identified in proliferative nestin- positive adult neural progenitor cells and in neurons of the neurogenic hippocampal dentate gyrus (DG), a structure associated to anxiety, critical for learning and memory functions and severely damaged in people with Alzheimer’s Disease (AD). The in vivo role of Pdpn in adult neurogenesis and anxiety-like behavior remained however unexplored. Using mice with disrupted Pdpn gene as a model organism and applying combined behavioral, molecular biological and electrophysiological assays, we here show that the absence of Pdpn selectively impairs long-term synaptic depression in the neurogenic DG without affecting the CA3-Schaffer’s collateral-CA1 synapses. Pdpn deletion also enhanced the proliferative capacity of DG neural progenitor cells and diminished survival of differentiated neuronal cells in vitro. In addition, mice with podoplanin gene disruption showed increased anxiety-like behaviors in experimentally validated behavioral tests as compared to wild type littermate controls. Together, these findings broaden our knowledge on the molecular mechanisms influencing hippocampal synaptic plasticity and neurogenesis in vivo and reveal Pdpn as a novel molecular target for future studies addressing general anxiety disorder and synaptic depression-related memory dysfunctions.
Published: 2020

112. A mathematical model of p62-ubiquitin aggregates in autophagy

Author: Julia Delacour, Marie Doumic, Sascha Martens, Christian Schmeiser, Gabriele Zaffagnini, Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Vienna [Vienna], Max Perutz Labs, Fakultät für Mathematik [Wien], Universität Wien, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), This work has been supported by the PhD program Signalling Mechanisms in Cellular Autophagy,funded by the Austrian Science Fund (FWF), project no. W1261. CS acknowledges support by FWF, grant nos. W1245 and SFB65. MD and JD have been partially supported by the ERC Starting Grant SKIPPERAD (number 306321)., European Project: 306321,EC:FP7:ERC,ERC-2012-StG_20111012,SKIPPERAD(2012), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: 0303 health sciences, Statistical Mechanics (cond-mat.stat-mech), Ubiquitin, Applied Mathematics, Proteins, FOS: Physical sciences, Biomolecules (q-bio.BM), Models, Theoretical, Agricultural and Biological Sciences (miscellaneous), Article, 92C40 Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Quantitative Biology - Biomolecules, 92C40, Modeling and Simulation, FOS: Biological sciences, Sequestosome-1 Protein, Autophagy, molecular biology, [MATH]Mathematics [math], Condensed Matter - Statistical Mechanics, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Aggregation of ubiquitinated cargo by oligomers of the protein p62 is an important preparatory step in cellular autophagy. In this work a mathematical model for the dynamics of these heterogeneous aggregates in the form of a system of ordinary differential equations is derived and analyzed. Three different parameter regimes are identified, where either aggregates are unstable, or their size saturates at a finite value, or their size grows indefinitely as long as free particles are abundant. The boundaries of these regimes as well as the finite size in the second case can be computed explicitly. The growth in the third case (quadratic in time) can also be made explicit by formal asymptotic methods. In the absence of rigorous results the dynamic stability of these structures has been investigated by numerical simulations. A comparison with recent experimental results permits a partial parametrization of the model. This work has been supported by the PhD program Signalling Mechanisms in Cellular Autophagy, funded by the Austrian Science Fund (FWF), project no. W1261. CS also acknowledges support by FWF, Grant Nos. W1245 and SFB65. MD and JD have been partially supported by the ERC Starting Grant SKIPPERAD (Number 306321). MD thanks the Wolfgang Pauli Institute for the sabbatical stay in Vienna during which this work has been initiated.
Published: 2020
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113. Vegetation management intensity and landscape diversity alter plant species richness, functional traits and community composition across European vineyards

Author: Hall, Rea M., Penke, Nicole, Kriechbaum, Monika, Kratschmer, Sophie, Jung, Vincent, Chollet, Simon, Guernion, Muriel, Nicolai, Annegret, Burel, Françoise, Fertil, Albin, Lora González, Ángel, Sánchez-Cuesta, Rafael, Guzmán, Gema, Gómez Calero, José Alfonso, Popescu, Daniela, Hoble, Adela, Bunea, Claudiu-Ioan, Zaller, Johann G., Winter, Silvia, University of Natural Resources and Life Sciences (BOKU), 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), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), University of Córdoba [Córdoba], Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Babes-Bolyai University [Cluj-Napoca] (UBB), Agence Nationale de la Recherche, ANR, Austrian Science Fund, FWF I 2044-B25 FWF, Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii, UEFISCDI, Bundesministerium für Bildung und Forschung, BMBF, Ministerio de Economía y Competitividad, MINECO, ANR-16-EBI3-0016,SoilMan,Ecosystem services driven by the diversity of soil biota – understanding and management -(2016), Austrian Science Fund, Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), Executive Unit for Financing Higher Education, Research, Development and Innovation (Romania), Federal Ministry of Education and Research (Germany), Plant Trait Database, German Centre for Integrative Biodiversity Research, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), 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), Université de Rennes (UR), Universidad de Córdoba = University of Córdoba [Córdoba], and ANR-14-EBID-0006,VineDivers,Biodiversity-based ecosystem services in vineyards: analysing interlinkages between plants, pollinators, soil biota and soil erosion across Europe(2014)
Subjects: [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Cover crops, Herbicides, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, Ecosystem services, Landscape, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agroecology, Tillage
Abstract: Land-use intensification at the field and landscape scale is a strong driver for declining biodiversity and ecosystem service provision. Vineyards are characterised by non-productive inter-rows, which could potentially host diverse plant communities. Mulching, tillage or herbicides are used to mitigate the competition between vines and the inter-row vegetation. As plant species with the same set of functional traits will respond similarly to environmental filters like management measures, knowledge about plant trait–environment-relations can be used to predict community and ecosystem processes which are essential for preserving ecosystem services like soil erosion mitigation. We hypothesized that higher vegetation management intensity reduces plant (functional) diversity, changes functional traits and community composition. Across Europe, four viticultural regions in Austria, France, Spain and Romania, which comprised 78 vineyards differing in vegetation management intensity (bare soil, temporary and permanent vegetation cover), were selected for sampling vascular plant diversity. Around each vineyard, the surrounding landscape composition and landscape diversity was investigated within a 750 m radius. Rao's quadratic entropy as a measure of functional diversity was calculated based on a selection of plant functional traits. The effects of management and landscape variables on species richness, functional traits, functional diversity and vegetation cover were analysed by generalized linear mixed models and random forests (RF). Furthermore, plant community composition was analysed with non-metric multidimensional scaling (NMDS). Higher management intensities resulted in lower species richness, functional diversity and vegetation cover. The country with the related divergent edaphoclimatic conditions was a significant factor affecting most diversity and functional trait parameters, whereas landscape diversity increased plant species richness only slightly. Vegetation management intensity had the highest explanatory power for species richness, functional diversity and most functional traits according to RF analysis. Consequently, plant functional traits like a higher coverage of ruderals and annuals could be clearly related to bare soil management. Furthermore, the type of cover crops influenced the relationship between annual and perennial plant species, Grime plant strategy types and species diversity. Accordingly, NMDS showed a separation between permanent vegetation cover and bare soil vineyards. The overall positive effect of extensive management and the use of diverse cover crops or spontaneous vegetation in vineyard inter-rows should be better implemented in agricultural policies to support both, biodiversity and ecosystem provision., This study was funded by the European BiodivERsA project VineDivers (www.vinedivers.eu) through the BiodivERsA/FACCE JPI (2013-2014 joint call) for research proposals, with the national funders: Austrian Science Fund (grant number I 2044-B25 FWF), French National Research Agency (ANR), Spanish Ministry of Economy and Competitiveness (MINECO), Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) and Federal Ministry of Education and Research (BMBF/Germany). We would like to thank all winegrowers who provided information regarding vineyard management and provided access to their vineyards as study sites. The study has been supported by the TRY initiative on plant traits (http://www.try-db.org). The TRY initiative and database is hosted, developed and maintained by J. Kattge and G. Bönisch (Max Planck Institute for Biogeochemistry, Jena, Germany). TRY is currently supported by DIVERSITAS/Future Earth and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig.
Published: 2020
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114. Neural Networks for Cross-Section Segmentation in Raw Images of Log Ends

Author: Rémi Decelle, Ehsaneddin Jalilian, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Applying Discrete Algorithms to Genomics and Imagery (ADAGIO), Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria), University of Salzburg, This research was made possible by support from both the French National Research Agency and the Austrian Science Fund (FWF), in the framework of the project TreeTrace, ANR-17-CE10-0016 and FWF International Project I-3653., ANR-17-CE10-0016,TreeTrace,Les empreintes biométriques des arbres : traçage de la forêt à la scierie et évaluation précoce de la qualité(2017), Decelle, Rémi, Les empreintes biométriques des arbres : traçage de la forêt à la scierie et évaluation précoce de la qualité - - TreeTrace2017 - ANR-17-CE10-0016 - AAPG2017 - VALID, 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), and 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)
Subjects: Pixel-wisesegmentation, Artificial neural network, business.industry, Computer science, Feature extraction, [SCCO.COMP]Cognitive science/Computer science, Pattern recognition, Image processing, 02 engineering and technology, Image segmentation, 010501 environmental sciences, 01 natural sciences, Wood quality, Tree (data structure), Sawmill scenes, Feature (computer vision), [SCCO.COMP] Cognitive science/Computer science, Deep convolutional neural networks, 0202 electrical engineering, electronic engineering, information engineering, RGB color model, 020201 artificial intelligence & image processing, Segmentation, Artificial intelligence, business, 0105 earth and related environmental sciences
Abstract: International audience; In this paper, wood cross-section (CS) segmentationof RGB images is treated. CS segmentation has already been studied for computed tomography images, but few study focuses on RGB images. CS segmentation in rough log ends is an important feature for the both assessment of wood quality and wood traceability. Indeed, it allows to extract other features like pith, eccentricity (distance between the pith and the geometriccentre) or annual tree rings which are related to mechanical strength. In image processing, neural networks have been widely used to solve the problem of objects segmentation. In this paper, we propose to compare different state-of-the-art neural networks for CS segmentation task. In particular, we consider U-Net, Mask R-CNN, RefineNet and SegNet. We create an imageset which has been split into 6 subsets . Considered neural networks have been trained on each subset in order to compare their performance on different type of images. Results show different behaviors between neural networks. On the one hand, overall U-Net learns better on small dataset than the others. On the other hand, RefineNet learns well on huge dataset. While SegNetis less efficient and Mask R-CNN does not provide a detailed segmentation. This offers a preliminary result on neural network performances for CS segmentation.
Published: 2019

115. Serum resistance and phase variation of a nasopharyngeal non-typeable Haemophilus influenzae isolate

Author: Sabine Lichtenegger, Philippe Glaser, Isabelle Bina, Sanel Durakovic, Stefan Schild, Joachim Reidl, Sarah Tutz, Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria, Institute of Molecular Biosciences, Karl-Franzens-Universität [Graz, Autriche], Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BioTechMed Graz [Graz, Autriche], Work was supported by the Austrian Science Fund (FWF) ERA-NET FWF I 662-B09 to SL, and JR. Clinical NTHi isolates were donatedby AGES-Graz (Agentur Gesundheit und ErnaehrungssicherheitGmbH/Zentrum fuer lebensmittelbedingte Infektionskrankheiten,Dr. Georg Steindl, AGES Graz) and the Institute for Hygieneand Microbiology (Dr. Thien-Tri Lam, University of Wuerzburg,Germany), University of Graz, Karl-Franzens-Universität Graz, and Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Mutant, Clone (cell biology), medicine.disease_cause, Haemophilus influenzae, MESH: Genotype, chemistry.chemical_compound, MESH: Child, Nasopharynx, MESH: Immune Evasion, Child, education.field_of_study, MESH: Blood Bactericidal Activity, General Medicine, Antigenic Variation, Phenotype, Endocytosis, 3. Good health, MESH: Multilocus Sequence Typing, Infectious Diseases, MESH: Endocytosis, MESH: Glycosyltransferases, MESH: Antigenic Variation, lpsA, Adult, Microbiology (medical), Blood Bactericidal Activity, Genotype, 030106 microbiology, Population, Biology, MESH: Alveolar Epithelial Cells, Microbiology, Cell Line, 03 medical and health sciences, medicine, Humans, education, Immune Evasion, Phase variation, Serum resistance, MESH: Humans, Glycosyltransferases, MESH: Adult, MESH: Haemophilus influenzae, MESH: Nasopharynx, MESH: Cell Line, Sialic acid, 030104 developmental biology, chemistry, Alveolar Epithelial Cells, Multilocus sequence typing, Multilocus Sequence Typing
Abstract: International audience; Haemophilus influenzae harbours a complex array of factors to resist human complement attack. As non-typeable H. influenzae (NTHi) strains do not possess a capsule, their serum resistance mainly depends on other mechanisms including LOS decoration. In this report, we describe the identification of a highly serum resistant, nasopharyngeal isolate (NTHi23) by screening a collection of 77 clinical isolates. For NTHi23, we defined the MLST sequence type 1133, which matches the profile of a previously published invasive NTHi isolate. A detailed genetic analysis revealed that NTHi23 shares several complement evading mechanisms with invasive disease isolates. These mechanisms include the functional expression of a retrograde phospholipid trafficking system and the presumable decoration of the LOS structure with sialic acid. By screening the NTHi23 population for spontaneous decreased serum resistance, we identified a clone, which was about 103-fold more sensitive to complement-mediated killing. Genome-wide analysis of this isolate revealed a phase variation in the N'-terminal region of lpsA, leading to a truncated version of the glycosyltransferase (LpsA). We further showed that a NTHi23 lpsA mutant exhibits a decreased invasion rate into human alveolar basal epithelial cells. Since only a small proportion of the NTHi23 population expressed the serum sensitive phenotype, resulting from lpsA phase-off, we conclude that the nasopharyngeal environment selected for a population expressing the intact and functional glycosyltransferase.
Published: 2017
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116. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

Author: Maria Theresia Pöschko, VV Rodin, Norbert Müller, Hervé Desvaux, Judith Schlagnitweit, Institute of Organic Chemistry, Johannes Kepler Universität Linz - Johannes Kepler University Linz [Autriche] (JKU), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the Austrian Science Funds (FWF) and the Agence Nationale de Recherche (ANR) in the joint project IMAGINE (FWF project number I1115-N19, ANR project 12-IS04-0006) and by the EGIDE-OAD AMADEUS Austrian-French exchange programme (no 28948WD and FR 11/2013). The Avance III 700 MHz NMR spectrometer was co-financed by the European Union through the INTERREG IV ETC-AT-CZ programme (EFRE RU2-EU-124/100-2010, project M00146 ‘RERI-uasb’)., ANR-12-IS04-0006,IMAGINE,Etudes RMN d'effets non-linéaires induits par l'aimantation(2012), Johannes Kepler University Linz [Linz] (JKU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Materials science, Science, General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Molecular physics, Noise (electronics), General Biochemistry, Genetics and Molecular Biology, Magnetization, Nuclear magnetic resonance, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Dispersion (optics), Spin (physics), Coupling, Multidisciplinary, Chemical shift, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Magnetostatics, equipment and supplies, 0104 chemical sciences, Erratum, 0210 nano-technology, human activities, Excitation
Abstract: The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements.
Published: 2017
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117. Tillage intensity or landscape features What matters most for wild bee diversity in vineyards?

