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266 results on '"Institute of Science and Technology [Austria] (IST Austria)"'

1. Gene Drives: Dynamics and Regulatory Matters—A Report from the Workshop 'Evaluation of Spatial and Temporal Control of Gene Drives,' April 4–5, 2019, Vienna

Author: Florence Débarre, Philipp W. Messer, Nicholas H. Barton, Marc F. Schetelig, Bernd Giese, Nikolai Windbichler, Johannes L. Frieß, Harald Meimberg, Christophe Boëte, University of Natural Resources and Applied Life Sciences (BOKU), Institute of Science and Technology Austria [Klosterneuburg, Austria] (IST), Department of Systems & Computational Biology [New York], Albert Einstein College of Medicine, Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), Department of Life Sciences, Imperial College London, 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 de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Natural Resources and Life Sciences (BOKU), Institute of Science and Technology [Austria] (IST Austria), Albert Einstein College of Medicine [New York], Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, German Federal Agency for Nature Conservation (BfN) [3518 84 0500], Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] - IST Austria (IST Austria), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
Subjects: [SDV]Life Sciences [q-bio], Population, Control (management), Biology, Risk Assessment, Population control, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, population dynamics, Humans, education, Gene, Risk management, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, education.field_of_study, Organisms, Genetically Modified, business.industry, Gene Drive Technology, Prospective risk, modeling, Gene drive, Risk analysis (engineering), Paradigm shift, gene drive, business, 030217 neurology & neurosurgery, population control
Abstract: International audience; Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modiﬁed organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this ﬁeld and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio-ecological systems. The recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.
Published: 2019

2. Shellability is NP-Complete

Author: Zuzana Patáková, Pavel Paták, Uli Wagner, Xavier Goaoc, Martin Tancer, Laboratoire d'Informatique Gaspard-Monge (LIGM), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Bézout-ESIEE Paris-École des Ponts ParisTech (ENPC)-Université Paris-Est Marne-la-Vallée (UPEM), Department of Mathematics and Statistics [Brno], Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI)-Masaryk University [Brno] (MUNI), Institute of Science and Technology [Austria] (IST Austria), Department of Applied Mathematics [Prague] (KAM), Charles University [Prague] (CU), Bettina Speckmann and Csaba D. Tóth, Université Paris-Est Marne-la-Vallée (UPEM)-École des Ponts ParisTech (ENPC)-ESIEE Paris-Fédération de Recherche Bézout-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] - IST Austria (IST Austria), Geometric Algorithms and Models Beyond the Linear and Euclidean realm (GAMBLE ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Computational Geometry (cs.CG), FOS: Computer and information sciences, Reduction (recursion theory), 0102 computer and information sciences, Collapsibility, 02 engineering and technology, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], Contractible space, 01 natural sciences, Combinatorics, Simplicial complex, Mathematics - Geometric Topology, Corollary, Artificial Intelligence, Simple (abstract algebra), FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, Mathematics - Combinatorics, [INFO]Computer Science [cs], [MATH]Mathematics [math], 0101 mathematics, Mathematics, 000 Computer science, knowledge, general works, Simplicial complexes, 010102 general mathematics, Geometric Topology (math.GT), 020207 software engineering, NP-completeness, 010201 computation theory & mathematics, Hardware and Architecture, Control and Systems Engineering, Computer Science, Computer Science - Computational Geometry, 020201 artificial intelligence & image processing, Combinatorics (math.CO), NP-complete, Partially ordered set, Software, Information Systems, Shellability
Abstract: We prove that for every $d\geq 2$, deciding if a pure, $d$-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every $d \ge 2$ and $k \ge 0$, deciding if a pure, $d$-dimensional, simplicial complex is $k$-decomposable is NP-hard. For $d \ge 3$, both problems remain NP-hard when restricted to contractible pure $d$-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable., Version 2: 17 pages, 11 figures. Improved readability at various places. Proof in Section 6 simplified
Published: 2018
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3. On a certain non-split cubic surface

Author: Yongqiang Zhao, Kevin Destagnol, Jie Wu, Jianya Liu, Régis de la Bretèche, Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG (UMR_7586)), Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] (IST Austria), Shandong University, Laboratoire d'Analyse et de Mathématiques Appliquées (LAMA), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Fédération de Recherche Bézout-Université Paris-Est Marne-la-Vallée (UPEM), Westlake University, Université Paris-Est Marne-la-Vallée (UPEM)-Fédération de Recherche Bézout-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), and Institute of Science and Technology [Austria] - IST Austria (IST Austria)
Subjects: asymptotic formula, Pure mathematics, Cubic surface, singular cubic surface, Mathematics::Commutative Algebra, Mathematics - Number Theory, General Mathematics, Mathematics::Number Theory, 010102 general mathematics, 0211 other engineering and technologies, 021107 urban & regional planning, 02 engineering and technology, Term (logic), 01 natural sciences, non-split toric surface, rational points, Bounded function, FOS: Mathematics, Asymptotic formula, Number Theory (math.NT), 0101 mathematics, [MATH]Mathematics [math], Manin-Peyre conjecture, Mathematics, descent on torsors
Abstract: In this note, we establish an asymptotic formula for the number of rational points of bounded height on the singular cubic surface $$ x_0(x_1^2 + x_2^2)=x_3^3 $$ with a power-saving error term, which verifies the Manin-Peyre conjectures for this surface., v2. 18 pages, one author added
Published: 2017

4. Bounding Helly Numbers via Betti Numbers

Author: Xavier Goaoc, Uli Wagner, Pavel Paták, Zuzana Patáková, Martin Tancer, Laboratoire d'Informatique Gaspard-Monge (LIGM), Université Paris-Est Marne-la-Vallée (UPEM)-École des Ponts ParisTech (ENPC)-ESIEE Paris-Fédération de Recherche Bézout-Centre National de la Recherche Scientifique (CNRS), Einstein Institute of Mathematics, The Hebrew University of Jerusalem (HUJ), Department of Applied Mathematics [Prague] (KAM), Charles University [Prague] (CU), Institute of Science and Technology [Austria] - IST Austria (IST Austria), Martin Loebl, Jaroslav Nešetřil, Robin Thomas, Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Bézout-ESIEE Paris-École des Ponts ParisTech (ENPC)-Université Paris-Est Marne-la-Vallée (UPEM), Institute of Science and Technology [Austria] (IST Austria), Department of Algebra (MFF-UK), and Lars Arge and János Pach
Subjects: Computational Geometry (cs.CG), FOS: Computer and information sciences, Discrete Mathematics (cs.DM), Betti number, 0102 computer and information sciences, Computer Science::Computational Geometry, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Primary 52A35, secondary 05E45, 55S91, 05D10, 57Q35, Combinatorics, 510 Mathematics, Integer, Bounding overwatch, Embedding of simplicial complexes, FOS: Mathematics, Algebraic Topology (math.AT), Mathematics - Combinatorics, Beta (velocity), Betti numbers, Family of sets, Mathematics - Algebraic Topology, 0101 mathematics, Physics, 000 Computer science, knowledge, general works, Ramsey’s theorem, 010102 general mathematics, Homological almost-embedding, 010201 computation theory & mathematics, Computer Science, Computer Science - Computational Geometry, Combinatorics (math.CO), Helly-type theorem, Singular homology, Computer Science - Discrete Mathematics
Abstract: We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers $b$ and $d$ there exists an integer $h(b,d)$ such that the following holds. If $\mathcal F$ is a finite family of subsets of $\mathbb R^d$ such that $\tilde\beta_i\left(\bigcap\mathcal G\right) \le b$ for any $\mathcal G \subsetneq \mathcal F$ and every $0 \le i \le \lceil d/2 \rceil-1$ then $\mathcal F$ has Helly number at most $h(b,d)$. Here $\tilde\beta_i$ denotes the reduced $\mathbb Z_2$-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these $\lceil d/2 \rceil$ first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex $K$, some well-behaved chain map $C_*(K) \to C_*(\mathbb R^d)$., Comment: 29 pages, 8 figures
Published: 2017

5. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly

Author: Jonas Ranft, Martin Behrndt, Thomas Risler, Carl-Philipp Heisenberg, Nicolas Minc, Pedro Campinho, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Physico-Chimie-Curie (PCC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Physik komplexer Systeme (MPI-PKS), Max-Planck-Gesellschaft, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] (IST Austria), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC), Institute of Science and Technology Austria (IST Austria), Institute of Science and Technology Austria, and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Embryo, Nonmammalian, Cell, Epiboly, MESH: Gastrulation, Epithelium, Cell Fusion, Cell elongation, Myosin, MESH: Animals, Tissues and Organs (q-bio.TO), Zebrafish, biology, Tension (physics), Chemistry, Cell Polarity, Biomechanical Phenomena, Cell biology, medicine.anatomical_structure, MESH: Epithelial Cells, Biological Physics (physics.bio-ph), MESH: Cell Division, MESH: Cell Polarity, Cell Division, MESH: Myosin Type II, MESH: Biomechanical Phenomena, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, MESH: Zebrafish Proteins, Models, Biological, medicine, Animals, MESH: Cell Shape, Physics - Biological Physics, MESH: Zebrafish, Cell Shape, Myosin Type II, Gastrulation, MESH: Models, Biological, MESH: Embryo, Nonmammalian, Epithelial Cells, Quantitative Biology - Tissues and Organs, Cell Biology, Zebrafish Proteins, biology.organism_classification, Spindle apparatus, MESH: Epithelium, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, MESH: Cell Fusion, FOS: Biological sciences, MESH: Anisotropy, Anisotropy, Wound healing
Abstract: Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the Enveloping Cell Layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly., Comment: Methods, supplementary information and associated references are available in the published online version of the paper at http://www.nature.com/doifinder/10.1038/ncb2869
Published: 2015
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6. On Generalized Heawood inequalities for manifolds: a Van Kampen–Flores-type nonembeddability result

Author: Goaoc, Xavier, Mabillard, Isaac, Paták, Pavel, Patáková, Zuzana, Tancer, Martin, Wagner, Uli, Arge, Lars, Pach, János, Laboratoire d'Informatique Gaspard-Monge (LIGM), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Bézout-ESIEE Paris-École des Ponts ParisTech (ENPC)-Université Paris-Est Marne-la-Vallée (UPEM), Institute of Science and Technology [Austria] (IST Austria), Einstein Institute of Mathematics, The Hebrew University of Jerusalem (HUJ), Department of Applied Mathematics [Prague] (KAM), Charles University [Prague] (CU), Charles University Grant SVV-2014-260103, CE-ITI (GACR P202/12/G061) of the Czech Science Foundation, Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948), European Project: 267165,EC:FP7:ERC,ERC-2010-AdG_20100224,DISCONV(2011), Université Paris-Est Marne-la-Vallée (UPEM)-École des Ponts ParisTech (ENPC)-ESIEE Paris-Fédération de Recherche Bézout-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Department of Algebra (MFF-UK), Lars Arge, János Pach, and Institute of Science and Technology [Austria] - IST Austria (IST Austria)
Subjects: General Mathematics, 0102 computer and information sciences, Type (model theory), [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Combinatorics, Van Kampen–Flores, 510 Mathematics, 05E45 (Primary), 57N35 (Secondary), FOS: Mathematics, Mathematics - Combinatorics, 0101 mathematics, Manifolds, Prime power, Klein bottle, Mathematics, Heawood graph, Conjecture, Simplex, 000 Computer science, knowledge, general works, 010102 general mathematics, Complete graph, Surface (topology), Embeddings, 010201 computation theory & mathematics, Computer Science, Heawood Inequality, Combinatorics (math.CO)
Abstract: The fact that the complete graph $K_5$ does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph $K_n$ embeds in a closed surface $M$ (other than the Klein bottle) if and only if $(n-3)(n-4)\leq 6b_1(M)$, where $b_1(M)$ is the first $\mathbb Z_2$-Betti number of $M$. On the other hand, van Kampen and Flores proved that the $k$-skeleton of the $n$-dimensional simplex (the higher-dimensional analogue of $K_{n+1}$) embeds in $\mathbb R^{2k}$ if and only if~$n \le 2k+1$. Two decades ago, K\"uhnel conjectured that the $k$-skeleton of the $n$-simplex embeds in a compact, $(k-1)$-connected $2k$-manifold with $k$th $\mathbb Z_2$-Betti number $b_k$ only if the following generalized Heawood inequality holds: $\binom{n-k-1}{k+1} \le \binom{2k+1}{k+1}b_k$. This is a common generalization of the case of graphs on surfaces as well as the van Kampen--Flores theorem (the special cases $k=1$ and $b_k=0$, respectively), and also closely related to the theory of face numbers of triangulated manifolds. In the spirit of K\"uhnel's conjecture, we prove that if the $k$-skeleton of the $n$-simplex embeds in a $2k$-manifold with $k$th $\mathbb Z_2$-Betti number $b_k$, then $n \le 2b_k\binom{2k+2}{k} + 2k + 4$. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that $M$ is $(k-1)$-connected. Our results generalize to maps without $q$-covered points, in the spirit of Tverberg's theorem, for $q$ a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.
Published: 2015

7. An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis

Author: Ursula Abad, Gladys Cloarec, Benjamin Gilles, Jiří Friml, Massimiliano Sassi, Xu Chen, Coralie Cellier, Olivier Ali, Olivier Hamant, Jan Traas, Christophe Godin, Teva Vernoux, Frédéric Boudon, Pascale Milani, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-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), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Department of Plant Biotechnology and Genetics, Universiteit Gent = Ghent University (UGENT), Image & Interaction (ICAR), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Joliot Curie, École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), European Project: 235447,GA,FP7-ERANET-2008-RTD,ERASYSBIO+(2008), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institute of Science and Technology Austria (IST Austria), Institute of Science and Technology Austria, Ghent University [Belgium] (UGENT), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Science and Technology [Austria] (IST Austria), Universiteit Gent = Ghent University [Belgium] (UGENT), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Meristem, Morphogenesis, Arabidopsis, Organogenesis, Katanin, Receptors, Cell Surface, F62 - Physiologie végétale - Croissance et développement, Biology, General Biochemistry, Genetics and Molecular Biology, Plant Growth Regulators, Auxin, Cell Wall, Botany, Plant Proteins, chemistry.chemical_classification, Adenosine Triphosphatases, Indoleacetic Acids, Agricultural and Biological Sciences(all), Arabidopsis Proteins, Biochemistry, Genetics and Molecular Biology(all), fungi, food and beverages, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Cell biology, Biomechanical Phenomena, chemistry, biology.protein, Plant hormone, General Agricultural and Biological Sciences, Cortical microtubule, Plant Shoots
Abstract: International audience; To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the indi-vidual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferenti-ated cells where complex changes in growth rates and direc-tions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an impor-tant role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dy-namics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, in-cluding AUXIN BINDING PROTEIN 1 and KATANIN 1. Numer-ical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.
Published: 2014