Author: Kratschmer, Sophie, Pachinger, B., Schwantzer, M., Paredes, Daniel, Guernion, M., Burel, F., Nicolai, Annegret, Strauss, Peter, Bauer, Thomas, Kriechbaum, Monika, Zaller, J.G., Winter, Silvia, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Spanish National Research Council (CSIC), 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), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes (UR), Institute for land and water management research, ANR, Agence Nationale de la Recherche, I 2044-B25 FWF, FWF, Austrian Science Fund, UEFISCDI, Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii, 2044-B25, BMBF, Bundesministerium für Bildung und Forschung, MINECO, Ministerio de Economía y Competitividad, Austrian Science Fund, Federal Ministry of Education and Research (Germany), Ministerio de Economía y Competitividad (España), University of Natural Resources and Life Sciences (BOKU), 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), and Université de Rennes 1 (UR1)
Subjects: Floral resources, Apiformes, Ecosystem services, Landscape, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Vineyard, Tillage
Abstract: Vineyard inter-rows can provide habitats for a range of plant and animal species especially when covered with vegetation. However, frequent tillage results in the degradation of habitat quality and the provision of biodiversity-based ecosystem services. Wild bees are important pollinators of crops and wild plants and depend on both, floral resources and suitable nesting sites, which are influenced by the landscape configuration. We examined effects of field and landscape parameters on wild bee species’ richness, abundance and functional traits in Austrian vineyards over two years using Generalised Linear Mixed models, Detrended Correspondence Analysis and Random Forests. Alternating tillage was compared with no tillage in two inter-rows per vineyard. Forage availability in these inter-rows was estimated by flower coverage at each sampling date, and landscape features were analysed within a radius of 750 m around the vineyards. Across all vineyards we found 84 wild bee species with a mean abundance (±SD) of 29 (±16.6). Forage availability had the strongest positive effect on wild bee diversity and abundance. In comparison to no tillage, alternating tillage slightly increased wild bee diversity and abundance. Eusocial wild bees were more abundant in untilled inter-rows, whereas solitary wild bees were more closely associated with alternating tilled vineyards. At the landscape scale, the percentage of artificial areas (mostly villages) and distance to semi-natural elements raised wild bee diversity and abundance. The proportion of woodland increased the abundance of wild bees, in particular of eusocial taxa. Solitary wild bee abundance was enhanced by the number of solitary trees. Pollination provided by wild bees in viticultural areas can be enhanced by maintaining a diversity of different soil management strategies to improve forage availability in vineyards. Furthermore, semi-natural elements such as fallows or solitary trees providing floral resources and nesting habitat should be preserved within viticultural landscapes., This research is part of the BiodivERsA project VineDivers (www.vinedivers.eu) and was funded through the BiodivERsA/FACCE JPI (2013-2014 joint call) for research proposals, with the national funders: Austrian Science Fund (grant number I 2044-B25FWF), French National Research Agency (ANR), Spanish Ministry of Economy and Competitiveness (MINECO), Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) and Federal Ministry of Education and Research (BMBF/Germany). The open access funding was provided by the Austrian Science Fund: I 2044-B25. We are grateful to Johann Grassl and to the winegrowers in the Neusiedlersee-Hügelland and Carnuntum region for allowing us to study their vineyards.
Published: 2018
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118. Ultraviolet exposure regulates skin metabolome based on the microbiome

Author: Vijaykumar Patra, Natalie Bordag, Yohann Clement, Harald Köfeler, Jean-Francois Nicolas, Marc Vocanson, Sophie Ayciriex, Peter Wolf, Medical University Graz, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Medical University of Graz, CheMod, Institut des Sciences Analytiques (ISA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANABIO-MS - Analyse biomoléculaire par spectrométrie de masse - Biological Analysis by Mass Spectrometry, BioTechMed-Graz, Graz University of Technology [Graz] (TU Graz)-Karl-Franzens-Universität Graz-Medical University Graz, and Austrian Science Fund (FWF, W1241)
Subjects: [STAT]Statistics [stat], Multidisciplinary, [SDV]Life Sciences [q-bio]
Abstract: Skin metabolites (
Published: 2023
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119. Shadow prices, fractional Brownian motion, and portfolio optimisation under transaction costs

Author: Junjian Yang, Christoph Czichowsky, Walter Schachermayer, Rémi Peyre, London School of Economics and Political Science (LSE), Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Fakultät für Mathematik [Wien], Universität Wien, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Rémi Peyre is partially supported by the Austrian Science Fund (FWF) under grant P25815., Walter Schachermayer is partially supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation and also partially supported by the Austrian Science Fund (FWF) under grants P25815 and P28661 and by the Vienna Science and Technology Fund (WWTF) under grant MA14-008., and Junjian Yang is partially supported by the Austrian Science Fund (FWF) under grant P25815
Subjects: Statistics and Probability, Mathematical optimization, MSC 2010: 91G10, 93E20, 60G48, Shadow price, [QFIN.PM]Quantitative Finance [q-fin]/Portfolio Management [q-fin.PM], fractional Brownian motion, [MATH.MATH-FA]Mathematics [math]/Functional Analysis [math.FA], 01 natural sciences, 91G10, 93E20, 60G48, FOS: Economics and business, 010104 statistics & probability, Mathematics::Probability, 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, 0502 economics and business, Economics, JEL: G - Financial Economics/G.G1 - General Financial Markets/G.G1.G11 - Portfolio Choice • Investment Decisions, QA Mathematics, 0101 mathematics, proportional transaction costs, Brownian motion, 050208 finance, Fractional Brownian motion, Mathematical finance, 05 social sciences, Financial market, Mathematical Finance (q-fin.MF), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Semimartingale, shadow prices, two-way crossing, Quantitative Finance - Mathematical Finance, Portfolio, Arbitrage, logarithmic utility, Statistics, Probability and Uncertainty, Mathematical economics, Finance
Abstract: We continue the analysis of our previous paper (Czichowsky/Schachermayer/Yang 2014) pertaining to the existence of a shadow price process for portfolio optimisation under proportional transaction costs. There, we established a positive answer for a continuous price process $S=(S_t)_{0\leq t\leq T}$ satisfying the condition $(NUPBR)$ of "no unbounded profit with bounded risk". This condition requires that $S$ is a semimartingale and therefore is too restrictive for applications to models driven by fractional Brownian motion. In the present paper, we derive the same conclusion under the weaker condition $(TWC)$ of "two way crossing", which does not require $S$ to be a semimartingale. Using a recent result of R.~Peyre, this allows us to show the existence of a shadow price for exponential fractional Brownian motion and $all$ utility functions defined on the positive half-line having reasonable asymptotic elasticity. Prime examples of such utilities are logarithmic or power utility.
Published: 2018
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120. Acyl-CoA-Binding Protein Is a Lipogenic Factor that Triggers Food Intake and Obesity

Author: Nektarios Tavernarakis, Mireia Niso-Santano, Lorenzo Galluzzi, Violeta Raverdy, Friedemann Loos, Guido Kroemer, François Pattou, Céline Cruciani-Guglielmacci, Patricia Boya, Justine Lallement, Frank Madeo, Jessica Denom, Ignacio Ramírez-Pardo, Karine Clément, Christophe Magnan, Isabelle Martins, Sylvère Durand, Raphaël G. P. Denis, Noélie Bossut, Maria Chiara Maiuri, Véronique Pelloux, Robert Caiazzo, Valentina Sica, Erwan Boedec, Alili Rohia, Stéphanie Migrenne-Li, José Manuel Bravo-San Pedro, Jonathan Pol, Nicolas Ramoz, Fernando Aranda, Philip Gorwood, Gerasimos Anagnostopoulos, Fanny Aprahamian, Carlos López-Otín, Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut Gustave Roussy (IGR), Université Paris-Saclay, Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III [Madrid] (ISC), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Unité de Biologie Fonctionnelle et Adaptative (BFA (UMR_8251 / U1133)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur l'Inflammation (CRI (UMR_S_1149 / ERL_8252 / U1149)), Clinique des maladies mentales et de l'encéphale (CMME - Service de psychiatrie), Hôpital Sainte-Anne-Université Paris Descartes - Paris 5 (UPD5), Institut de psychiatrie et neurosciences (U894 / UMS 1266), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Apoptose, cancer et immunité (U848), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Weill Medical College of Cornell University [New York], Sandra and Edward Meyer Cancer Center [New-York], Yale University School of Medicine, BioTechMed-Graz, Graz University of Technology [Graz] (TU Graz)-Medical University Graz-Karl-Franzens-Universität [Graz, Autriche], Institute of Molecular Biosciences, Karl-Franzens-Universität [Graz, Autriche], University of Crete [Heraklion] (UOC), Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Foundation for Research and Technology - Hellas (FORTH), Universidad de Oviedo [Oviedo], Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), University of Science & Technology of China [Suzhou], Karolinska Institutet [Stockholm], The authors thank CRC Core Facilities (CGB, CHIC, and CEF). G.K. is supported by the Ligue Contre le Cancer (équipe labelisée), Agence National de la Recherche (ANR) – projets blancs, Cancéropôle Île-de-France, Chancelerie Des universités de Paris (Legs Poix), the European Research Council (ERC), Inserm Transfert, Fondation Carrefour, Institut National du Cancer (INCa), Inserm (HTE), Institut Universitaire de France, Leducq Foundation, the Labex immuno-Oncology, the RHU Torino Lumière, the Seattle Foundation, and the SIRICs SOCRATE and CARPEM. C.M. and C.C.-G. are supported by Agence National de la Recherche (ANR-16-CE14-0026, fat4brain proposal), C.L.-O. is supported by 'Juan de Madariaga fellowship', S.B. is supported by the Swedish Research Council Vetenskapsrådet (2015-05468) and the Austrian Science Fund FWF (P27183-B24), and F.M. is supported by the Austrian Science Fund FWF (grants P23490-B20, P29262, P24381, P29203, and P27893), DKplus Metabolic and Cardiovascular Diseases (W1226), Austrian Science Ministry, Karl Franzens University ('Unkonventionelle Forschung' and 'flysleep'), NAWI Graz, and BioTechMed-Graz flagship project 'EPIAge.' K.C. is supported by ANR MICRO-Obes and AP/HP (PHRC Microbaria). L.G. is supported by an intramural startup from the Department of Radiation Oncology of Weill Cornell Medical College (New York, US) and by Sotio a.c. (Prague, Czech Republic)., The authors thank PreclinICAN (Institute of Cardiometabolism and Nutrition, IHU-ICAN, Paris, France) and 'Plateforme Imageries du Vivant' INSERM UMR 970 (PARCC-HEGP) for analyses of mouse whole-body composition and Functional & Physiological Exploration Platform (FPE) of the Unit 'Biologie Fonctionnelle et Adaptative' (University Paris Diderot, Sorbonne Paris Cité, BFA, UMR 8251 CNRS, Paris, France) for metabolic analyses., Ligue Nationale contre le Cancer (France), Agence Nationale de la Recherche (France), Chancellerie des Universités de Paris, European Research Council, Institut National du Cancer (France), Fondation Leducq, Swedish Research Council, Austrian Science Fund, Federal Ministry of Science, Research and Economy (Austria), Bravo-San-Pedro, José Manuel [0000-0002-5781-1133], Sica, Valentina [0000-0003-2770-5847], Martins, Isabelle [0000-0003-0885-613X], Pol, Jonathan G. [0000-0002-8355-7562], Loos, Friedemann [0000-0002-5976-5978], Maiuri, Maria Chiara [0000-0001-9760-7674], Niso-Santano, Mireia [0000-0002-6506-422X], Aranda, Fernando [0000-0002-9364-474X], Gorwood, Philip [0000-0003-1845-3676], Ramoz, Nicolas [0000-0002-8070-9938], Cleḿent, Karine [0000-0002-2489-3355], Pelloux, Véronique [0000-0003-3630-4746], Raverdy, Violeta [0000-0001-5754-2028], Denis, Raphaël G.P. [0000-0002-7677-7460], Boya, Patricia [0000-0003-3045-951X], Galluzzi, Lorenzo [0000-0003-2257-8500 ], Madeo, Frank [0000-0002-5070-1329], Cruciani-Guglielmacci, Céline [0000-0002-2562-5360], Tavernarakis, Nektarios [0000-0002-5253-1466 ], López-Otín, Carlos [0000-0001-6964-1904], Magnan, Christophe [0000-0002-7044-2571], Kroemer, Guido [0000-0002-9334-4405], CCSD, Accord Elsevier, Université Paris Descartes - Paris 5 (UPD5)-Hôpital Sainte-Anne, Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Yale School of Medicine [New Haven, Connecticut] (YSM), Graz University of Technology [Graz] (TU Graz)-Karl-Franzens-Universität Graz-Medical University Graz, Karl-Franzens-Universität Graz, École Pratique des Hautes Études (EPHE), Centre de Psychiatrie et Neurosciences (U894), ANR-16-CE14-0026,Fat4Brain,Le métabolisme des lipides dans le cerveau est un regulateur essentiel de l'homéostasie énergétique(2016), Bravo-San Pedro, J. M., Sica, V., Martins, I., Pol, J., Loos, F., Maiuri, M. C., Durand, S., Bossut, N., Aprahamian, F., Anagnostopoulos, G., Niso-Santano, M., Aranda, F., Ramirez-Pardo, I., Lallement, J., Denom, J., Boedec, E., Gorwood, P., Ramoz, N., Clement, K., Pelloux, V., Rohia, A., Pattou, F., Raverdy, V., Caiazzo, R., Denis, R. G. P., Boya, P., Galluzzi, L., Madeo, F., Migrenne-Li, S., Cruciani-Guglielmacci, C., Tavernarakis, N., Lopez-Otin, C., Magnan, C., Kroemer, G., Bravo-San-Pedro, José Manuel, Sica, Valentina, Martins, Isabelle, Pol, Jonathan G., Loos, Friedemann, Maiuri, Maria Chiara, Niso-Santano, Mireia, Aranda, Fernando, Gorwood, Philip, Ramoz, Nicolas, Cleḿent, Karine, Pelloux, Véronique, Raverdy, Violeta, Denis, Raphaël G.P., Boya, Patricia, Galluzzi, Lorenzo, Madeo, Frank, Cruciani-Guglielmacci, Céline, Tavernarakis, Nektarios, López-Otín, Carlos, Magnan, Christophe, and Kroemer, Guido
Subjects: Male, 0301 basic medicine, obesity, Anorexia Nervosa, Physiology, Mice, Obese, Weight Gain, Eating, Mice, 0302 clinical medicine, lipid metabolism, Acyl-CoA-binding protein, Beta oxidation, media_common, Diazepam Binding Inhibitor, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 2. Zero hunger, 0303 health sciences, Leptin Deficiency, Chemistry, Fatty Acids, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Anorexia, 3. Good health, anorexia, Lipogenesis, Female, medicine.symptom, Human, autophagy, medicine.medical_specialty, media_common.quotation_subject, Context (language use), Cell Line, 03 medical and health sciences, Internal medicine, Macroautophagy, Weight Loss, Autophagy, medicine, Animals, Humans, Obesity, Molecular Biology, 030304 developmental biology, Animal, Lipogenesi, Appetite, Cell Biology, Weight Lo, Mice, Inbred C57BL, Lipid metabolism, 030104 developmental biology, Endocrinology, Fatty Acid, 030217 neurology & neurosurgery
Abstract: 24 p.-6 fig.-1 tab.-1 graph. abst., Autophagy facilitates the adaptation to nutritional stress. Here, we show that short-term starvation of cultured cells or mice caused the autophagy-dependent cellular release of acyl-CoA-binding protein (ACBP, also known as diazepam-binding inhibitor, DBI) and consequent ACBP-mediated feedback inhibition of autophagy. Importantly, ACBP levels were elevated in obese patients and reduced in anorexia nervosa. In mice, systemic injection of ACBP protein inhibited autophagy, induced lipogenesis, reduced glycemia, and stimulated appetite as well as weight gain. We designed three approaches to neutralize ACBP, namely, inducible whole-body knockout, systemic administration of neutralizing antibodies, and induction of antiACBP autoantibodies in mice. ACBP neutralization enhanced autophagy, stimulated fatty acid oxidation, inhibited appetite, reduced weight gain in the context of a high-fat diet or leptin deficiency, and accelerated weight loss in response to dietary changes. In conclusion, neutralization of ACBP might constitute a strategy for treating obesity and its co-morbidities., G.K. is supported by the Ligue Contre le Cancer (équipe labelisée); Agence National de la Recherche (ANR) – projets blancs; Cancéropôle Île-de-France; Chancelerie Des universités de Paris (Legs Poix); the European Research Council (ERC); Inserm Transfert, Fondation Carrefour; Institut National du Cancer (INCa); Inserm (HTE); Institut Universitaire de France; Leducq Foundation; the Labex immuno-Oncology; the RHU Torino Lumière; the Seattle Foundation; and the SIRICs SOCRATE and CARPEM. C.M. and C.C.-G. are supported by Agence National de la Recherche (ANR-16-CE14-0026, fat4brain proposal); C.L.-O. is supported by “Juan de Madariaga fellowship”; S.B. is supported by the Swedish Research Council Vetenskapsrådet (2015-05468) and the Austrian Science Fund FWF (P27183-B24); and F.M. is supported by the Austrian Science Fund FWF (grants P23490-B20, P29262, P24381, P29203, and P27893), DKplus Metabolic and Cardiovascular Diseases (W1226), Austrian Science Ministry, Karl Franzens University (“Unkonventionelle Forschung” and “flysleep”), NAWI Graz, and BioTechMed-Graz flagship project “EPIAge.” K.C. is supported by ANR MICRO-Obes and AP/HP (PHRC Microbaria). L.G. is supported by an intramural startup from the Department of Radiation Oncology of Weill Cornell Medical College (New York, US) and by Sotio a.c. (Prague, Czech Republic).
Published: 2019
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121. T-DNA alleles of the receptor kinase THESEUS1 with opposing effects on cell wall integrity signaling

Author: Rodnay Sormani, Herman Höfte, Julia Richter, David Merz, Marie-Theres Hauser, Tobias Eder, Martine Gonneau, Marjolaine Martin, Clara Sánchez-Rodríguez, Kian Hématy, Department of Applied Genetics and Cell Biology, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ERL 3559 - Du gène à la graine, Centre National de la Recherche Scientifique (CNRS), Department of Biology, Austrian Science Fund, French National Research Agency [FWF-SFB F3707-B22, ANR-FWF I 1725-B16], and Hauser, Marie-Theres
Subjects: 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Cell elongation, Cellulose synthesis, Cell wall integrity signaling, CrRLK1L receptor, Gene silencing, Isoxaben, Plant Science, Lignin, chemistry.chemical_compound, gene silencing, Cell Wall, Gene Expression Regulation, Plant, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Receptor, Genes, Dominant, Genetics, Kinase, cellulose synthesis, Plants, Genetically Modified, Phenotype, Research Papers, 3. Good health, Cell biology, ddc:580, cell wall integrity signaling, Benzamides, Growth and Development, Growth inhibition, Signal Transduction, DNA, Bacterial, Receptors, Cell Surface, Biology, isoxaben, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Allele, Cellulose, Gene, Alleles, Arabidopsis Proteins, 030104 developmental biology, Protein kinase domain, chemistry, Seedlings, Botanical sciences, Protein Kinases
Abstract: Antagonistic growth effects of two T-DNA alleles in THESEUS1 correlate with the expression of a predicted functional THE1 protein lacking the kinase domain and antisense transcripts, respectively., Perturbation of cellulose synthesis in plants triggers stress responses, including growth retardation, mediated by the cell wall integrity-sensing receptor-like kinase (RLK) THESEUS1 (THE1). The analysis of two alleles carrying T-DNA insertions at comparable positions has led to conflicting conclusions concerning the impact of THE1 signaling on growth. Here we confirm that, unlike the1-3 and other the1 alleles in which cellular responses to genetic or pharmacological inhibition of cellulose synthesis are attenuated, the1-4 showed enhanced responses, including growth inhibition, ectopic lignification, and stress gene expression. Both the1-3 and the1-4 express a transcript encoding a predicted membrane-associated truncated protein lacking the kinase domain. However, the1-3, in contrast to the1-4, strongly expresses antisense transcripts, which are expected to prevent the expression of the truncated protein as suggested by the genetic interactions between the two alleles. Seedlings overexpressing such a truncated protein react to isoxaben treatment similarly to the1-4 and the full-length THE overexpressor. We conclude that the1-4 is a hypermorphic allele; that THE1 signaling upon cell wall damage has a negative impact on cell expansion; and that caution is required when interpreting the phenotypic effects of T-DNA insertions in RLK genes.
Published: 2017
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122. Multidimensional Heilbronn sets

Author: Madritsch, Manfred G., Tichy, Robert F., Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut für Analysis und Computational Number Theory (Technische Universität Graz), Parts of this research work were done when the first author was a visiting professor at the Department of Analysis and Number Theory,Graz University of Technology. The author thanks this institution and the doctoral school ``Discrete Mathematics' funded by FWF., For the realization of the present paper the first author received support from the Conseil Régional de Lorraine. The second author acknowledges support of the project F 5510-N26 within the special research area ``Quasi Monte-Carlo Methods and applications' founded by FWF (Austrian Science Fund)., and Madritsch, Manfred
Subjects: [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT], [MATH.MATH-NT] Mathematics [math]/Number Theory [math.NT]
Abstract: 19 pages; We show in the context of $\mathbb{Z}^k$-actions that every van der Corput set is a Heilbronn set. Furthermore we establish Diophantine inequalities of the Heilbronn type for generalized polynomials $g$ in particular for sequences $\nu(n)=\lfloor n^c\rfloor+n^k$ with $c>1$ a non-integral real number and $k\in\mathbb{N}$, as well as for $\nu(p)$ where $p$ runs through all prime numbers.
Published: 2016

123. Geometrical models for a class of reducible Pisot substitutions

Author: Milton Minervino, Benoît Loridant, Montanuniversität Leoben (MUL), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), JSPS/FWF Project 'Topology of planar and higher dimensional self-replicating tiles' of the Japan Society for the Promotion of Science (JSPS), I3346, Austrian Science Fund (FWF), and ANR-12-IS01-0002,FAN,Fractals et Numération(2012)
Subjects: Class (set theory), Dynamical systems theory, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Rauzy fractals, Stepped surfaces, 0102 computer and information sciences, Dynamical Systems (math.DS), 01 natural sciences, Theoretical Computer Science, Combinatorics, Set (abstract data type), Fractal, FOS: Mathematics, Discrete Mathematics and Combinatorics, 0101 mathematics, Mathematics - Dynamical Systems, Mathematics, 010102 general mathematics, A domain, Substitutive systems, Tilings, Computational Theory and Mathematics, 010201 computation theory & mathematics, 28A80 52C23 37B10, Dual polyhedron, Geometry and Topology
Abstract: We set up a geometrical theory for the study of the dynamics of reducible Pisot substitutions. It is based on certain Rauzy fractals generated by duals of higher dimensional extensions of substitutions. We obtain under certain hypotheses geometric representations of stepped surfaces and related polygonal tilings, as well as self-replicating and periodic tilings made of Rauzy fractals. We apply our theory to an infinite family of substitutions. For this family, we analyze and interpret in a new combinatorial way the codings of a domain exchange defined on the associated fractal domains. We deduce that the symbolic dynamical systems associated with this family of substitutions behave dynamically as first returns of toral translations., Comment: 42 pages, 15 figures, revised version to appear in Discrete & Computational Geometry
Published: 2016
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124. Common Genetic Polymorphisms within NFκB-Related Genes and the Risk of Developing Invasive Aspergillosis

Author: Carmen Belén Lupiañez, María Teresa Villaescusa, Agostinho Carvalho, Jan Springer, Michaela Lackner, José Manuel Sánchez-Maldonado, Luz María Canet, Cristina Cunha, Juana Segura-Catena, Laura Alcazar-Fuoli, Carlos Solano, Luana Fianchi, Livio Pagano, Leonardo Potenza, José María Aguado, Mario Luppi, Manuel Cuenca-Estrella, Cornelia Lass-Flörl, Hermann Einsele, Lourdes Vázquez, PCRAGA Study Group, Rafael Ríos-Tamayo, Jurgen Loeffler, Manuel Jurado, Juan Sainz, Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (España), FWF Austrian Science Fund, Fundação para a Ciência e Tecnologia (Portugal), Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Universidade do Minho, PCRAGA StudyGroup, PCRAGA Study Group, [Lupiañez,CB, Sánchez-Maldonado,JM, Canet,LM, Segura-Catena,J, Ríos-Tamayo,R, Jurado,M, Sainz,J] Genomic Oncology Area, GENYO, Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government,Granada, Spain. [Lupiañez,CB, Sainz,J] Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain. [Villaescusa,M, Vázquez,L] Hematology Department, University Hospital of Salamanca, Salamanca, Spain. [Villaescusa,MT] Hematology Department, Jiménez Díaz Foundation, Madrid, Spain. [Carvalho,A, Cunha,C] Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho. 6ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal. [Springer,J, Einsele,H, Loeffler,J] Universitätsklinikum Würzburg, Klinik II, Würzburg, Germany. [Lackner,M, Lass-Flörl,C] Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria. [Alcazar-Fuoli,L: Cuenca-Estrella,M] Mycology Reference Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain. [Solano,C] Hematology Department, Clinic University Hospital of Valencia, Valencia, Spain. [Fianchi,L, Pagano,L] Istituto di Ematologia, Università Cattolica del S. Cuore, Rome, Italy. [Potenza,L, Luppi,M] Istituto di Ematologia, Università Cattolica del S. Cuore, Rome, Italy. Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy. [Aguado,JM] Unit of Infectious Diseases, University Hospital 12 de Octubre, Research Institute of Hospital 12 de Octubre (i+12), Madrid., This study was supported by grants PI12/02688 from Fondo de Investigaciones Sanitarias (Instituto de Salud Carlos III, Madrid, Spain), the ERA-NET PathoGenoMics (03159000A, Ministerio de Ciencia e Innovación PIM2010EPA-00756, Madrid, Spain), the Collaborative Research Center / Transregio 124 FungiNet, the Austrian Science Fundation (FWF I-656-B09), the Fundação para a Ciência e Tecnologia (FCT), cofunded by Programa Operacional Regional do Norte (ON.2—O Novo Norte), the Quadro de Referência Estratégico Nacional (QREN) through the Fundo Europeu de Desenvolvimento Regional (FEDER) and the Projeto Estratégico – LA 26 – 2013–2014 (PEst-C/SAU/LA0026/2013). Agostinho Carvalho and Cristina Cunha were supported by the Fundação para a Ciência e Tecnologia (FCT), Portugal (IF/00735/2014 and SFRH/BPD/96176/2013, respectively).The PCRAGA trial was supported by an unrestricted grant from Pfizer. This study was also supported by Astellas Pharma Inc. and a donation from Consuelo González Moreno, an acute myeloid leukemia survivor., Austrian Science Fund, Fundação para a Ciência e a Tecnologia (Portugal), and European Regional Development Fund
Subjects: 0301 basic medicine, Polimorfismo de nucleótido simple, Medicina Básica [Ciências Médicas], lcsh:QR1-502, Diseases::Bacterial Infections and Mycoses::Mycoses::Hyalohyphomycosis::Aspergillosis [Medical Subject Headings], Genetic Susceptibility, NF kappa B-related genes, lcsh:Microbiology, susceptibility, Diseases::Bacterial Infections and Mycoses::Infection::Opportunistic Infections [Medical Subject Headings], Phenomena and Processes::Genetic Phenomena::Genotype::Haplotypes [Medical Subject Headings], Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], Infecciones oportunistas, Invasive Aspergillosis, NFκB-related genes, genetic polymorphisms, interaction, Diseases::Pathological Conditions, Signs and Symptoms::Pathologic Processes::Disease Attributes::Disease Susceptibility [Medical Subject Headings], Genotype, Chemicals and Drugs::Carbohydrates::Glycosides::Nucleotides [Medical Subject Headings], Original Research, Genetics, education.field_of_study, Phenomena and Processes::Genetic Phenomena::Phenotype::Genetic Markers [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Surgical Procedures, Operative::Transplantation::Cell Transplantation::Stem Cell Transplantation::Hematopoietic Stem Cell Transplantation [Medical Subject Headings], Humanos, 3. Good health, Nucleótidos, Ciências Médicas::Medicina Básica, Haplotipos, Phenomena and Processes::Genetic Phenomena::Genotype [Medical Subject Headings], Trasplante de células madre hematopoyéticas, Microbiology (medical), Marcadores genéticos, nfkb pathway, Population, Single-nucleotide polymorphism, Biology, Microbiology, 03 medical and health sciences, Genetic predisposition, SNP, ddc:610, Allele, education, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Polymorphism, Genetic::Polymorphism, Single Nucleotide [Medical Subject Headings], Science & Technology, Haplotype, Susceptibilidad a enfermedades, Organisms::Eukaryota::Fungi::Mitosporic Fungi::Aspergillus [Medical Subject Headings], Hematologic Diseases, Settore MED/15 - MALATTIE DEL SANGUE, 030104 developmental biology, Aspergilosis, Genetic marker, Invasive Aspergillosis, genetic polymorphisms, susceptibility, NFκB-related genes, interaction, Immunology, Genotipo, Stem Cell Transplantation
Abstract: Invasive Aspergillosis (IA) is an opportunistic infection caused by Aspergillus, a ubiquitously present airborne pathogenic mold. A growing number of studies suggest a major host genetic component in disease susceptibility. Here, we evaluated whether 14 single-nucleotide polymorphisms within NF kappa B1, NF kappa B2, RelA, RelB, Rel, and IRF4 genes influence the risk of IA in a population of 834 high-risk patients (157 IA and 677 non IA) recruited through a collaborative effort involving the aspBlOmics consortium and four European clinical institutions. No significant overall associations between selected SNPs and the risk of IA were found in this large cohort. Although a hematopoietic stem cell transplantation (HSCT)-stratified analysis revealed that carriers of the IRF4(rs12203592T/T) genotype had a six-fold increased risk of developing the infection when compared with those carrying the C allele (ORREC = 6.24, 95%CI 1.25-31.2, P = 0.026), the association of this variant with IA risk did not reach significance at experiment-wide significant threshold. In addition, we found an association of the IRF4(AATC) and IRF4(GGTC) haplotypes (not including the IRF4(rs12203592T/T) risk allele) with a decreased risk of IA but the magnitude of the association was similar to the one observed in the single-SNP analysis, which indicated that the haplotypic effect on IA risk was likely due to the IRF4(rs12203592) SNP Finally, no evidence of significant interactions among the genetic markers tested and the risk of IA was found. These results suggest that the SNPs on the studied genes do not have a clinically relevant impact on the risk of developing IA., This study was supported by grants PI12/02688 from Fond de Investigaciones Sanitarias (Institute de Salud Carlos III, Madrid, Spain), the ERA-NET PathoGenoMics (03159000A; Ministerio de Ciencia e Innovation PIM2010EPA-00756, Madrid, Spain), the Collaborative Research Center / Transregio 124 FungiNet, the Austrian Science Fundation (FWF I-656-B09), the Fundacao para a Ciencia e Tecnologia (FCT), cofundcd by Programa Operacional Regional do Norte (ON.2-O Novo Norte), the Quadro de Referencia Estrategico Nacional (QREN) through the Fundo Europeu de Desenvolvimento Regional (FEDER) and the Projeto Estrategico - LA 26 - 2013-2014 (PEst-C/SAU/LA0026/2013). Agostinho Carvalho and Cristina Cunha were supported by the Fundacao para a e Tecnologia (FCT), Portugal (IF/00735/2014 and SFRH/BPD/96176/2013, respectively). The PCRAGA trial was supported by an unrestricted grant from Pfizer, which had no involvement or control over the collection, analysis, and interpretation of data; the writing of the report; or the decision to submit the paper for publication. This study was also supported by Astellas Pharma Inc. and a donation from Consuelo Gonzalez Moreno, an acute myeloid leukemia survivor., info:eu-repo/semantics/publishedVersion
Published: 2016