8. A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes

Author: Mario Brameshuber, Gerhard J. Schütz, Jürgen Danzberger, Elena Heister, Barbara Unterauer, Peter Hinterdorfer, Constanze Lamprecht, Stefan Wieser, Andreas Ebner, Birgit Plochberger, Emmanuel Flahaut, Verena Ruprecht, Christian Rankl, Petar Lukanov, Johannes Kepler Universität Linz (JKU), Christian-Albrechts-Universität zu Kiel (CAU), Vienna University of Technology (TU Wien), Institute of Science and Technology [Austria] (IST Austria), Agilent Technologies, University of Surrey (UNIS), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Center for Advanced Bioanalysis - CBL (AUSTRIA), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Technische Universität Wien - TU Wien (AUSTRIA), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Agilent Technologies (USA), Christian-Albrechts-Universität zu Kiel - CAU (GERMANY), Institute of Science and Technology Austria - IST Austria (AUSTRIA), Linz Johannes Kepler University (AUSTRIA), University of Surrey (UNITED KINGDOM), Centre Interuniversitaire de Recherche et d'Ingénierie des Matériaux - CIRIMAT (Toulouse, France), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: Materials science, Matériaux, media_common.quotation_subject, Carbon nanotubes, Médecine humaine et pathologie, Bioengineering, Nanotechnology, 02 engineering and technology, Carbon nanotube, Microscopy, Atomic Force, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, 03 medical and health sciences, Molecular recognition, Cytosol, Drug Delivery Systems, Folic Acid, law, Cell Line, Tumor, Molecule, Humans, General Materials Science, Electrical and Electronic Engineering, Receptor, Internalization, 030304 developmental biology, media_common, 0303 health sciences, Nanotubes, Carbon, Particle tracking, Mechanical Engineering, Nocodazole, Force spectroscopy, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Molecular Docking Simulation, Mechanics of Materials, Docking (molecular), Biophysics, AFM, 0210 nano-technology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.
Published: 2014

9. A map of cell type‐specific auxin responses

Author: Kenneth D. Birnbaum, Dominique C. Bergmann, Bastiaan O. R. Bargmann, Mark Estelle, Idan Efroni, Tal Nawy, Goh Choe, Steffen Vanneste, Jiří Friml, Gabriel Krouk, Eilon Shani, Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Department of Cell and Developmental Biology (UCSD), University of California [San Diego] (UC San Diego), University of California-University of California, Department of Plant Biotechnology and Genetics [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Plant Biotechnology and Bioinformatics, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Science and Technology [Austria] (IST Austria), Howard Hughes Medical Institute (HHMI), Ghent University [Belgium] (UGENT), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology Austria (IST Austria), Howard Hughes Medical Institute, and Stanford University [Stanford]
Subjects: 0106 biological sciences, FUNCTIONAL GENOMIC ANALYSIS, root apical meristem, LATERAL ROOT INITIATION, SOYBEAN GH3 PROMOTER, Arabidopsis, HAIR DEVELOPMENT, Plant Roots, 01 natural sciences, Transcriptome, Gene Expression Regulation, Plant, signaling gradient, Transcriptional regulation, heterocyclic compounds, TRANSCRIPTION FACTOR, 581 Botany, DOMINANT EXPRESSION PATTERNS, Genetics, Regulation of gene expression, chemistry.chemical_classification, 0303 health sciences, Vegetal Biology, biology, AUX/IAA PROTEINS, Applied Mathematics, PLANT DEVELOPMENT, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Computational Theory and Mathematics, Organ Specificity, General Agricultural and Biological Sciences, Signal Transduction, Information Systems, Cell type, Meristem, Article, General Biochemistry, Genetics and Molecular Biology, development, 03 medical and health sciences, Auxin, GENE FAMILY-MEMBERS, ARABIDOPSIS ROOT, 030304 developmental biology, Indoleacetic Acids, auxine, General Immunology and Microbiology, Arabidopsis Proteins, Gene Expression Profiling, fungi, Biology and Life Sciences, biology.organism_classification, racine, Gene expression profiling, chemistry, arabidopsis halleri, Biologie végétale, 010606 plant biology & botany
Abstract: A map of cell type-specific auxin responses The transcriptional response to auxin was analyzed in four root cell types. The newly obtained data were cross-referenced with spatial expression maps to examine auxin's role in regulating gene expression in the root meristem., The majority of the thousands of auxin-responsive genes in the Arabidopsis thaliana root show a spatial bias in their induction or repression by auxin treatment. Auxin promotes the expression of cell-identity markers for the developing xylem and quiescent center, whereas it inhibits markers for the maturing xylem, cortex and trichoblasts. Relative induction or repression by auxin predicts expression along the longitudinal axis of the root., In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.
Published: 2013

10. Modeling adhesion-independent cell migration

Author: Diane Peurichard, Christian Schmeiser, Michael Sixt, Anne Reversat, Gaspard Jankowiak, Johann Radon Institute for Computational and Applied Mathematics (RICAM), Austrian Academy of Sciences (OeAW), 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 de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institute of Science and Technology [Austria] (IST Austria), Fakultät für Mathematik [Wien], Universität Wien, This work has been supported by the Vienna Science and Technol-ogy Fund, Grant no. LS13-029. Gaspard Jankowiak and Christian Schmeiser also acknowledge support by the Austrian Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences Mathématiques de Paris, and by Paris-Sciences-et-Lettres., Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Flow (psychology), Quantitative Biology::Cell Behavior, Quantitative Biology::Subcellular Processes, 03 medical and health sciences, Mathematics - Analysis of PDEs, 0302 clinical medicine, Variational methods, Simple (abstract algebra), Cell Behavior (q-bio.CB), FOS: Mathematics, Actin polymerization, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], AMS Subject Classification: 35K40, 35K51, 35Q92, 35A15, 2C17, Cellular cortex, [MATH]Mathematics [math], 030304 developmental biology, Physics, 0303 health sciences, Applied Mathematics, Degenerate energy levels, Internal pressure, 35K40, 35K51, 35Q92, 35A15, 2C17, Cell migration, Mechanics, Adhesion, Cell motility modelling, Weak solutions, Nonlinear system, Polymerization, FOS: Biological sciences, Modeling and Simulation, Quantitative Biology - Cell Behavior, 030217 neurology & neurosurgery, Analysis of PDEs (math.AP)
Abstract: A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modelled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modelled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility., Comment: 22 pages and 9 figures
Published: 2020

11. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography

Author: Joseph Atherton, Melissa Stouffer, Fiona Francis, Carolyn A. Moores, Francis, Fiona, King‘s College London, University of London [London], Institut du Fer à Moulin (IFM - Inserm U1270 - SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), and Institute of Science and Technology [Austria] - IST Austria (IST Austria)
Subjects: Neurons, Electron Microscope Tomography, genetic structures, [SDV]Life Sciences [q-bio], Growth Cones, Doublecortin, Microtubule, Cell Biology, Neuron, Microtubules, Actins, Axons, [SDV] Life Sciences [q-bio], Mice, Neuron Growth cone Cytoskeleton Actin Microtubule Doublecortin, Animals, sense organs, Cytoskeleton, Actin, Growth cone
Abstract: Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration.
Published: 2022