125. Influence of plant traits, soil microbial properties, and abiotic parameters on nitrogen turnover of grassland ecosystems

Author: Richard D. Bardgett, Thomas Pommier, Arnaud Foulquier, Sandra Lavorel, Catherine Baxendale, Bello Mouhamadou, Michael Schloter, Marie-Noëlle Binet, Franck Poly, Jean-Christophe Clément, Marie-Pascale Colace, Ute Krainer, Eva-Maria Kastl, Michael Bahn, Amélie A. M. Cantarel, Nicolas Legay, Karl Grigulis, 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), Université Grenoble Alpes (UGA), Lancaster Environment Centre, Soil and Ecosystem Ecology Laboratory, Institute of Ecology, Technische Universität Berlin (TUB), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), Research Unit for Environmental Genomics, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz-Zentrum München (HZM), Station alpine Joseph Fourier - UMS 3370 (SAJF), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF), Faculty of Life Sciences, Michael Smith Building, University of Manchester, ERA-Net BiodivERsA project VITAL [ANR-08-BDVA-008], ANR, FWF, NERC [NE/G002258/2], BMBF, Austrian Science Fund (FWF) [I 242-B17], ECO-SERVE project, NWO, FCT, MINECO, FORMAS, SNSF, 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]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Technische Universität Berlin (TU), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Station alpine Joseph Fourier - UMS 3370 (SAJF ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Universität Innsbruck [Innsbruck], 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), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Faculty of Life Sciences University of Manchester, University of Manchester [Manchester], UMR 5553 Laboratoire d’Ecologie Alpine, Centre National de la Recherche Scientifique ( CNRS ), Université Grenoble Alpes ( UGA ), Technical University of Berlin, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Helmholtz-Zentrum München ( HZM ), UMS 3370 Station Alpine Joseph Fourier, Université Joseph Fourier (Grenoble 1) ( UJF ), Lancaster University, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique ( INRA ), Station alpine Joseph Fourier - UMS 3370 ( SAJF ), and Centre National de la Recherche Scientifique ( CNRS ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Grenoble Alpes ( UGA )
Subjects: 0106 biological sciences, leaf traits, Soil biology, [SDV]Life Sciences [q-bio], ammonia‐oxidizing archaea and bacteria, water availability, 010603 evolutionary biology, 01 natural sciences, complex mixtures, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Mesocosm, nitrite reducers, Nutrient, lcsh:QH540-549.5, Ammonia-oxidizing Archaea And Bacteria, Arbuscular Mycorrhizal Colonization, Ecosystem Properties, Grasslands, Leaf Traits, Nitrite Oxidizers, Nitrite Reducers, Nutrient Availability, Root Traits, Water Availability, Ecosystem, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV ] Life Sciences [q-bio], Ecology, Soil organic matter, grasslands, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, nitrite oxidizers, ammonia-oxidizing archaea and bacteria, root traits, Agronomy, Soil water, 040103 agronomy & agriculture, arbuscular mycorrhizal colonization, 0401 agriculture, forestry, and fisheries, Environmental science, ecosystem properties, lcsh:Ecology, nutrient availability, Soil fertility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Although it is known that multiple interactions among plant functional traits, microbial properties , and abiotic soil parameters influence the nutrient turnover, the relative contribution of each of these groups of variables is poorly understood. We manipulated grassland plant functional composition and soil nitrogen (N) availability in a multisite mesocosm experiment to quantify their relative effects on soil N turnover. Overall, root traits, arbuscular mycorrhizal colonization, denitrification potential, as well as N availability and water availability, best explained the variation in measured ecosystem properties, especially the trade-off between nutrient sequestration and plant biomass production. Their relative contributions varied with soil N availability. In relatively N-poor soils (10–20 μg·N·g −1 soil), N turnover was mainly controlled by microbial properties and abiotic soil parameters, whereas in the relatively N-rich soils (110–120 μg·N·g −1 soil), N turnover was mainly controlled by plant traits and microbial properties. This experiment is a strong demonstration of the importance of functional characteristics of both plants and soil microbes, and their interplay with soil N availability, for N turnover in grassland soils.
Published: 2016
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126. Application of photon detectors in the VIP2 experiment to test the Pauli Exclusion Principle

Author: E. Sbardella, Edoardo Milotti, K. Piscicchia, Johann Zmeskal, Carolina Berucci, J.-P. Egger, Alberto Clozza, Catalina Curceanu, E. Widmann, Laura Sperandio, Sergio Bartalucci, S. Di Matteo, L. De Paolis, Diana Sirghi, Mario Bragadireanu, A. Pichler, T. Ishiwatari, A. d'Ufflzi, Sergio Bertolucci, Hexi Shi, Florin Sirghi, Alessandro Scordo, D. Pietreanu, Michael Cargnelli, O. Vazquez-Doce, C. Guaraldo, Matthias Laubenstein, M. Iliescu, T. Ponta, Johann Marton, M. Bazzi, Laboratori Nazionali di Frascati (LNF), Istituto Nazionale di Fisica Nucleare (INFN), Horia Hulubei National Institute of Physics and Nuclear Engineering (NIPNE), IFIN-HH, Laboratori Nazionali del Gran Sasso (LNGS), Stefan Meyer Institut für subatomare Physik (SMI), Dipartimento di Fisica [Trieste], Università degli studi di Trieste, Enrico Fermi Center for Study and Research | Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, National Institut for Nuclear Physics and Engineering (IFIN HH), National Institut for Nuclear Physics and Engineering, 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 de Neuchâtel (UNINE), 581589, John Templeton Foundation, P25529-N20, FWF, Austrian Science Fund, W1252-N27, FWF, Austrian Science Fund, Centro Studi e Ricerche 'Enrico Fermi' (Centro Fermi), Centro Studi e Ricerche e Museo Storico Della Fisica, Università degli studi di Trieste = University of Trieste, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Pichler, A., Bartalucci, S., Bazzi, M., Bertolucci, S., Berucci, C., Bragadireanu, M., Cargnelli, M., Clozza, A., Curceanu, C., De Paolis, L., Di Matteo, S., D'Ufflzi, A., Egger, J. P., Guaraldo, C., Iliescu, M., Ishiwatari, T., Laubenstein, M., Marton, J., Milotti, Edoardo, Pietreanu, D., Piscicchia, K., Ponta, T., Sbardella, E., Scordo, A., Shi, H., Sirghi, D., Sirghi, F., Sperandio, L., Vazquez Doce, O., Widmann, E., and Zmeskal, J.
Subjects: History, Particle physics, Physics - Instrumentation and Detectors, Photon, Silicon drift detector, Underground laboratory, FOS: Physical sciences, Photodetector, 02 engineering and technology, Electron, Active shielding, Scintillator, Silicon photomultiplier, Astrophysics, 01 natural sciences, Education, Pauli exclusion principle, Physics and Astronomy (all), symbols.namesake, 0103 physical sciences, Detectors and Experimental Techniques, Silicon Drift Detector, 010306 general physics, Physics, Plastic scintillator, [PHYS]Physics [physics], Photons, Photodetectors, Instrumentation and Detectors (physics.ins-det), 021001 nanoscience & nanotechnology, Pauli principle, Particle beams, Computer Science Applications, Cosmology, Orders of magnitude, Orders of magnitude (time), Quantum theory, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, symbols, Silicon detectors, 0210 nano-technology
Abstract: The Pauli Exclusion Principle (PEP) was introduced by the austrian physicist Wolfgang Pauli in 1925. Since then, several experiments have checked its validity. From 2006 until 2010, the VIP (VIolation of the Pauli Principle) experiment took data at the LNGS underground laboratory to test the PEP. This experiment looked for electronic 2p to 1s transitions in copper, where 2 electrons are in the 1s state before the transition happens. These transitions violate the PEP. The lack of detection of X-ray photons coming from these transitions resulted in a preliminary upper limit for the violation of the PEP of $4.7 \times 10^{-29}$. Currently, the successor experiment VIP2 is under preparation. The main improvements are, on one side, the use of Silicon Drift Detectors (SDDs) as X-ray photon detectors. On the other side an active shielding is implemented, which consists of plastic scintillator bars read by Silicon Photomultipliers (SiPMs). The employment of these detectors will improve the upper limit for the violation of the PEP by around 2 orders of magnitude. The Pauli Exclusion Principle (PEP) was introduced by the austrian physicist Wolfgang Pauli in 1925. Since then, several experiments have checked its validity. From 2006 until 2010, the VIP (Violation of the Pauli Principle) experiment took data at the LNGS underground laboratory to test the PEP. This experiment looked for electronic 2p to Is transitions in copper, where 2 electrons are in the Is state before the transition happens. These transitions violate the PEP. The lack of detection of X-ray photons coming from these transitions resulted in a preliminary upper limit for the violation of the PEP of 4.7 × 10(-29). Currently, the successor experiment VIP2 is under preparation. The main improvements are, on one side, the use of Silicon Drift Detectors (SDDs) as X-ray photon detectors. On the other side an active shielding is implemented, which consists of plastic scintillator bars read by Silicon Photomultipliers (SiPMs). The employment of these detectors will improve the upper limit for the violation of the PEP by around 2 orders of magnitude. The Pauli Exclusion Principle (PEP) was introduced by the austrian physicist Wolfgang Pauli in 1925. Since then, several experiments have checked its validity. From 2006 until 2010, the VIP (VIolation of the Pauli Principle) experiment took data at the LNGS underground laboratory to test the PEP. This experiment looked for electronic 2p to 1s transitions in copper, where 2 electrons are in the 1s state before the transition happens. These transitions violate the PEP. The lack of detection of X-ray photons coming from these transitions resulted in a preliminary upper limit for the violation of the PEP of $4.7 \times 10^{-29}$. Currently, the successor experiment VIP2 is under preparation. The main improvements are, on one side, the use of Silicon Drift Detectors (SDDs) as X-ray photon detectors. On the other side an active shielding is implemented, which consists of plastic scintillator bars read by Silicon Photomultipliers (SiPMs). The employment of these detectors will improve the upper limit for the violation of the PEP by around 2 orders of magnitude.
Published: 2015
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127. Leaf water potential measurements using the pressure chamber: Synthetic testing of assumptions towards best practices for precision and accuracy

Author: Celia M. Rodriguez‐Dominguez, Alicia Forner, Sebastia Martorell, Brendan Choat, Rosana Lopez, Jennifer M. R. Peters, Sebastian Pfautsch, Stefan Mayr, Madeline R. Carins‐Murphy, Scott A. M. McAdam, Freya Richardson, Antonio Diaz‐Espejo, Virginia Hernandez‐Santana, Paulo E. Menezes‐Silva, Jose M. Torres‐Ruiz, Timothy A. Batz, Lawren Sack, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Museo Nacional de Ciencias Naturales, Departamento de Biogeografía y Cambio Global, Laboratorio Internacional de Cambio Global (LINC-Global), Spanish National Research Council (CSIC), Université des îles Baléares (UIB), Western Sydney University, Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Hawkesbury Institute for the Environment [Richmond] (HIE), Institute of Botany [Innsbruck], Leopold Franzens Universität Innsbruck - University of Innsbruck, School of Biological Sciences [Hobart], University of Tasmania [Hobart, Australia] (UTAS), Purdue University [West Lafayette], Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Perdue University, Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, SKA South Africa751918-AgroPHYSAustrian Science Fund (FWF)P32203National Science Foundation (NSF)1457279, European Project: 624473,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,HYDROPIT(2015), European Commission, Austrian Research Promotion Agency, National Science Foundation (US), Rodríguez Domínguez, Celia M., Forner, Alicia, Choat, B., López, Rosana, Peters, J.M.R., Pfautsch, S., Carins Murphy, Madeline R., McAdam S.A.M., Richardson, Freya, Díaz-Espejo, Antonio, Hernández Santana, V., Menezes-Silva, Paulo E., Torres Ruiz, José Manuel, Sack, Lawren, Rodríguez Domínguez, Celia M. [0000-0003-2352-0829], Forner, Alicia [0000-0002-7123-6403], Choat, B.[0000-0002-9105-640X], López, Rosana [0000-0003-3553-9148], Peters, J.M.R. [0000-0003-4627-7788], Pfautsch, S. [0000-0002-4390-4195], Carins Murphy, Madeline R. [0000-0003-4370-9485], McAdam S.A.M. [0000-0002-9625-6750], Richardson, Freya [0000-0003-2460-3423], Díaz-Espejo, Antonio [0000-0002-4711-2494], Hernández Santana, V. [0000-0001-9018-8622], Menezes-Silva, Paulo E. [0000-0002-8122-3489], Torres Ruiz, José Manuel [0000-0003-1367-7056], and Sack, Lawren [0000-0002-7009-7202]
Subjects: Physiology, Water stress, Reproducibility of Results, Water, plant water relations, Plant water relations, pressure bomb, Plant Science, Leaf water potential, leaf water potential, Droughts, Plant Leaves, water stress, Pressure bombpressure chamber, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plant water status, Plant water status, pressure chamber
Abstract: 25 páginas.- 8 figuras.- 2 tablas.- 66 referencias.- Additional supporting information can be found online in the Supporting Information section at the end of this article., eaf water potential (psi(leaf)), typically measured using the pressure chamber, is the most important metric of plant water status, providing high theoretical value and information content for multiple applications in quantifying critical physiological processes including drought responses. Pressure chamber measurements of psi(leaf) (psi(leafPC)) are most typical, yet, the practical complexity of the technique and of the underlying theory has led to ambiguous understanding of the conditions to optimize measurements. Consequently, specific techniques and precautions diversified across the global research community, raising questions of reliability and repeatability. Here, we surveyed specific methods of psi(leafPC) from multiple laboratories, and synthesized experiments testing common assumptions and practices in psi(leafPC) for diverse species: (i) the need for equilibration of previously transpiring leaves; (ii) leaf storage before measurement; (iii) the equilibration of psi(leaf) for leaves on bagged branches of a range of dehydration; (iv) the equilibration of psi(leaf) across the lamina for bagged leaves, and the accuracy of measuring leaves with artificially 'elongated petioles'; (v) the need in psi(leaf) measurements for bagging leaves and high humidity within the chamber; (vi) the need to avoid liquid water on leaf surfaces; (vii) the use of 'pulse' pressurization versus gradual pressurization; and (viii) variation among experimenters in psi(leafPC) determination. Based on our findings we provide a best practice protocol to maximise accuracy, and provide recommendations for ongoing species-specific tests of important assumptions in future studies., European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 751918-AgroPHYS; Marie Curie Fellowship (FP7-PEOPLE-2013-IOF-624473); Austrian research agency (FWF) project P32203; National Science Foundation (Grant IOS-#1457279)
Published: 2022
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128. Incongruence between transcriptional and vascular pathophysiological cell states

Author: Macarena Fernández-Chacón, Severin Mühleder, Alvaro Regano, Lourdes Garcia-Ortega, Susana F. Rocha, Carlos Torroja, Maria S. Sanchez-Muñoz, Mariya Lytvyn, Verónica Casquero-Garcia, Macarena De Andrés-Laguillo, Lars Muhl, Michael M. Orlich, Konstantin Gaengel, Emilio Camafeita, Jesús Vázquez, Alberto Benguría, M. Luisa Iruela-Arispe, Ana Dopazo, Fátima Sánchez-Cabo, Hannah Carter, Rui Benedito, Unión Europea. Comisión Europea. European Research Council (ERC), Ministerio de Ciencia e Innovación. Centro de Excelencia Severo Ochoa (España), Ministerio de Ciencia e Innovación (España), Fundación La Caixa, Knut and Alice Wallenberg Foundation, Instituto de Salud Carlos III, Fundación ProCNIC, Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Ministerio de Economía y Competitividad (España), and FWF Austrian Science Fund
Abstract: Research in R.B.’s laboratory was supported by the European Research Council Starting Grant AngioGenesHD (638028) and Consolidator Grant AngioUnrestUHD (101001814), the CNIC Intramural Grant Program Severo Ochoa (11-2016-IGP-SEV-2015-0505), the Ministerio de Ciencia e Innovación (MCIN) (SAF2013-44329-P, RYC-2013- 13209, and SAF2017-89299-P) and ‘La Caixa’ Banking Foundation (HR19-00120). J.V.’s laboratory was supported by MCIN (PGC2018- 097019-B-I00 and PID2021-122348NB-I00) and La Caixa (HR17-00247 and HR22-00253). K.G.’s laboratory was supported by Knut and Alice Wallenberg Foundation (2020.0057) and Vetenskapsrådet (2021-04896). The CNIC is supported by Instituto de Salud Carlos III, MCIN, and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MCIN/ AEI/10.13039/501100011033). Microscopy experiments were performed at the Microscopy and Dynamic Imaging Unit, CNIC, ICTS-ReDib, co-funded by MCIN/AEI/10.13039/501100011033 and FEDER ‘Una manera de hacer Europa’ (ICTS-2018-04-CNIC-16). M.F.-C. was supported by PhD fellowships from La Caixa (CX_E-2015-01) and Boehringer Ingelheim travel grants. S.M. was supported by the Austrian Science Fund (J4358). A.R. was supported by the Youth Employment Initiative (PEJD-2019-PRE/BMD-16990). L.G.-O. was supported by the Spanish Ministry of Economy and Competitiveness (PRE2018-085283). We thank S. Bartlett (CNIC) for English editing, as well as the members of the Transgenesis, Microscopy, Genomics, Citometry and Bioinformatic units at CNIC. We also thank F. Radtke (Swiss Institute for Experimental Cancer Research), R. H. Adams (Max Planck Institute for Molecular Biomedicine), F. Alt (Boston Children’s Hospital, Harvard Medical School), T. Honjo (Kyoto University Institute for Advanced Studies), I. Flores (CNIC), J. Lewis (Cancer Research UK London Research Institute), S. Habu (Tokai University School of Medicine), T. Gridley (Maine Health Institute for Research) and C. Brakebusch (Biotech Research and Innovation Centre) for sharing the Dll4floxed, Notch1floxed, Notch2floxed, Cdh5(PAC)-creERT2, Myc floxed, Rbpj floxed, p21−/−, Jag1floxed, Dll1floxed, Jag2floxed and Rac1floxed mice. Sí
Published: 2023
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129. Tracing Isomanifolds in R^d in Time Polynomial in d using Coxeter–Freudenthal–Kuhn Triangulations

Author: Jean-Daniel Boissonnat, Siargey Kachanovich, Mathijs Wintraecken, Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria), Université Côte d'Azur (UCA), Austrian Science Fund (FWF): M 3073, ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 339025,EC:FP7:ERC,ERC-2013-ADG,GUDHI(2014), and European Project: 754411,ISTplus(2017)
Subjects: isomanifolds/solution manifolds/isosurfacing, General Computer Science, PL approximations, Coxeter triangulation Freudenthal--Kuhn triangulation permutahedron PLapproximations isomanifolds/solution manifolds/isosurfacing MSC codes. 65D18 68U05, General Mathematics, permutahedron, PLapproximations, isomanifolds/solution manifolds/isosurfacing MSC codes. 65D18, Coxeter triangulation, [INFO]Computer Science [cs], Freudenthal--Kuhn triangulation, 68U05
Abstract: International audience; Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of $\mathbb{R}^d$ defined as the zero set of a multivariate multivalued smooth function $f: \mathbb{R}^d\rightarrow \mathbb{R}^{d-n}$, where $n$ is the intrinsic dimension of the manifold and we assume that $0$ is a regular value. A natural way to approximate a smooth isomanifold $\mathcal{M}=f^{-1}(0)$ is to consider its Piecewise-Linear (PL) approximation $\hat{\mathcal{M}}$ based on atriangulation $\mathcal{T}$ of the ambient space $\mathbb{R}^d$, whose longest edge has length $D$. In thispaper, we describe a simple algorithm to trace isomanifolds from a given starting point {on each connected component}. The algorithm works for arbitrary dimensions $n$ and $d$, and $D$. Our main result is that, when$f$ (or $\mathcal{M}$) has bounded complexity, the complexity of the algorithm is polynomial in $d$ and $\delta=1/D$ (and unavoidably exponential in $n$). Since it is known that for $\delta = \Omega (d^{2.5})$, $\hat{\mathcal{M}}$ is $O(D^2)$-close and isotopic to $\mathcal{M}$, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in $d$.Combining this algorithm with dimensionality reduction techniques, the dependency on $d$ in the size of $\mathcal{M}$ can be completely removed with high probability. We also show that the algorithm can handleisomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art.
Published: 2023
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130. Of mice, flies--and men? Comparing fungal infection models for large-scale screening efforts

Author: Martin E. A. Richter, Ekkehard Hiller, Bernhard Hube, Lydia Kasper, Sascha Brunke, Dominique Ferrandon, Christophe d'Enfert, Jessica Quintin, Steffen Rupp, Karl Kuchler, Ilse D. Jacobsen, Tobias Schwarzmüller, Department of Microbial Pathogenicity Mechanisms [Jena], Hans Knoell Institute, Center for Sepsis Control & Care, Jena University Hospital, Réponse immunitaire et developpement chez les insectes (RIDI - UPR 9002), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Escuela de Ciencas Biologicas, Pontificia Universidad Catolica del Ecuador, Research Group Microbial Immunology, Hans Knöll Institute, Jena University Hospital [Jena], Fraunhofer Institute for Interfacial Engineering and Biotechnology (Fraunhofer IGB), Fraunhofer (Fraunhofer-Gesellschaft), Medizinische Universität Wien = Medical University of Vienna, Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), This work was supported via institutional support from CNRS, by the DeutscheForschungsgemeinschaft (DFG) and the Austrian Science Foundation (FWF) via a joint DACH project of the B.H. and K.K. laboratories (DFG HU 528/17-1 and FWF-I-746-B11), and by the German Federal Ministry of Education and Health (BMBF)and the FWF via the ERA-Net Pathogenomics project FunPath (BMBF-FKZ:0313931B and FWF-API-0125). The work of S.B., M.E.R. and B.H. was further supported by the German Federal Ministry of Education and Health (BMBF) Germany via the Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC, FKZ: 01EO1002). Work in the K.K. laboratory was supported by the Austrian Science Foundation FWF by a grant from the Christian Doppler Society., Université de Strasbourg (UNISTRA)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Brunke, Sascha, Quintin, Jessica, Pontificia Universidad Católica del Ecuador, Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), RIBIERRE, Helene, and Publica
Subjects: MESH: Gene Ontology, Male, [SDV]Life Sciences [q-bio], Mutant, Medicine (miscellaneous), lcsh:Medicine, MESH: Logistic Models, Candida glabrata, MESH: Virulence, medicine.disease_cause, Polymerase Chain Reaction, Mice, Immunology and Microbiology (miscellaneous), [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, Mutant library, Drosophila melanogaster, Alternative infection models, Signature-tagged mutagenesis, Fungal virulence factors, MESH: Candida glabrata, Pathogen, MESH: Organ Specificity, 0303 health sciences, Mutation, Virulence, 3. Good health, [SDV] Life Sciences [q-bio], Organ Specificity, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RB1-214, Research Article, MESH: Mutation, Neuroscience (miscellaneous), Biology, General Biochemistry, Genetics and Molecular Biology, Microbiology, MESH: Drosophila melanogaster, 03 medical and health sciences, MESH: Mycoses, medicine, lcsh:Pathology, Animals, Humans, Drosophila, MESH: Mice, 030304 developmental biology, MESH: Humans, 030306 microbiology, lcsh:R, fungi, MESH: Polymerase Chain Reaction, biology.organism_classification, MESH: Male, Disease Models, Animal, Gene Ontology, Logistic Models, Mycoses, MESH: Disease Models, Animal
Abstract: Studying infectious diseases requires suitable hosts for experimental in vivo infections. Recent years have seen the advent of many alternatives to murine infection models. However, the use of non-mammalian models is still controversial because it is often unclear how well findings from these systems predict virulence potential in humans or other mammals. Here, we compare the commonly used models, fruit fly and mouse (representing invertebrate and mammalian hosts), for their similarities and degree of correlation upon infection with a library of mutants of an important fungal pathogen, the yeast Candida glabrata. Using two indices, for fly survival time and for mouse fungal burden in specific organs, we show a good agreement between the models. We provide a suitable predictive model for estimating the virulence potential of C. glabrata mutants in the mouse from fly survival data. As examples, we found cell wall integrity mutants attenuated in flies, and mutants of a MAP kinase pathway had defective virulence in flies and reduced relative pathogen fitness in mice. In addition, mutants with strongly reduced in vitro growth generally, but not always, had reduced virulence in flies. Overall, we demonstrate that surveying Drosophila survival after infection is a suitable model to predict the outcome of murine infections, especially for severely attenuated C. glabrata mutants. Pre-screening of mutants in an invertebrate Drosophila model can, thus, provide a good estimate of the probability of finding a strain with reduced microbial burden in the mouse host., Summary: Can the fitness of deletion mutants in a murine model be predicted by their virulence in Drosophila melanogaster? For a fungal pathogen, the answer is, mostly, yes.
Published: 2015
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131. Whose Dharma? Śaiva and Śākta Community Rules (samayas) and Dharmaśāstric Prescriptions

Author: Törzsök, Judit, Mondes Iranien et Indien - UMR 7528, Université Sorbonne Nouvelle - Paris 3-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National des Langues et Civilisations Orientales (Inalco)-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund (FWF) VISCOM SFB Project, Tantric communities in context, Austrian Science Fund (FWF) VISCOM SFB Project, and Törzsök, Judit
Subjects: sakta tantra, dharmasastra, samaya rules, orthopraxy, tantric community, women, [SHS.RELIG] Humanities and Social Sciences/Religions, [SHS.RELIG]Humanities and Social Sciences/Religions
Abstract: In the tantric context, samayas are the rules a Śaiva or Śākta neophyte is to follow after he is introduced into his new community and receives an initiation name. The samaya rules are therefore part of what defines the Śaiva or Śākta Śaiva tantric community, at least according to the scriptures. This paper attempts to see what these rules are, how they are related to mainstream brahmanical rules prescribed by Dharmaśāstras and in what way they may actually demarcate various Śaiva and Śākta communities. Before turning to the samayas themselves, a nontantric Śaiva story is presented, which clearly shows that in spite of their overall conformity to traditional brahmanical prescriptions, lay Śaivas also saw themselves as following a different set of laws and rules. Then three different types of samaya sets will be examined: those of the Śaiva Siddhānta, the heterogeneous lists of early Śākta scriptures and the strictly 'nondualist' rules of later Śāktas. While these rules cannot reveal the exact relation of the respective communities to their contemporary society or to each other, they may betray something about the way in which these communities saw themselves within a larger context., Les règles d'une communité appartiennent à son identité. Cette étude examine les façons dont différents textes shivaïtes (laïc ou puranique, shivaïte général du Siddhānta, śākta ancien, śākta de la branche ésotérique kaula) conçoivent et constituent leurs règles communautaires et quel est le rapport de ces règles à celles de l’orthopraxie préscrites dans les Dharmaśāstra. Il est étonnant de constater que les textes du culte ancien des Yoginī incluent plusieurs règles de l'orthopraxie malgré leur opposition explicite à d'autres. Ceci pourrait s'exliquer par l'intention des auteurs d'être reconnu et respecté dans un contexte social orthopraxique qui avait tendance à refuser le tantrisme.
Published: 2015