12. Towards best practices in research Role of academic core facilities

Author: Leonardo, Restivo, Björn, Gerlach, Michael, Tsoory, Lior, Bikovski, Sylvia, Badurek, Claudia, Pitzer, Isabelle C, Kos-Braun, Anne-Laure Mj, Mausset-Bonnefont, Jonathan, Ward, Michael, Schunn, Lucas Pjj, Noldus, Anton, Bespalov, Vootele, Voikar, Biosciences, Neuroscience Center, Helsinki Institute of Life Science HiLIFE, Department of Fundamental Neurosciences, [University of Lausanne], Université de Lausanne (UNIL), PAASP GmbH, Weizmann Institute of Science [Rehovot, Israël], Tel Aviv University [Tel Aviv], Vienna Biocenter Core Facilities, Partenaires INRAE, University of Heidelberg, Medical Faculty, Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Goethe-University Frankfurt am Main, Institute of Science and Technology [Austria] (IST Austria), Noldus Information Technology B.V., Helsinki Institute of Life Science (HiLIFE), University of Helsinki, and Bonnefont, Anne-Laure
Subjects: [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, education, 1182 Biochemistry, cell and molecular biology, Methods & Resources, Science Policy & Publishing, Science & Society, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Academic Core Facilities are optimally situated to improve the quality of preclinical research by implementing quality control measures and offering these to their users.
Published: 2021

13. Metamachines of Pluripotent Colloids

Author: Antoine Aubret, Jeremie Palacci, Quentin Martinet, Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), University of California [San Diego] (UC San Diego), University of California, and Institute of Science and Technology [Austria] (IST Austria)
Subjects: Computer science, Science, Distributed computing, FOS: Physical sciences, General Physics and Astronomy, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Affordable and Clean Energy, Colloids, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], Microscale chemistry, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Focus (computing), [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Multidisciplinary, business.industry, Active particles, Control reconfiguration, Self-assembly, General Chemistry, Energy consumption, Modular design, Stem Cell Research, 021001 nanoscience & nanotechnology, Active matter, body regions, Applied physics, Template, [PHYS.COND.CM-GEN]Physics [physics]/Condensed Matter [cond-mat]/Other [cond-mat.other], [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Soft Condensed Matter (cond-mat.soft), Generic health relevance, 0210 nano-technology, business, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials., Mobile micromachines have the potential to probe and manipulate matter at small scales emulating the biological machinery of living organisms. Here, the authors take advantage of the anisotropy of self-propelled colloidal heterodimers to control anisotropic and reprogrammable interactions between particles.
Published: 2021

14. How do Chaperones Bind (Partly) Unfolded Client Proteins?

Author: Iva Sučec, Paul Schanda, Beate Bersch, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institute of Science and Technology [Austria] (IST Austria), ANR-18-CE92-0032,MitoMemProtImp,Etudes structurales et fonctionnelles de l'import et le transfert à travers l'espace inter-membranaire des protéines membranaires mitochondriales(2018), European Project: 311318,EC:FP7:ERC,ERC-2012-StG_20111109,PROTDYN2FUNCTION(2013), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: QH301-705.5, Complex formation, Sequence (biology), Computational biology, Review, Intrinsically disordered proteins, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Cellular protein, holdase, 03 medical and health sciences, chaperone-client complexes, NMR spectroscopy, enthalpy, conformational ensemble, Fuzzy complex, Molecular Biosciences, Interaction type, Biology (General), Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, 030302 biochemistry & molecular biology, Chaperone (protein), biology.protein, fuzzy complex, entropy
Abstract: International audience; Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.
Published: 2021

15. Scaling limit of the homogenization commutator for correlated coefficient fields

Author: Duerinckx, Mitia, Fischer, Julian, Gloria, Antoine, Département de Mathématique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Laboratoire de Mathématiques d'Orsay (LMO), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] (IST Austria), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

16. The Topological Correctness of PL Approximations of Isomanifolds

Author: Mathijs Wintraecken, Jean-Daniel Boissonnat, 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), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 339025,EC:FP7:ERC,ERC-2013-ADG,GUDHI(2014), Institute of Science and Technology [Austria] (IST Austria), and ANR-19-P3IA-0002,3IA Côte d'Azur,Nice - Interdisciplinary Institute for Artificial Intelligence(2019)
Subjects: 0209 industrial biotechnology, Generalization, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Boundary (topology), Isotopy, 02 engineering and technology, 0102 computer and information sciences, Topology, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Fréchet distance, 020901 industrial engineering & automation, [MATH.MATH-GT]Mathematics [math]/Geometric Topology [math.GT], Piecewise-linear approximation, 0202 electrical engineering, electronic engineering, information engineering, Isomanifolds, 0101 mathematics, PL-approximations, Mathematics, Triangulation (topology), and phrases PL-approximations, Zero set, Multivalued function, Applied Mathematics, 010102 general mathematics, Codimension, Isomanifold, Ambient space, Computational Mathematics, Solution manifolds, Computational Theory and Mathematics, 010201 computation theory & mathematics, [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], Topological correctness, 020201 artificial intelligence & image processing, Topological conjugacy, Analysis
Abstract: Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary., LIPIcs, Vol. 164, 36th International Symposium on Computational Geometry (SoCG 2020), pages 20:1-20:18
Published: 2021

17. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination

Author: Beatriz Vicoso, Marwan Elkrewi, Mikhail A. Moldovan, Marion Picard, Institute of Science and Technology [Austria] (IST Austria), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Splicing factor, Genetic linkage, Genetics, Homologous chromosome, Animals, Humans, Molecular Biology, Gene, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, U2AF2, 0303 health sciences, Genome, Sex Chromosomes, biology, AcademicSubjects/SCI01130, Chromosome, Genomics, biology.organism_classification, Evolutionary biology, Primary sex determination, Schistosoma, Female, Schistosoma mansoni
Abstract: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. Keywords: sex chromosomes, evolutionary strata, W-linked gene, sex determining gene, schistosome parasites.
Published: 2021

18. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum

Author: Andi H. Hansen, Natalia Mora, Natalia Danda, Justine Guegan, Luca Tiberi, Simon Hippenmeyer, Mathilde Bertrand, Marica Anderle, Tingting Zhang, Carmen Streicher, Tengyuan Liu, Ximena Contreras, Bassem A. Hassan, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institute of Science and Technology [Austria] (IST Austria), University of Trento [Trento], HAL-SU, Gestionnaire, Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: 0301 basic medicine, DOUBLE MARKERS, EXPRESSION, Cerebellum, GLIOGENESIS, MOSAIC ANALYSIS, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Notch signaling pathway, Biology, Cell fate determination, Inhibitory postsynaptic potential, General Biochemistry, Genetics and Molecular Biology, NEUROGENESIS, 03 medical and health sciences, 0302 clinical medicine, [SDV.BDD] Life Sciences [q-bio]/Development Biology, medicine, Humans, human cerebellar organoids, SPECIFICATION, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Notch signaling, 030304 developmental biology, Progenitor, neural stem cells, Neurons, 0303 health sciences, Science & Technology, Receptors, Notch, Neurogenesis, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Cell Differentiation, neuronal diversity, Cell Biology, STEM, Embryonic stem cell, mouse cerebellum, Neural stem cell, 030104 developmental biology, medicine.anatomical_structure, DIFFERENTIATION, MEDULLOBLASTOMA, Excitatory postsynaptic potential, Neuroscience, Life Sciences & Biomedicine, INTEGRATION, 030217 neurology & neurosurgery
Abstract: SUMMARYBrain neurons arise from relatively few progenitors capable of giving rise to an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis in both the cortex and the cerebellum is that excitatory neurons and inhibitory neurons derive from separate, spatially segregated, progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both excitatory and inhibitory lineages exist and how such a fate decision may be regulated is unknown. Using cerebellar development as a model, we discover that individual embryonic cerebellar progenitors give rise to both inhibitory and excitatory lineages. We find that gradations of Notch activity levels determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate. Daughters with intermediate levels of Notch activity become fate restricted to generate inhibitory neurons, while daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors.Graphical summary
Published: 2021

19. Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome

Author: Céline Cosseau, Jérôme Boissier, Christoph Grunau, Beatriz Vicoso, Ronaldo de Carvalho Augusto, Nathalie Arancibia, David Roquis, Marion Picard, Ingo Bulla, Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), and Institute of Science and Technology [Austria] (IST Austria)
Subjects: chromatin landscape, Gene dosage, Chromosomes, Female heterogamety, Chromatin remodeling, Epigenesis, Genetic, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Dosage Compensation, Genetic, Genetics, Animals, Dosage compensation, Epigenetics, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Z chromosome, female heterogamety, biology, histone modifications, Histone modifications, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Schistosoma mansoni, Chromatin, Histone, dosage compensation, biology.protein, Female, Chromatin landscape, 030217 neurology & neurosurgery, Heterogametic sex, Research Article
Abstract: Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.
Published: 2019

20. Roadmap on multiscale coupling of biochemical and mechanical signals during development

Author: Ed Munro, Kasumi Kishi, Sham Tlili, Jean-Léon Maître, Stefano Di Talia, Yonit Maroudas-Sacks, Aryeh Warmflash, Paolo Caldarelli, Anna Kicheva, Zev J. Gartner, Timothy E. Saunders, Idse Heemskerk, Antoine Fruleux, Alan R. Rodrigues, Benjamin Stormo Stormo, Bassma Khamaisi, Amy Gladfelter Gladfelter, Edouard Hannezo, Jerome Gros, Pierre-François Lenne, David Sprinzak, Arezki Boudaoud, Laura Bocanegra-Moreno, Yuchen Long, Arthur Michaut, Amy E. Shyer, Kinneret Keren, Nicolas Minc, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), University of Chicago, University of Michigan Medical School [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Rice University [Houston], Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), National University of Singapore (NUS), Cellule Pasteur UPMC, Institut Pasteur [Paris] (IP)-Sorbonne Université (SU), Régulation Dynamique de la Morphogénèse - Dynamic Regulation of Morphogenesis, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Technion - Israel Institute of Technology [Haifa], University of California [San Francisco] (UC San Francisco), University of California (UC), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Rockefeller University [New York], Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Duke University Medical Center, Tel Aviv University (TAU), The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints, the members of the Gartner Lab for helpful discussions, the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022)., ANR-19-CE13-0024,Embryonics,Rôle de la mécanique dans l'auto-organisation et la plasticité embryonnaire(2019), ANR-11-LABX-0044,DEEP,Développement, Epigénèse, Epigénétique et potentiel de vie(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-16-CONV-0001,CENTURI,CenTuri : Centre Turing des Systèmes vivants(2016), ANR-17-CE13-0032,MechaResp,Réponses cellulaires et tissulaires aux forces mécaniques au cours de la morphogenèse(2017), ANR-19-CE13-0022,AdGastrulo,Intégration de signaux biochimiques et mécaniques aux contacts adhésifs cellulaires pendant la morphogenèse mammifère : une approche quantitative utilisant un système auto-organisé minimal(2019), European Project: 680037,H2020,ERC-2015-STG,GROWTHPATTERN(2016), European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), European Project: 337635,EC:FP7:ERC,ERC-2013-StG,LIMBCELLDYNAMICS(2014), European Project: 647073,H2020,ERC-2014-CoG,FORCASTER(2015), European Project: 757557,ERC-2017-STG ,MECHABLASTO(2018), European Project: 851288,ERC-2019-STG,DEMOS(2020), European Project: 682161,ERC-2015-CoG ,MorphoNotch(2016), Institute of Science and Technology [Austria] (IST Austria), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Institut Pasteur [Paris]-Sorbonne Université (SU), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of California [San Francisco] (UCSF), University of California, Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Tel Aviv University [Tel Aviv], and Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cognitive science, Force generation, 0303 health sciences, Computer science, [SDV]Life Sciences [q-bio], Biophysics, morphogenesis, Cell Biology, Models, Biological, Article, Biomechanical Phenomena, Dynamic coupling, 03 medical and health sciences, Coupling (physics), 0302 clinical medicine, Development (topology), Multiscale coupling, Structural Biology, embryogenesis, signalling, Molecular Biology, Biological sciences, 030217 neurology & neurosurgery, Signal Transduction, 030304 developmental biology
Abstract: The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.
Published: 2021

21. Decay of streaks and rolls in plane Couette–Poiseuille flow

Author: Tom Mullin, Ramiro Godoy-Diana, José Eduardo Wesfreid, Tao Liu, Benoît Semin, Lukasz Klotz, Physique et mécanique des milieux hétérogenes (UMR 7636) (PMMH), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institute of Science and Technology [Austria] (IST Austria), and University of Oxford [Oxford]
Subjects: Physics, Turbulence, Plane (geometry), Mechanical Engineering, Flow (psychology), Fluid Dynamics (physics.flu-dyn), FOS: Physical sciences, Reynolds number, Physics - Fluid Dynamics, Mechanics, Approx, Condensed Matter Physics, Hagen–Poiseuille equation, 01 natural sciences, 010305 fluids & plasmas, Exponential function, Physics::Fluid Dynamics, symbols.namesake, Mechanics of Materials, 0103 physical sciences, symbols, Vector field, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], 010306 general physics
Abstract: We report the results of an experimental investigation into the decay of turbulence in plane Couette-Poiseuille flow using 'quench' experiments where the flow laminarises after a sudden reduction in Reynolds number $Re$. Specifically, we study the velocity field in the streamwise-spanwise plane. We show that the spanwise velocity containing rolls, decays faster than the streamwise velocity, which displays elongated regions of higher or lower velocity called streaks. At final Reynolds numbers above 425, the decay of streaks displays two stages: first a slow decay when rolls are present and secondly a more rapid decay of streaks alone. The difference in behaviour results from the regeneration of streaks by rolls, called the lift-up effect. We define the turbulent fraction as the portion of the flow containing turbulence and this is estimated by thresholding the spanwise velocity component. It decreases linearly with time in the whole range of final $Re$. The corresponding decay slope increases linearly with final $Re$. The extrapolated value at which this decay slope vanishes is $Re_{a_z}\approx 656\pm10$, close to $Re_g\approx 670$ at which turbulence is self-sustained. The decay of the energy computed from the spanwise velocity component is found to be exponential. The corresponding decay rate increases linearly with $Re$, with an extrapolated vanishing value at $Re_{A_z}\approx 688\pm10$. This value is also close to the value at which the turbulence is self-sustained, showing that valuable information on the transition can be obtained over a wide range of $Re$., 22 pages, 15 figures
Published: 2021

22. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels

Author: John J. Welch, Alexis Simon, Tahani El Ayari, Christelle Fraïsse, Petr Strelkov, Nicolas Bierne, Cathy Liautard-Haag, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), St. Petersburg State University, Universitetskaya Emb. 7/9, St. Petersburg 199034, Russia., Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Kapitana Egorova Str. 16, Murmansk 183038, Russia., University of Cambridge [UK] (CAM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institute of Science and Technology [Austria] (IST Austria), Department of Genetics, University of Cambridge, Downing St. Cambridge, CB23EH, UK., Simon, Alexis [0000-0002-6176-5045], Fraïsse, Christelle [0000-0001-8441-5075], El Ayari, Tahani [0000-0003-2631-2099], Strelkov, Petr [0000-0002-6030-7034], Bierne, Nicolas [0000-0003-1856-3197], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, 0301 basic medicine, Genetic Speciation, Concordance, local introgression, Introgression, Single-nucleotide polymorphism, Biology, Genetic Introgression, 010603 evolutionary biology, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, Gene flow, 03 medical and health sciences, hybrid zones, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, 14. Life underwater, secondary contact, Allele, Ecology, Evolution, Behavior and Systematics, genomic clines, Mytilus, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Haplotype, Local scale, Cline (biology), biology.organism_classification, 030104 developmental biology, Evolutionary biology
Abstract: When the ranges of closely-related lineages are large, and overlapping, we can often study introgression at many “replicated” contacts, with different locations and spatial scales. Here we analysed multiple contact zones of the M. edulis complex of marine mussel species, which represent a mosaic distribution of heterogeneously differentiated, semi-isolated genomes. Our aim was to contrast ongoing introgression at the heart of hybrid zones, with past introgression between similar parental populations, at increasing distance from the contact. Using a panel of ancestry-informative SNPs derived from a previous genomic study, we first confirm, with a broader sampling, that local introgression, affecting one but not all of the populations compared, is both widespread and heterogeneous across the genome. Some outlier loci show patterns of complete introgression in certain populations, and an absence of introgression in others. Genomic cline analyses reveal a globally high concordance among loci at a local scale, albeit with signals of asymmetric introgression at a few loci. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants, or less loaded alleles. Given the mosaic structure of the M. edulis complex, with a succession of genetic barriers to gene flow, variants with enhanced introgression through one barrier can be trapped, maybe transiently, at the next barrier, confining introgression locally. This makes the Mytilus complex an ideal model of the heterogeneous porosity of species barriers.
Published: 2021