132. Native Wolbachia from Aedes albopictus Blocks Chikungunya Virus Infection In Cellulo

Author: Patrick Potier, Florence-Hélène Tran, Vincent Raquin, Yoann Saucereau, Patrick Mavingui, Claire Valiente Moro, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), Cyclotron Réunion Océan Indien (CYROI), Université de La Réunion (UR)-Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Agence Nationale de la Recherche (ANR) [ANR-2010-BLAN-170101], Fondation pour la Recherche et la Biodiversite (FRB) [FRBCD-AOOI-07-12], Action Concertee InterPasteurienne (ACIP) [A-10-2009], ERA-Net BiodivERsA network, ANR France [ANR-13-EBID-0007-01], FWF Austria [FWF I-1437], DFG Germany [DFG KL 2087/6-1], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Univ, Réunion
Subjects: Aedes albopictus, viruses, Host cells, lcsh:Medicine, Dengue virus, Biology, Virus Replication, medicine.disease_cause, Mosquitoes, Virus, Microbiology, Aedes, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, Viral replication, Animals, Humans, Chikungunya, Symbiosis, lcsh:Science, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Pathogen, Multidisciplinary, lcsh:R, fungi, Correction, virus diseases, biochemical phenomena, metabolism, and nutrition, Arboviral infection, biology.organism_classification, Virology, Phenotype, 3. Good health, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chikungunya Fever, Wolbachia, lcsh:Q, Chikungunya infection, Chikungunya virus, Arboviruses, Research Article
Abstract: International audience; Wolbachia, a widespread endosymbiont of terrestrial arthropods, can protect its host against viral and parasitic infections, a phenotype called "pathogen blocking". However, in some cases Wolbachia may have no effect or even enhance pathogen infection, depending on the host-Wolbachia-pathogen combination. The tiger mosquito Aedes albopictus is naturally infected by two strains of Wolbachia, wAlbA and wAlbB, and is a competent vector for different arboviruses such as dengue virus (DENV) and Chikungunya virus (CHIKV). Interestingly, it was shown in some cases that Ae. albopictus native Wolbachia strains are able to inhibit DENV transmission by limiting viral replication in salivary glands, but no such impact was measured on CHIKV replication in vivo. To better understand the Wolbachia/CHIKV/Ae. albopictus interaction, we generated a cellular model using Ae. albopictus derived C6/36 cells that we infected with the wAlbB strain. Our results indicate that CHIKV infection is negatively impacted at both RNA replication and virus assembly/secretion steps in presence of wAlbB. Using FISH, we observed CHIKV and wAlbB in the same mosquito cells, indicating that the virus is still able to enter the cell in the presence of the bacterium. Further work is needed to decipher molecular pathways involved in Wolbachia-CHIKV interaction at the cellular level, but this cellular model can be a useful tool to study the mechanism behind virus blocking phenotype induced by Wolbachia. More broadly, this underlines that despite Wolbachia antiviral potential other complex interactions occur in vivo to determine mosquito vector competence in Ae. albopictus.
Published: 2015
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133. Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae

Author: Domman, Daryl, Collingro, Astrid, Lagkouvardos, Ilias, Gehre, Lena, Weinmaier, Thomas, Rattei, Thomas, Subtil, Agathe, Horn, Matthias, University of Vienna, Austria, Biologie des Interactions Cellulaires (BIC), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), This work was supported byAustrian Science Fund FWF grants Y277-B06 and I1628-B22, European Research Council ERC StG EVOCHLAMY (281633), and Marie Curie Initial Training Network Symbiomics.Genome sequencing was performed at the NorwegianSequencing Center, European Project : 281633, EVOCHLAMY, University of Vienna [Vienna], Biologie cellulaire de l'Infection microbienne - Cellular Biology of Microbial Infection, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund FWF grants Y277-B06 and I1628-B22, European Project: 281633,EC:FP7:ERC,ERC-2011-StG_20101109,EVOCHLAMY(2012), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Genetic, gene families, intracellular bacteria, Chlamydiaceae, F-box, Gene Dosage, Ubiquitination, Genetic Variation, effector proteins, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Protein Structure, Tertiary, Evolution, Molecular, [SDV] Life Sciences [q-bio], [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Multigene Family, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], birth and death model, Bacterial Secretion Systems, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Discoveries, Genome, Bacterial, Phylogeny
Abstract: International audience; Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.
Published: 2014
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134. A catalogue of 1,167 genomes from the human gut archaeome

Author: Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-François Brugère, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger, Christian-Albrechts University of Kiel, Institute for Microbiology, Medical University Graz, Institut Pasteur [Paris] (IP), Biologie Évolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Wellcome Trust Sanger Institute [Cambridge], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), BioTechMed-Graz, Graz University of Technology [Graz] (TU Graz)-Karl-Franzens-Universität Graz-Medical University Graz, The research was funded in whole, or in part, by the Austrian Science Fund (FWF) (P 32697, P 30796 given to C.M.E.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S. received partial funding from the Kiel Marine science cluster at the Christian-Albrechts-University (CAU) and the German Ministry of Education and Science, BMBF (no. 031B0851B), which is highly appreciated. C.M.C. and A.W. used the resources of the high-memory computer nodes and computation support from the Computing Center of CAU Kiel. A.A. and R.F. were supported by EMBL. J.F.B. thanks Hub Innovergne for a grant (‘Investissements d’Avenir’, no. 16-IDEX-0001 CAP 20–25). G.B. and S.G. thank the Institut Pasteur and the French National Research Agency (ANR) for their support through grants Methevol (grant no. ANR-19-CE02-0005-01) and Archevol (grant no. ANR-16-CE02-0005-01)., C.M.E. and A.M. thank the Medical University of Graz for the computational resources of the MedBioNode and the Life Science Compute Cluster (LiSC) operated by the Computational Systems Biology group at the University of Vienna. We thank the Medical University of Graz ZMF Galaxy Team: Core Facility Computational Bioanalytics, Medical University of Graz, funded by the Austrian Federal Ministry of Education, Science and Research, Hochschulraum-Strukturmittel 2016 grant as part of BioTechMed Graz. We thank K. Bick for discussion on taxonomic naming, and the scientific support provided by Z. Hameed, ANR-19-CE02-0005,METHEVOL,Caractérisation de nouveaux acteurs et des transitions évolutives dans le métabolisme du méthane, un métabolisme clef dans l'évolution du domaine Archaea(2019), and ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016)
Subjects: Adult, Male, Microbiology (medical), Adolescent, Immunology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Applied Microbiology and Biotechnology, Microbiology, Article, Young Adult, Genome, Archaeal, Genetics, Humans, Child, Phylogeny, Microbiota, Infant, Newborn, Infant, Cell Biology, Middle Aged, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gastrointestinal Microbiome, Child, Preschool, Female, Databases, Nucleic Acid, Microbial genetics
Abstract: The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-quality genomes) recovered from human gastrointestinal tract, sampled across 24 countries and rural and urban populations. We identified previously undescribed taxa including 3 genera, 15 species and 52 strains. Based on distinct genomic features, we justify the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the previously undescribed ‘Candidatus Methanobrevibacter intestini’. Patterns derived from 28,581 protein clusters showed significant associations with sociodemographic characteristics such as age groups and lifestyle. We additionally show that archaea are characterized by specific genomic and functional adaptations to the host and carry a complex virome. Our work expands our current understanding of the human archaeome and provides a large genome catalogue for future analyses to decipher its impact on human physiology., Recovery of 1,167 nonredundant archaeal genomes from the human gut microbiomes reveals previously undescribed genera, associations with sociodemographic factors and the presence of an archaeal virome.
Published: 2021
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135. Optimisation of the total population size for logistic diffusive equations: bang-bang property and fragmentation rate

Author: Idriss Mazari, Grégoire Nadin, Yannick Privat, Institute for Analysis and Scientific Computing [Wien], Vienna University of Technology (TU Wien), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Recherche Mathématique Avancée (IRMA), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), TOkamaks and NUmerical Simulations (TONUS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), I Mazari was partially supported by the Austrian Science Fund (FWF) projects I4052-N32 and F65. I. Mazari, G. Nadin and Y. Privat were partially supported by the Project 'Analysis and simulation of optimal shapes - application to lifesciences' of the Paris City Hall., ANR-18-CE40-0013,SHAPO,Optimisation de forme(2018), CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), 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)-Inria Nancy - Grand Est, Institut Universitaire de France (IUF), and Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)
Subjects: Applied Mathematics, shape optimization, 010102 general mathematics, calculus of variations, bilinear optimal control, 01 natural sciences, 010101 applied mathematics, optimal control, 35Q92,49J99,34B15, Mathematics - Analysis of PDEs, Optimization and Control (math.OC), FOS: Mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], AMS: 35Q92,49J99,34B15, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, diffusive logistic equation, Mathematics - Optimization and Control, Analysis, Analysis of PDEs (math.AP)
Abstract: International audience; In this article, we give an in-depth analysis of the problem of optimising the total population size for a standard logistic-diffusive model. This optimisation problem stems from the study of spatial ecology and amounts to the following question: assuming a species evolves in a domain, what is the best way to spread resources in order to ensure a maximal population size at equilibrium? {In recent years, many authors contributed to this topic.} We settle here the proof of two fundamental properties of optimisers: the bang-bang one which had so far only been proved under several strong assumptions, and the other one is the fragmentation of maximisers. Here, we prove the bang-bang property in all generality using a new spectral method. The technique introduced to demonstrate the bang-bang character of optimizers can be adapted and generalized to many optimization problems with other classes of bilinear optimal control problems where the state equation is semilinear and elliptic. We comment on it in a conclusion section.Regarding the geometry of maximisers, we exhibit a blow-up rate for the $BV$-norm of maximisers as the diffusivity gets smaller: if $\Omega$ is an orthotope and if $m_\mu$ is an optimal control, then $\Vert m_\mu\Vert_{BV}\gtrsim \sqrt{\mu}$. The proof of this results relies on a very fine energy argument.
Published: 2021
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136. Deriving a genetic regulatory network from an optimization principle

Author: Sokolowski, Thomas R, Gregor, Thomas, Bialek, William, Tkačik, Gašper, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Frankfurt Institute for Advanced Studies (FIAS ), Department of Physics, Princeton University (DPPU), Princeton University, Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Rockefeller University [New York], This work was supported in part by the Human Frontiers Science Program, the Austrian Science Fund (FWF P28844), U.S. National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by National Institutes of Health Grants R01GM097275, U01DA047730, and U01DK127429, by the Simons Foundation, and and by the John Simon Guggenheim Memorial Foundation.
Subjects: Biological Physics (physics.bio-ph), Molecular Networks (q-bio.MN), FOS: Biological sciences, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, Quantitative Biology - Molecular Networks, Physics - Biological Physics
Abstract: Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only been applied in very simplified setups. Here, in contrast, we explore a mechanistically-detailed class of models for the gap gene network of the Drosophila embryo, and determine its 50+ parameters by optimizing the information that gene expression levels convey about nuclear positions, subject to physical constraints on the number of available molecules. Optimal networks recapitulate the architecture and spatial gene expression profiles of the real organism. Our framework makes precise the many tradeoffs involved in maximizing functional performance, and allows us to explore alternative networks to address the questions of necessity vs contingency. Multiple solutions to the optimization problem may be realized in closely related organisms., 8 pages, 5 vigures
Published: 2023

137. Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

Author: Coiro, Mario, Allio, Rémi, Mazet, Nathan, Seyfullah, Leyla, Condamine, Fabien, University of Vienna [Vienna], Department of Palaeontology, Ronin Institute for Independent Scholarship (Ronin Institute), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), MC has been supported by the Austrian Science Fund (FWF), Lise Meitner project no. M3168. The visit of MC to the NRM and the NHM was funded by the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 226506 (SYNTHESYS project SE-TAF-5774 and project GB-TAF-5763). The computational results presented have been achieved in part using the Vienna Scientific Cluster (VSC). This project benefited from an Investissements d'Avenir' program managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-0025) and the ANR GAARAnti project (ANR-17-CE31-0009)., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-17-CE31-0009,GAARAnti,Pont terrestre 'GAARlandia' vs voies de dispersion à travers les Petites Antilles–Couplage entre dynamique de la subduction et processus de l'évolution des espèces dans le domaine des Caraïbes.(2017), and European Project: 226506,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,SYNTHESYS(2009)
Subjects: total-evidence analysis, fossil leaves, historical biogeography, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Greenland, Antarctica, Cycadales, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: We dedicate this study to the memory of our esteemed colleague Nathalie S. Nagalingum.; International audience; The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian totalevidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
Published: 2023
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138. Positive dimensional parametric polynomial systems, connectivity queries and applications in robotics

Author: Jose Capco, Josef Schicho, Mohab Safey El Din, Capco, Jose, Algorithmes efficaces et exacts pour la planification de trajectoire en robotique - - ECARP2019 - ANR-19-CE48-0015 - AAPG2019 - VALID, ANR (ANR-19-CE48-0015) FWF (I 4452-N). - ECARP - INCOMING, University of Innsbruck, Research Institute for Symbolic Computation (RISC), Johannes Kepler Universität Linz (JKU), Polynomial Systems (PolSys), LIP6, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ANR-19-CE48-0015,ECARP,Algorithmes efficaces et exacts pour la planification de trajectoire en robotique(2019), European Project: ECARP, and Leopold Franzens Universität Innsbruck - University of Innsbruck
Subjects: [INFO.INFO-SC]Computer Science [cs]/Symbolic Computation [cs.SC], Algebra and Number Theory, [INFO.INFO-SC] Computer Science [cs]/Symbolic Computation [cs.SC], [INFO.INFO-RB] Computer Science [cs]/Robotics [cs.RO], [MATH.MATH-AG] Mathematics [math]/Algebraic Geometry [math.AG], [INFO] Computer Science [cs], Semi-algebraic sets, Polynomial systems, Computer Science::Robotics, Computational Mathematics, Kinematic singularity, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], [INFO]Computer Science [cs], [MATH.MATH-AG]Mathematics [math]/Algebraic Geometry [math.AG], Roadmaps
Abstract: International audience; In this paper we introduce methods and algorithms that will help us solve connectivity queries of parameterized semi-algebraic sets. Answering these connectivity queries is applied in the design of robotic structures having similar kinematic properties (e.g. topology of the kinematic-singularity-free space). From these algorithms one also obtain solutions to connectivity queries of a specific parameter which is in turn related to kinematic-singularity free path-planning of a specific manipulator belonging to the family of robots with these properties; i.e. we obtain paths joining two given singularity free configurations lying in the same connected component of the singularity-free space. We prove in the paper how one reduces the problems related to connectivity queries of parameterized semi-algebraic sets to closed and bounded semi-algebraic sets. We then design an algorithm using computer-algebra methods for "solving" positive dimensional polynomial system depending on parameters. The meaning of solving here means partitioning the parameter space into semi-algebraic components over which the number of connected components of the semi-algebraic set defined by the input system is invariant. The complexity of this algorithm is singly exponential in the dimension of the ambient space. The algorithm scales enough to analyze automatically the family of UR-series robots. Finally we provide manual analysis of the family of UR-series robots, proving that the number of connected components of the complementary of kinematic singularity set of a generic UR-robot is eight.
Published: 2023
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139. The reach of subsets of manifolds

Author: Jean-Daniel Boissonnat, Mathijs Wintraecken, Université Côte d'Azur (UCA), Understanding the Shape of Data (DATASHAPE), 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)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), The Austrian science fund (FWF) M-3073, ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 339025,EC:FP7:ERC,ERC-2013-ADG,GUDHI(2014), and European Project: 754411,ISTplus(2017)
Subjects: Computational Mathematics, 53-08 , 53A99 , 68U05 , 65D18, comparison theory, Applied Mathematics, [INFO]Computer Science [cs], Geometry and Topology, Reach, surfaces, [MATH]Mathematics [math], Manifolds
Abstract: International audience; Kleinjohann [1] and Bangert [2] extended the reach rch(S) from subsets S of Euclidean space to the reach rch M (S) of subsets S of Riemannian manifolds M, where M is smooth (we'll assume at least C^3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann's and Bangert's extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p ∈ M and q ∈ S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp^{ −1}_p (S)) at q, assuming that rch M (S) and the geodesic distance d_ M (p, q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.
Published: 2023
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140. Proprioceptors in extraocular muscles

Author: Blumer, Roland, Carrero Rojas, Génova, Martín Calvo, Paula, Streicher, Johannes, Rodríguez de la Cruz, Rosa María, Pastor Loro, Ángel Manuel, Universidad de Sevilla. Departamento de Fisiología, Austrian Science Fund (FWF), Ministerio de Ciencia e Innovación (MICIN). España, and Junta de Andalucía
Subjects: Muscle spindles, Palisade endings, Golgi tendon organs, Proprioception, Eye muscle
Abstract: New Findings: What is the topic of this review? This review aims to evaluate the literature on proprioceptors and particular nerve specializations (palisade endings) in mammalian extraocular muscles (EOMs) and to reconsider current knowledge of their structure and function. What advances does it highlight? Classical proprioceptors (muscle spindles and Golgi tendon organs) are absent in the EOMs of most mammals. Instead, palisade endings are present in most mammalian EOMs. For many years, palisade endings were considered to be sensory but recent studies show that they combine sensory and motor features. The functional significance of palisade endings is still debated. Abstract: Proprioception is the sense that lets us perceive the location, movement and action of the body parts. The proprioceptive apparatus includes specialized sense organs (proprioceptors) which are embedded in the skeletal muscles. The eyeballs are moved by six pairs of eye muscles and binocular vision depends on fine-tuned coordination of the optical axes of both eyes. Although experimental studies indicate that the brain has access to eye position information, both classical proprioceptors (muscle spindles and Golgi tendon organ) are absent in the extraocular muscles of most mammalian species. This paradox of monitoring extraocular muscle activity in the absence of typical proprioceptors seemed to be resolved when a particular nerve specialization (the palisade ending) was detected in the extraocular muscles of mammals. In fact, for decades there was consensus that palisade endings were sensory structures that provide eye position information. The sensory function was called into question when recent studies revealed the molecular phenotype and the origin of palisade endings. Today we are faced with the fact that palisade endings exhibit sensory as well as motor features. This review aims to evaluate the literature on extraocular muscle proprioceptors and palisade endings and to reconsider current knowledge of their structure and function. Austrian Science Fund (FWF) P15478, P20881, P32463-B Ministerio de Ciencia e Innovación PGC2018-094654-B-100, PID2021-124300NB-I00 Junta de Andalucía P20_00529
Published: 2023

141. Some aspects of infinite-dimensional Geometry: Theory and Applications

Author: Tumpach, Alice Barbara, University of Lille, FWF Grant I-5015N, Lille University, and Stephane de Bièvre
Subjects: Infinite-dimensional manifolds, orbites coadjointes de dimension infinie, Banach Poisson-Lie groups, infinite-dimensional coadjoint orbits, variétés Riemanniannes de dimension infinie, Shape analysis of curves and surfaces, crochet de Poisson, infinite-dimensional Riemannian manifolds, Poisson brackets, géometrie en dimension infinie, Groupes de Poisson-Lie banachiques, Analyse des courbes et des surfaces, [INFO]Computer Science [cs], [MATH]Mathematics [math]
Abstract: We present some recent developments of infinite-dimensional Geometry, and show some applications in Shape Analysis. The first chapter is an introduction to the universal Teichmüller space and to its connexion to infinite-dimensional coadjoint orbits on one hand, and Shape Analysis via the fingerprint map on the other hand.Chapter II presents applications of infinite-dimensional Riemannian Geoemtry for Form Recognition and Shape Analysis of curves and surfaces.Chapter III is devoted to infinite-dimensional Poisson Geometry and its pathologies,notably we set the foundations of the theory of Banach Poisson--Lie groups.
Published: 2022

142. Hotspots of Cenozoic Tropical Marine Biodiversity

Author: Moriaki Yasuhara, Huai-Hsuan May Huang, Markus Reuter, Skye Yunshu Tian, Jonathan D. Cybulski, Aaron O’Dea, Briony L. Mamo, Laura J. Cotton, Emanuela Di Martino, Ran Feng, Clay R. Tabor, Gabriel Reygondeau, Qianshuo Zhao, Mark T. Warne, Kyawt K. T. Aye, Jingwen Zhang, Anne Chao, Chih-Lin Wei, Fabien L. Condamine, Adam T. Kocsis, Wolfgang Kiessling, Mark J. Costello, Derek P. Tittensor., Chhaya Chaudhary, Marina C. Rillo, Hideyuki Doi, Yun-wei Dong, Thomas M. Cronin, Erin E. Saupe, Heike K. Lotze, Kenneth G. Johnson, Willem Renema, John M. Pandolfi, Mathias Harzhauser, Jeremy B. C. Jackson, Yuanyuan Hong, School of biological sciences (Hong Kong, Chine), The University of Hong Kong (HKU), Smithsonian Institution, Universität Greifswald - University of Greifswald, Smithsonian Tropical Research Institute, University of Bologna/Università di Bologna, Macquarie University, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Oslo (UiO), University of Connecticut (UCONN), University of British Columbia (UBC), Ocean University of China (OUC), Deakin University [Burwood], National Tsing Hua University [Hsinchu] (NTHU), National Taiwan University [Taiwan] (NTU), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), MTA-MTM-ELTE Research Group for Paleontology, Eötvös Loránd University (ELTE)-Hungarian Academy of Sciences (MTA), Faculty of Biosciences and Aquaculture [Bodø], University of Nordland, Dalhousie University [Halifax], United Nations Environment Programme (UNEP) World Conservation Monitoring Center (WCMC) (UNEP WCMC), Alfred Wegener Institute [Potsdam], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, University of Hyogo, Qingdao National Laboratory for Marine Science and Technology, US Geological Survey [Salt Lake City], United States Geological Survey [Reston] (USGS), University of Oxford, The Natural History Museum [London] (NHM), Naturalis Biodiversity Center [Leiden], Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), University of Queensland [Brisbane], Natural History Museum [Vienna] (NHM), American Museum of Natural History (AMNH), Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch], This work is a product of the PSEEDS (Palaeobiology as the Synthetic Ecological, Evolutionary, and Diversity Sciences) project and is partly supported by grants from the Research Grants Council of the Hong Kong Special Administrative Region, China (project codes: HKU 17300821, HKU 17300720, HKU 17302518, C7050-18E, C7013-19G), the Marine Conservation Enhancement Fund (project code: MCEF20002_L01), the Marine Ecology Enhancement Fund (project code: MEEF2021001), the Small Equipment Grant of the University of Hong Kong, the Seed Funding Programme for Basic Research of the University of Hong Kong (project codes: 202011159122, 201811159076), the Faculty of Science RAE Improvement Fund of the University of Hong Kong, the Seed Funding of the HKU-TCL Joint Research Centre for Artificial Intelligence of the University of Hong Kong and the SKLMP Seed Collaborative Research Fund (SKLMP/SCRF/0031) (to M.Y.), by the Sistema Nacional de Investigadores (SENACYT) (to A.O), by the Australian Research Council Centre of Excellence for Coral Reef Studies (to J.M.P.), by the Austrian Science Fund (FWF, project code: P 29158-N29) (to M.R.), and by State Key Laboratory of Palaeobiology and Stratigraphy and Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (project code: 203108) (to Y.H.)., Stephen J. Hawkins, A. Louise Allcock, Peter A. Todd, Stephen E. Swearer‬, Maria Byrne, Louise B. Firth, Anaëlle J. Lemasson, Cathy H. Lucas, Ezequiel M. Marzinelli, Peter J. Mumby, Bayden D. Russell, I. Philip Smith, and Hawkins, S. J.
Subjects: Species diversity gradients, Global patterns, [SDV]Life Sciences [q-bio], Tropics, Neogene, Paleobiology, Fossil records, Paleogene
Abstract: International audience; Hotspots of tropical marine biodiversity are areas that harbour disproportionately large numbers of species compared to surrounding regions. The richness and location of these hotspots have changed throughout the Cenozoic. Here, we review the global dynamics of Cenozoic tropical marine biodiversity hotspots, including the four major hotspots of the Indo-Australian Archipelago (IAA), western Tethys (present Mediterranean), Arabian Sea and Caribbean Sea. Our review supports the ‘Hopping Hotspots’ model, which proposes that the locations of peak biodiversity are related to Tethyan faunal elements and track broad-scale shallow-marine habitats and high coastal complexity created by the collision of tectonic plates. A null hypothesis is the ‘Whack-A-Mole’ model, which proposes that hotspots occur in habitats suitable for high diversity regardless of taxonomic identity or faunal elements. Earlier ‘Centre-of’ theories (e.g. centres of origin with diversity decreasing with distance from supposed areas of exceptionally high rates of speciation, for which easy connection to adjacent regions to the east and west is important) were based on the analysis of recent biotas with no palaeontological foundation, and may better explain diversity dynamics within a hotspot rather than those between hotspots. More recently, however, human disturbance is massively disrupting these natural patterns.
Published: 2022
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143. Mosquito sex and mycobiota contribute to fructose metabolism in the Asian tiger mosquito Aedes albopictus

Author: Morgane Guégan, Edwige Martin, Van Tran Van, Benjamin Fel, Anne-Emmanuelle Hay, Laurent Simon, Noémie Butin, Floriant Bellvert, Feth el Zahar Haichar, Claire Valiente Moro, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Équipe 3 - Écologie, Évolution, Écosystemes Souterrains (E3S), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-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 de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul FluxoMet (TBI-MetaToul), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-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)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie, adaptation et pathogénie (MAP), 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)-Centre National de la Recherche Scientifique (CNRS), French National Programme EC2CO-Biohefect/Ecodyn//Dril/MicrobiEen (<>) ERA-NET BiodivERsA ANR-13-EBID-0007-01Austrian Science Fund (FWF)I-1437German Research Foundation (DFG)European Commission KL 2087/6-1, ANR-18-CE32-0005,DIORE,Régulation de la dénitrification par la nature des exsudats racinaires(2018), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-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)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ROSSI, Sabine, and Régulation de la dénitrification par la nature des exsudats racinaires - - DIORE2018 - ANR-18-CE32-0005 - AAPG2018 - VALID
Subjects: Microbiology (medical), Male, Sugar assimilation, Microbiota, Stable isotope probing, Fructose, Microbiology, Gastrointestinal Microbiome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Mosquito, FungiC-13 metabolomic, Aedes, Animals, Carbohydrate Metabolism, Female, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: Background Plant floral nectars contain natural sugars such as fructose, which are a primary energy resource for adult mosquitoes. Despite the importance of carbohydrates for mosquito metabolism, a limited knowledge is available about the pathways involved in sugar assimilation by mosquitoes and their associated microbiota. To this end, we used 13C-metabolomic and stable isotope probing approaches coupled to high-throughput sequencing to reveal fructose-related mosquito metabolic pathways and the dynamics of the active gut microbiota following fructose ingestion. Results Our results revealed significant differences in metabolic pathways between males and females, highlighting different modes of central carbon metabolism regulation. Competitive and synergistic interactions of diverse fungal taxa were identified within the active mycobiota following fructose ingestion. In addition, we identified potential cross-feeding interactions between this. Interestingly, there is a strong correlation between several active fungal taxa and the presence of fructose-derived metabolites. Conclusions Altogether, our results provide novel insights into mosquito carbohydrate metabolism and demonstrate that dietary fructose as it relates to mosquito sex is an important determinant of mosquito metabolism; our results also further highlight the key role of active mycobiota interactions in regulating the process of fructose assimilation in mosquitoes. This study opens new avenues for future research on mosquito-microbiota trophic interactions related to plant nectar-derived sugars. Graphical Abstract
Published: 2022
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144. Connector theory for reusing model results to determine materials properties

Author: Marco Vanzini, Ayoub Aouina, Martin Panholzer, Matteo Gatti, Lucia Reining, LSI - Spectroscopie théorique (ST), Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), European Theoretical Spectroscopy Facility (ETSF), Johannes Kepler Universität Linz - Johannes Kepler University Linz [Autriche] (JKU), Uni Software Plus GmbH, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), the Austrian science Fund FWF under Project No. J 3855-N27, and European Project: 320971,EC:FP7:ERC,ERC-2012-ADG_20120216,SEED(2013)
Subjects: electron-gas, kinetic-energy, Computer Science Applications, gradient approximation, Mechanics of Materials, Modeling and Simulation, linear-response, systems, General Materials Science, exchange-energy, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], density-functional theory, accurate, nonlocal approximation, expressions
Abstract: The success of Density Functional Theory (DFT) is partly due to that of simple approximations, such as the Local Density Approximation (LDA), which uses results of a model, the homogeneous electron gas, to simulate exchange-correlation effects in real materials. We turn this intuitive approximation into a general and in principle exact theory by introducing the concept of a connector: a prescription how to use results of a model system in order to simulate a given quantity in a real system. In this framework, the LDA can be understood as one particular approximation for a connector that is designed to link the exchange-correlation potentials in the real material to that of the model. Formulating the in principle exact connector equations allows us to go beyond the LDA in a systematic way. Moreover, connector theory is not bound to DFT, and it suggests approximations also for other functionals and other observables. We explain why this very general approach is indeed a convenient starting point for approximations. We illustrate our purposes with simple but pertinent examples.
Published: 2022
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145. Biochemical characterization of the major N-acetylmuramidase from Lactobacillus buchneri

Author: Christian Obinger, Christina Schäffer, Julia Anzengruber, Paul Messner, Monika Debreczeny, Jos Vanderleyden, Marie-Pierre Chapot-Chartier, Ingmar Claes, Stefan Hofbauer, Pascal Courtin, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Catholique de Louvain = Catholic University of Louvain (UCL), Department of Chemistry, Univ Bodenkultur Wien, Dept Chem, A-1190 Vienna, Austria, Partenaires INRAE, Univ Bodenkultur Wien, NanoGlycobiol Unit, Dept Nano Biotechnol, A-1190 Vienna, Austria, Austrian Science Fund, FWF [P21954-B20, P24305-B20], PhD programme 'BioToP - Biomolecular Technology of Proteins' (Austrian Science Fund, FWF) [W1224], Hochschuljubilaumsstiftung der Stadt Wien [H-2442/2012], INRA (France), and Region Ile de France
Subjects: Glycoside Hydrolases, biology, Peptidoglycan, biology.organism_classification, Microbiology, Protein Structure, Secondary, Article, Bacterial cell structure, Cell wall, Lactobacillus, Protein Transport, chemistry.chemical_compound, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Bacterial Proteins, Lactobacillus rhamnosus, chemistry, Biochemistry, Cell Wall, Enzyme Stability, Hydrolase, Glycoside hydrolase, Lactobacillus buchneri
Abstract: Bacterial cell wall hydrolases are essential for peptidoglycan remodelling in regard to bacterial cell growth and division. In this study, peptidoglycan hydrolases (PGHs) of differentLactobacillus buchneristrains were investigated. First, the genome sequence ofL. buchneriCD034 andL. buchneriNRRL B-30929 was analysedin silicofor the presence of PGHs. Of 23 putative PGHs with different predicted hydrolytic specificities, the glycosyl hydrolase family 25 domain-containing homologuesLbGH25B andLbGH25N fromL. buchneriCD034 and NRRL B-30929, respectively, were selected and characterized in detail. Zymogram analysis confirmed hydrolysing activity on bacterial cell walls for both enzymes. Subsequent reversed-phase HPLC and MALDI-TOF MS analysis of the peptidoglycan breakdown products fromL. buchneristrains CD034 and NRRL B-30929, and fromLactobacillus rhamnosusGG, which served as a reference, revealed thatLbGH25B andLbGH25N haveN-acetylmuramidase activity. Both enzymes were identified as cell wall-associated proteins by means of immunofluorescence microscopy and cellular fractionation, as well as by the ability of purified recombinantLbGH25B andLbGH25N to bind toL. buchnericell wallsin vitro. Moreover, similar secondary structures mainly composed of β-sheets and nearly identical thermal stabilities withTmvalues around 49 °C were found for the twoN-acetylmuramidases by far-UV circular dichroism spectroscopy. The functional and structural data obtained are discussed and compared to related PGHs. In this study, a majorN-acetylmuramidase fromL. buchneriwas characterized in detail for the first time.
Published: 2014
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146. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

Author: Catherine Baxendale, Nicolas Legay, Jean-Christophe Clément, Maxime Dumont, Cindy Arnoldi, Karl Grigulis, Thomas Pommier, Ute Krainer, Sandra Lavorel, F. Poly, Eva-Maria Kastl, Michael Schloter, Michael Bahn, Richard D. Bardgett, Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Lancaster Environment Centre, Lancaster University, Ecology, University of Innsbruck, University of Innsbruck, Helmholtz-Zentrum München ( HZM ), Faculty of Life Sciences [Manchester], University of Manchester [Manchester], Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Helmholtz-Zentrum München (HZM), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), ERA-Net BiodivERsA project VITAL (ANR-08-BDVA-008), ANR, FWF, NERC, BMBF, Austrian Science Fund (FWF) (I 242-B17), 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)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-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)
Subjects: 0106 biological sciences, leaf traits, soil microbial community, Plant Science, Plant Roots, 01 natural sciences, Soil, Abundance (ecology), bacteria, Soil Microbiology, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Community structure, food and beverages, Biodiversity, 04 agricultural and veterinary sciences, Plants, nitrite oxidizers, Grassland, Nitrification, Phenotype, Denitrification, Oxidation-Reduction, Soil microbiology, Nitrogen, Biology, 010603 evolutionary biology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, nitrite reducers, Botany, Ecosystem, Relative species abundance, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, plant functional traits, denitrifiers, Plant community, Original Articles, Plant Components, Aerial, 15. Life on land, Archaea, Ammonia-oxidizing archaea, root traits, Microbial population biology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, nutrient availability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aims: Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
Published: 2014
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147. On the Tuning of High-Resolution NMR Probes

Author: Pöschko, Maria Theresia, Schlagnitweit, Judith, Huber, Gaspard, Nausner, Martin, Horničáková, Michaela, Desvaux, Hervé, Müller, Norbert, Johannes Kepler Universität Linz (JKU), Institute of Organic Chemistry, Johannes Kepler Universität Linz - Johannes Kepler University Linz [Autriche] (JKU), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), This research was supported - by the Austrian Science Funds (FWF) and the Agence Nationale de Recherche (ANR) in the joint project IMAGINE (FWF project number I1115-N19, ANR project 12-IS04-0006) - by the EGIDE-ÖAD AMADEUS Austrian-French exchange program (no. 28948WD and FR 11/2013)., ANR-12-IS04-0006,IMAGINE,Etudes RMN d'effets non-linéaires induits par l'aimantation(2012), Johannes Kepler University Linz [Linz] (JKU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: analytical methods magnetic properties NMR spectroscopy radiation damping spin noise, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract: International audience; Three optimum conditions for the tuning of NMR probes are compared: the conventional tuning optimum, which is based on radio-frequency pulse efficiency, the spin noise tuning optimum based on the line shape of the spin noise signal, and the newly introduced frequency shift tuning optimum, which minimizes the frequency pushing effect on strong signals. The latter results if the radiation damping feedback field is not in perfect quadrature to the precessing magnetization. According to the conventional RLC (resistor–inductor–capacitor) resonant circuit model, the optima should be identical, but significant deviations are found experimentally at low temperatures, in particular on cryogenically cooled probes. The existence of different optima with respect to frequency pushing and spin noise line shape has important consequences on the nonlinearity of spin dynamics at high polarization levels and the implementation of experiments on cold probes.
Published: 2014
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148. Attosecond emission from chromium plasma

Author: F. Lepetit, Stefan Haessler, J.-F. Hergott, Pascal Salières, O. Gobert, Bertrand Carré, L. B. Elouga Bom, M. Perdrix, Tsuneyuki Ozaki, Institut National de la Recherche Scientifique [Québec] (INRS), Service des Photons, Atomes et Molécules (SPAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Photonics Institute, Vienna University of Technology (TU Wien), Austrian Science Fund (FWF) M1260-N16, Austrian Science Fund (FWF) 21463-N22, ANR-09-BLAN-0031,ATTO-WAVE(2009), and European Project: 238362,EC:FP7:PEOPLE,FP7-PEOPLE-ITN-2008,ATTOFEL(2009)
Subjects: Physics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS]Physics [physics]/Physics [physics], [PHYS.PHYS.PHYS-ATOM-PH]Physics [physics]/Physics [physics]/Atomic Physics [physics.atom-ph], business.industry, Attosecond, Nonlinear optics, Plasma, Laser, 7. Clean energy, 01 natural sciences, Atomic and Molecular Physics, and Optics, law.invention, 010309 optics, Optics, law, Harmonics, 0103 physical sciences, Femtosecond, Group delay dispersion, High harmonic generation, Atomic physics, 010306 general physics, business
Abstract: International audience; We present the first measurement of the attosecond emission generated from underdense plasma produced on a solid target. We generate high-order harmonics of a femtosecond Ti:sapphire laser focused in a weakly ionized underdense chromium plasma. Using the " Reconstruction of Attosecond Beating by Interference of Two-photon Transitions " (RABITT) technique, we show that the 11 th to the 19 th harmonic orders form in the time domain an attosecond pulse train with each pulse having 300 as duration, which is only 1.05 times the theoretical Fourier transform limit. Measurements reveal a very low positive group delay dispersion of 4200 as 2. Beside its fundamental interest, high-order harmonic generation in plasma plumes could thus provide an intense source of attosecond pulses for applications.
Published: 2011
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149. The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

Author: Erzsébet Fekete, Lukas Hartl, Irina S. Druzhinina, Stéphane Le Crom, Lea Atanasova, Bernhard Seiboth, Erzsébet Sándor, Thomas Portnoy, Antoine Margeot, Levente Karaffa, Rita Linke, Christian P. Kubicek, BMC, Ed., IFP Energies nouvelles (IFPEN), GenomiqueENS (Genomique ENS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Austrian Center of Industrial Biotechnology [Vienna, Austria] (Institute of Chemical Engineering), Vienna University of Technology (TU Wien), Research Area Gene Technology and Applied Biochemistry [Vienna, Austria] (Institute of Chemical Engineering), Biochemical Engineering Department [Debrecen, Hungary] (Faculty of Science & Technology), University of Debrecen Egyetem [Debrecen], Plant Protection Department [Debrecen, Hungary] (Faculty of Agriculture and Food Sciences & Environmental Management), This work was supported by grants from the Austrian Science Foundation (FWF P-19143 and FWF P-19421) to CPK and BS, respectively. Work by SLC was supported by the Infrastructures en Biologie Santé et Agronomie (IBISA). TP is recipient of a Fondation Tuck Enerbio PhD. Fellowship. Work by LK, EF and ES was supported by the Hungarian Scientific Research Fund (OTKA, K67667) and the National Office for Research and Technology (NKTH, A2-2006-0017). EF is supported by a Bolyai János Research Scholarship (BO/00519/09/8)., Plateforme Génomique de l'IBENS, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), University of Debrecen, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Catabolite repression, Biológiai tudományok, Gene Knockout Techniques, MESH: Protein Structure, Tertiary, Természettudományok, Hypocrea, Transcription (biology), MESH: Up-Regulation, Trichoderma reesei, MESH: Gene Knockout Techniques, 2. Zero hunger, Genetics, 0303 health sciences, biology, Up-Regulation, Cell biology, MESH: Glucose, Phenotype, MESH: Repressor Proteins, Hypocreales, MESH: Genome, Fungal, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Fungal Proteins, Genome, Fungal, Research Article, Biotechnology, MESH: Mutation, lcsh:QH426-470, lcsh:Biotechnology, Repressor, MESH: Carbon, MESH: Hypocreales, MESH: Phenotype, Chromatin remodeling, Fungal Proteins, 03 medical and health sciences, Mediator, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, 030304 developmental biology, Binding Sites, 030306 microbiology, biology.organism_classification, Carbon, Protein Structure, Tertiary, Repressor Proteins, lcsh:Genetics, Glucose, MESH: Binding Sites, Mutation
Abstract: Background The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known. Results Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. Conclusions Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
Published: 2011
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150. Microstructure, plasticité et ductilité d'un alliage TNM+ densifié par frittage SPS

Author: Michael Musi, Christophe Deshayes, Guy Molénat, Louise Toualbi, Benjamin Galy, Petra Spoerk-Erdely, Muriel Hantcherli, Jean-Philippe Monchoux, Marc Thomas, Helmut Clemens, Alain Couret, Montanuniversität Leoben (MUL), Physique de la Plasticité et Métallurgie (CEMES-PPM), Centre d'élaboration de matériaux et d'études structurales (CEMES), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), DMAS, ONERA, Université Paris Saclay [Châtillon], ONERA-Université Paris-Saclay, Austrian-French project 'Hi-TiAl - 18-CE91-0008-01' co-supported by the French Agence Nationale de la Recherche (ANR) and the Fonds zur Förderung der wissenschaftlichen Forschung (FWF), ANR-18-CE91-0008,Hi-TiAl,Amélioration des propriétés mécaniques à haute température des alliages TiAl par l'incorporation d'éléments d'addition(2018), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS]Physics [physics], titanium aluminides, plasticité, microstructure, heat treatments, Metals and Alloys, SPS, mechanical properties, intermétalliques, [SPI]Engineering Sciences [physics], transmission electron microscopy, [CHIM]Chemical Sciences, General Materials Science
Abstract: International audience; This work presents a study of the microstructure and mechanical properties of a TNM+ alloy (Ti-43.5Al-4Nb-1Mo-0.1B-0.3C-0.3Si, in at.%) densified by Spark Plasma Sintering (SPS), in comparison to the as-SPSed TNM alloy, which contains neither carbon nor silicon. Tensile tests at room temperature and 800 °C, as well as creep tests at 800 °C and 200 MPa, were performed. The microstructures and the fracture surfaces of deformed samples were studied by scanning and transmission electron microscopies, as well as by X-ray diffraction. The deformation mechanisms were investigated by means of in situ straining experiments and post-mortem analyses of deformed samples, both performed by transmission electron microscopy. Contrary to the TNM alloy, the as-SPSed microstructure of the TNM+ alloy does not contain β/βo phase due to the incorporation of carbon. At room temperature, the TNM+ alloy exhibits a yield stress of 520 MPa but a poor ductility of less than 0.1% of plastic strain. The incorporation of carbon and silicon leads to an increase in the creep resistance of the alloy at 800 °C. Despite the fact that iron inclusions are responsible for the premature failure of some samples during tensile tests, the TNM+ alloy is found to be able to deform plastically at room temperature by the glide of ordinary dislocations and by twinning.; Ce travail présente une étude de la microstructure et des propriétés mécaniques d'un alliage TNM+ (Ti-43.5Al-4Nb-1Mo-0.1B-0.3C-0.3Si, en at.%) densifié par Spark Plasma Sintering (SPS), en comparaison avec l'alliage TNM brut de SPS qui ne contient ni carbone ni silicium. Des essais de traction à température ambiante et 800°C ainsi que des essais de fluage à 800°C et 200 MPa ont été réalisés. Les microstructures et les surfaces de rupture des échantillons déformés ont été étudiées par microscopie électronique à balayage et à transmission, ainsi que par diffraction des rayons X. Les mécanismes de déformation ont été étudiés au moyen d'expériences de déformation in situ et d'analyses post-mortem d'échantillons déformés, toutes deux réalisées par microscopie électronique à transmission. Contrairement à l'alliage TNM, la microstructure brute de SPS de l'alliage TNM+ ne contient pas de phase bêta/bêta0 en raison de l'incorporation de carbone. Malgré le fait que les inclusions de fer soient responsables de la rupture prématurée de certains échantillons lors des essais de traction, l'alliage TNM+ est capable de se déformer plastiquement à température ambiante. L'incorporation de carbone et de silicium conduit à une augmentation de la résistance au fluage de l'alliage à 800°C.
Published: 2022
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