23. The many bits of positional information

Author: Thomas Gregor, Gašper Tkačik, Institute of Science and Technology [Austria] (IST Austria), Department of Physics, Princeton University (DPPU), Princeton University, Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844)., Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Information Theory, Subject (philosophy), MESH: Biological Evolution, Review, Space (commercial competition), Biology, Information theory, Models, Biological, 03 medical and health sciences, Lewis Wolpert, 0302 clinical medicine, Developmental biology, Animals, Humans, MESH: Animals, Molecular Biology, Body Patterning, 030304 developmental biology, Cognitive science, 0303 health sciences, MESH: Humans, Interpretation (philosophy), Perspective (graphical), MESH: Models, Biological, MESH: Information Theory, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Drosophila embryo, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Field (geography), Focus (linguistics), Variable (computer science), Pattern formation, Shannon information, 030217 neurology & neurosurgery, MESH: Body Patterning
Abstract: Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?
Published: 2021

24. Modulation of plant root growth by nitrogen source‐defined regulation of polar auxin transport

Author: Andrea Vega, Rashed Abualia, Eleonore Bouguyon, José Antonio O’Brien, Alexander W. Johnson, Shutang Tan, Eva Benková, Livio Antonielli, Yuzhou Zhang, Christina Artner, Marco Marconi, Krzysztof Wabnik, Rodrigo A. Gutiérrez, Alain Gojon, Krisztina Ötvös, Jiri Friml, Candela Cuesta, Juan Carlos Montesinos, Institute of Science and Technology [Austria] (IST Austria), AIT Austrian Inst Technol GmbH, Ctr Hlth & Bioresources, Bioresources Unit, Partenaires INRAE, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pontificia Universidad Católica de Chile (UC), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: root development, Cell division, Nitrogen, [SDV]Life Sciences [q-bio], Arabidopsis, post‐translational modification, Plant Biology, chemistry.chemical_element, Biology, Plant Roots, Article, General Biochemistry, Genetics and Molecular Biology, Dephosphorylation, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, nutrients, Auxin, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ammonium, Phosphorylation, Membrane & Intracellular Transport, Molecular Biology, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Indoleacetic Acids, General Immunology and Microbiology, Arabidopsis Proteins, General Neuroscience, auxin transport, Biological Transport, Articles, 15. Life on land, 6. Clean water, post-translational modification, chemistry, Biophysics, protein trafficking, Elongation, Polar auxin transport, Development & Differentiation, Flux (metabolism), 030217 neurology & neurosurgery
Abstract: Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments., Arabidopsis roots adjust their growth to the type of nitrogen source via phosphorylation of auxin carrier PIN2 and adjustment of auxin distribution between neighboring tissues.
Published: 2021

25. Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict

Author: Beatriz Vicoso, Marion Anne Lise Picard, Stéphanie Bertrand, Hector Escriva, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institute of Science and Technology [Austria] (IST Austria)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, invertebrate species, Modes of reproduction, Range (biology), media_common.quotation_subject, sex determination, Review, QH426-470, Biology, 010603 evolutionary biology, 01 natural sciences, Models, Biological, 03 medical and health sciences, Phylogenetics, Genetics, Animals, Subphylum, Genetics (clinical), genetic conflicts, Invertebrate, media_common, Ecological niche, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Reproduction, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex Determination Processes, Biological Evolution, Invertebrates, Sexual reproduction, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, modes of reproduction, Evolutionary biology, Female, Diversity (politics)
Abstract: International audience; About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.
Published: 2021
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26. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism

Author: Lise C. Noack, Tom Beeckman, Jiří Friml, Laia Armengot, Zachary L. Nimchuk, Ana I. Caño-Delgado, Maria Mar Marquès-Bueno, Barbara K. Möller, Matthieu Pierre Platre, Davy Opdenacker, Vincent Bayle, Mengying Liu, Steffen Vanneste, Lesia Rodriguez, Yvon Jaillais, Joseph Bareille, European Research Council, European Commission, Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), National Science Foundation (US), Research Foundation - Flanders, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Science and Technology [Austria] (IST Austria), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Centre for Research in Agricultural Genomics (CRAG), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: 0301 basic medicine, EFFLUX, [SDV]Life Sciences [q-bio], PROTEIN, Plant Roots, chemistry.chemical_compound, 0302 clinical medicine, Loss of Function Mutation, Arabidopsis, CELL-SURFACE, Brassinosteroid, Auxin, Receptor-like kinase, chemistry.chemical_classification, Anionic lipids, biology, food and beverages, Plants, Genetically Modified, ARABIDOPSIS, Transmembrane protein, gravitropism, Cell biology, receptor-like kinase, Gain of Function Mutation, INTRACELLULAR TRAFFICKING, Plant hormone, Signal transduction, ABP1, General Agricultural and Biological Sciences, Gravitation, Signal Transduction, EXPRESSION, ENDOCYTOSIS, Gravitropism, Protein Serine-Threonine Kinases, anionic lipids, Endocytosis, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, RHO, ROP6, Report, Indoleacetic Acids, Arabidopsis Proteins, fungi, Membrane Proteins, Biology and Life Sciences, RECEPTOR-LIKE KINASES, biology.organism_classification, root, TMK, MAKR, 030104 developmental biology, chemistry, Root, brassinosteroid, auxin, 030217 neurology & neurosurgery
Abstract: Summary Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface., Graphical Abstract, Highlights • MAKR2 is co-expressed with PIN2 and regulates the pace of root gravitropism • MAKR2 controls PIN2 asymmetric accumulation at the root level during gravitropism • MAKR2 binds to and is a negative regulator of the TMK1 receptor kinase • Auxin antagonizes the MAKR2 inhibition of TMK1 by delocalizing MAKR2 in the cytosol, Marquès-Bueno, Armengot et al. show that the unstructured protein MAKR2 controls the dynamics of the root gravitropic response by acting as a negative regulator of the TMK1 receptor kinase. In addition, the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner.
Published: 2021

27. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel

Author: Schulte, Linda, Mao, Jiafei, Reitz, Julian, Sreeramulu, Sridhar, Kudlinzki, Denis, Hodirnau, Victor-Valentin, Meier-Credo, Jakob, Saxena, Krishna, Buhr, Florian, Langer, Julian D., Blackledge, Martin, Frangakis, Achilleas S., Glaubitz, Clemens, Schwalbe, Harald, Institute of Organic Chemistry and Chemical Biology, Goethe-Universität Frankfurt am Main, Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany, Institute for Biophysics, Buchmann Institute for Molecular Life Science, Institute of Science and Technology [Austria] (IST Austria), Max Planck Institute of Biophysics [Frankfurt am Main] (MPIBP), Max-Planck-Gesellschaft, Center for Biomolecular Magnetic Resonance, Goethe-Universität Frankfurt am Main-Institute for Organic Chemistry and Chemical Biology, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Reitz, Julian [0000-0002-0393-0655], Meier-Credo, Jakob [0000-0003-1026-1573], Blackledge, Martin [0000-0003-0935-721X], Frangakis, Achilleas S [0000-0002-8067-6611], Glaubitz, Clemens [0000-0002-3554-6586], Schwalbe, Harald [0000-0001-5693-7909], Apollo - University of Cambridge Repository, and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Models, Molecular, MESH: Oxidation-Reduction, Protein Folding, Magnetic Resonance Spectroscopy, MESH: Mutation, Protein Conformation, Science, MESH: Protein Folding, Article, Mass Spectrometry, MESH: Protein Conformation, ddc:570, MESH: S-Nitrosothiols, MESH: Disulfides, Cysteine, Disulfides, gamma-Crystallins, lcsh:Science, MESH: Glutathione, MESH: Mass Spectrometry, S-Nitrosothiols, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH: gamma-Crystallins, MESH: Magnetic Resonance Spectroscopy, Cryoelectron Microscopy, food and beverages, MESH: Cysteine, Glutathione, Protein Biosynthesis, MESH: Protein Biosynthesis, Mutation, ddc:540, lcsh:Q, Molecular modelling, MESH: Cryoelectron Microscopy, Structural biology, Solution-state NMR, Oxidation-Reduction, Ribosomes, MESH: Ribosomes, MESH: Models, Molecular
Abstract: Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding., As protein synthesis takes place, newly synthesized polypeptide chain passes through the ribosomal exit tunnel, which can accommodate up to 70 residues in the case of a helical peptide. Here the authors show that oxidation of cysteine residues in the nascent chain can occur within the ribosome exit tunnel, where sufficient space exists for the formation of disulfide bonds.
Published: 2020

28. Long-range Temporal Correlations in the Broadband Resting state Activity of the Human Brain revealed by Neuronal Avalanches

Author: Fabrizio Lombardi, Hans J. Herrmann, Oren Shriki, Lucilla de Arcangelis, Institute of Science and Technology [Austria] (IST Austria), Lombardi, F, Shriki, O, Herrmann, H. J., and de Arcangelis, L
Subjects: 0209 industrial biotechnology, Brain activity and meditation, Cognitive Neuroscience, Context (language use), 02 engineering and technology, Electroencephalography, 01 natural sciences, 03 medical and health sciences, [SCCO]Cognitive science, 020901 industrial engineering & automation, 0302 clinical medicine, Artificial Intelligence, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, medicine, Feature (machine learning), 010306 general physics, Scaling, Physics, medicine.diagnostic_test, Resting state fMRI, Quantitative Biology::Neurons and Cognition, Magnetoencephalography, Human brain, Computer Science Applications, medicine.anatomical_structure, 020201 artificial intelligence & image processing, Neuroscience, 030217 neurology & neurosurgery
Abstract: Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.
Published: 2020

29. Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyr-Based Motif

Author: Isabelle Vanhoutte, Eugenia Russinova, Lucas Alves Neubus Claus, Rajesh Kumar, Peng Wang, Wei Siao, Daniël Van Damme, Jiří Friml, Derui Liu, Xiuyang Zhao, Grégory Vert, Alexander W. Johnson, Klaas Yperman, Sara Martins, Kyle W. Bender, Universiteit Gent = Ghent University (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Signalisation Cellulaire et Ubiquitination, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), European Project: 1009584(2010), Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Science and Technology [Austria] (IST Austria), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: POLAR LOCALIZATION, 0106 biological sciences, 0301 basic medicine, ADAPTER COMPLEX, Endocytic cycle, Amino Acid Motifs, MESH: Cell Membrane / metabolism, Arabidopsis, Plant Science, 01 natural sciences, chemistry.chemical_compound, MESH: Amino Acid Motifs, MESH: Endocytosis / physiology, Internalization, media_common, MESH: Arabidopsis / metabolism, TYROSINE PHOSPHORYLATION, biology, Signal transducing adaptor protein, CLATHRIN-MEDIATED ENDOCYTOSIS, ARABIDOPSIS, Plants, Genetically Modified, Endocytosis, Cell biology, MESH: Arabidopsis Proteins / genetics, FACTOR RECEPTOR, MESH: Protein Domains, MESH: Arabidopsis / genetics, EPIDERMAL-GROWTH-FACTOR, CELLULOSE SYNTHASE, MESH: Mutation, SORTING SIGNALS, media_common.quotation_subject, Green Fluorescent Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Clathrin, In Brief, 03 medical and health sciences, MESH: Arabidopsis Proteins / metabolism, Protein Domains, MESH: Arabidopsis Proteins / chemistry, Kinase activity, MESH: Protein Kinases / chemistry, Arabidopsis Proteins, Cell Membrane, fungi, Biology and Life Sciences, Tyrosine phosphorylation, Cell Biology, Receptor-mediated endocytosis, MESH: Protein Kinases / genetics, MESH: Protein Kinases / metabolism, 030104 developmental biology, chemistry, MESH: Plants, Genetically Modified, MESH: Tyrosine / chemistry, Mutation, biology.protein, Tyrosine, MESH: Green Fluorescent Proteins / genetics, Protein Kinases, STRUCTURAL EXPLANATION, 010606 plant biology & botany
Abstract: Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles via the recognition of motifs based on Tyr or di-Leu in their cytoplasmic tails. However, in plants, very little is known about how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis (Arabidopsis thaliana), the brassinosteroid (BR) receptor BR INSENSITIVE1 (BRI1) undergoes endocytosis, which depends on clathrin and AP-2. Here, we demonstrate that BRI1 binds directly to the medium AP-2 subunit (AP2M). The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed Tyr-based endocytic motifs. The Tyr-to-Phe substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2–dependent internalization of PM proteins via the recognition of functional Tyr motifs also operates in plants.
Published: 2020

30. The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes

Author: Himani Sachdeva, Christelle Fraïsse, Institute of Science and Technology [Austria] (IST Austria), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Faculty of Mathematics [Vienna], University of Vienna [Vienna], Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Universität Wien
Subjects: 0106 biological sciences, Gene Flow, Male, Introgression, Hemizygosity, Biology, Genetic Introgression, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, Genetics, Animals, Allele, ComputingMilieux_MISCELLANEOUS, Alleles, 030304 developmental biology, Investigation, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Dosage compensation, Autosome, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Sex Chromosomes, Models, Genetic, modeling, Reproductive isolation, Cline (biology), speciation, Evolutionary biology, Female, Heterogametic sex
Abstract: Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
Published: 2020

31. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis

Author: Alexander W. Johnson, Jiří Friml, Sebastian Y. Bednarek, Grégory Vert, Walter A. Kaufmann, Madhumitha Narasimhan, Nataliia Gnyliukh, Institute of Science and Technology [Austria] (IST Austria), Signalisation Cellulaire et Ubiquitination, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Biochemistry Department [Madison], and University of Wisconsin-Madison
Subjects: 0106 biological sciences, Quantitative imaging, media_common.quotation_subject, education, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, clathrin-mediated endocytosis, Endocytosis, 01 natural sciences, law.invention, 03 medical and health sciences, Confocal microscopy, law, Arabidopsis, Fluorescence microscope, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Internalization, 030304 developmental biology, media_common, 0303 health sciences, biology, Cell Biology, Receptor-mediated endocytosis, biology.organism_classification, metal-replica electron, quantitative imaging, Function (biology), 010606 plant biology & botany
Abstract: International audience; Statement: We present detailed novel quantitative imaging protocols and review 15 pharmacological and genetic manipulation to provide standardized experimental approaches 16 for the investigation of plant clathrin-mediated endocytosis at multiple scales. Abstract 18 Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects 19 of plant growth, development, intra-and inter-cellular signaling, nutrient uptake and 20 pathogen defense. Despite these significant roles, little is known about the precise molecular 21 details of how it functions in planta. In order to facilitate the direct quantitative study of plant 22 CME, here we review current routinely used methods and present refined, standardized 23 quantitative imaging protocols which allow the detailed characterization of CME at multiple 24 scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the 25 imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed 26 characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and 27 analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal 28 interplay of endocytosis components during single CME events; (iii) a semi-automated 29 analysis to allow the quantitative characterization of global internalization of cargos in whole 30 plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools 31 to interrogate the molecular mechanisms and function of CME in intact plant samples. 32 2
Published: 2020

32. Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity

Author: Mirza Ahad Baig, Alessia Milani, Corentin Travers, Danny Hendler, Institute of Science and Technology [Austria] (IST Austria), Ben-Gurion University of the Negev (BGU), Laboratoire Bordelais de Recherche en Informatique (LaBRI), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)
Subjects: amortized step complexity, 020203 distributed computing, Theoretical computer science, Computer science, max array, 0102 computer and information sciences, 02 engineering and technology, Object (computer science), Snapshot algorithm, 01 natural sciences, atomic snapshot, Shared memory, 010201 computation theory & mathematics, 0202 electrical engineering, electronic engineering, information engineering, Key (cryptography), [INFO]Computer Science [cs], CCS Concepts: • Theory of computation → Concurrent algorithms Additional Key Words and Phrases: shared memory, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract: We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.
Published: 2020

33. ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics

Author: Pieter Collins, Fabian Immler, Niklas Kochdumper, Christian Schilling, Luis Benet, Alexandre Chapoutot, Julien Alexandre Dit Sandretto, David P. Sanders, Xin Chen, Daniel Freire, Matthias Althoff, Luca Geretti, Marcelo Forets, Department of Computer Science [Verona] (UNIVR | DI), University of Verona (UNIVR), Unité d'Informatique et d'Ingénierie des Systèmes (U2IS), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Instituto de Matematicas (UNAM), Universidad Nacional Autónoma de México (UNAM), University of Dayton, Department of data science and Knowledge Engineering [Maastricht], Maastricht University [Maastricht], Universidad de la República (UDELAR), Computer Science Department - Carnegie Mellon University, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Mathematics, Massachusetts Institute of Technology, Cambridge MA 02139, United States, and Institute of Science and Technology [Austria] (IST Austria)
Subjects: Nonlinear system, justITSELF, Hybrid systems, Continuous systems, Computer science, Hybrid system, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Nonlinear systems, Applied mathematics, Arch, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS, ddc
Abstract: We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.
Published: 2020

34. The 16th Data Release of the Sloan Digital Sky Surveys : First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

Author: Romina Ahumada, Carlos Allende Prieto, Andrés Almeida, Friedrich Anders, Scott F. Anderson, Brett H. Andrews, Borja Anguiano, Riccardo Arcodia, Eric Armengaud, Marie Aubert, Santiago Avila, Vladimir Avila-Reese, Carles Badenes, Christophe Balland, Kat Barger, Jorge K. Barrera-Ballesteros, Sarbani Basu, Julian Bautista, Rachael L. Beaton, Timothy C. Beers, B. Izamar T. Benavides, Chad F. Bender, Mariangela Bernardi, Matthew Bershady, Florian Beutler, Christian Moni Bidin, Jonathan Bird, Dmitry Bizyaev, Guillermo A. Blanc, Michael R. Blanton, Médéric Boquien, Jura Borissova, Jo Bovy, W. N. Brandt, Jonathan Brinkmann, Joel R. Brownstein, Kevin Bundy, Martin Bureau, Adam Burgasser, Etienne Burtin, Mariana Cano-Díaz, Raffaella Capasso, Michele Cappellari, Ricardo Carrera, Solène Chabanier, William Chaplin, Michael Chapman, Brian Cherinka, Cristina Chiappini, Peter Doohyun Choi, S. Drew Chojnowski, Haeun Chung, Nicolas Clerc, Damien Coffey, Julia M. Comerford, Johan Comparat, Luiz da Costa, Marie-Claude Cousinou, Kevin Covey, Jeffrey D. Crane, Katia Cunha, Gabriele da Silva Ilha, Yu Sophia Dai, Sanna B. Damsted, Jeremy Darling, James W. Davidson, Roger Davies, Kyle Dawson, Nikhil De, Axel de la Macorra, Nathan De Lee, Anna Bárbara de Andrade Queiroz, Alice Deconto Machado, Sylvain de la Torre, Flavia Dell’Agli, Hélion du Mas des Bourboux, Aleksandar M. Diamond-Stanic, Sean Dillon, John Donor, Niv Drory, Chris Duckworth, Tom Dwelly, Garrett Ebelke, Sarah Eftekharzadeh, Arthur Davis Eigenbrot, Yvonne P. Elsworth, Mike Eracleous, Ghazaleh Erfanianfar, Stephanie Escoffier, Xiaohui Fan, Emily Farr, José G. Fernández-Trincado, Diane Feuillet, Alexis Finoguenov, Patricia Fofie, Amelia Fraser-McKelvie, Peter M. Frinchaboy, Sebastien Fromenteau, Hai Fu, Lluís Galbany, Rafael A. Garcia, D. A. García-Hernández, Luis Alberto Garma Oehmichen, Junqiang Ge, Marcio Antonio Geimba Maia, Doug Geisler, Joseph Gelfand, Julian Goddy, Violeta Gonzalez-Perez, Kathleen Grabowski, Paul Green, Catherine J. Grier, Hong Guo, Julien Guy, Paul Harding, Sten Hasselquist, Adam James Hawken, Christian R. Hayes, Fred Hearty, S. Hekker, David W. Hogg, Jon A. Holtzman, Danny Horta, Jiamin Hou, Bau-Ching Hsieh, Daniel Huber, Jason A. S. Hunt, J. Ider Chitham, Julie Imig, Mariana Jaber, Camilo Eduardo Jimenez Angel, Jennifer A. Johnson, Amy M. Jones, Henrik Jönsson, Eric Jullo, Yerim Kim, Karen Kinemuchi, Charles C. Kirkpatrick IV, George W. Kite, Mark Klaene, Jean-Paul Kneib, Juna A. Kollmeier, Hui Kong, Marina Kounkel, Dhanesh Krishnarao, Ivan Lacerna, Ting-Wen Lan, Richard R. Lane, David R. Law, Jean-Marc Le Goff, Henry W. Leung, Hannah Lewis, Cheng Li, Jianhui Lian, Lihwai Lin, Dan Long, Penélope Longa-Peña, Britt Lundgren, Brad W. Lyke, J. Ted Mackereth, Chelsea L. MacLeod, Steven R. Majewski, Arturo Manchado, Claudia Maraston, Paul Martini, Thomas Masseron, Karen L. Masters, Savita Mathur, Richard M. McDermid, Andrea Merloni, Michael Merrifield, Szabolcs Mészáros, Andrea Miglio, Dante Minniti, Rebecca Minsley, Takamitsu Miyaji, Faizan Gohar Mohammad, Benoit Mosser, Eva-Maria Mueller, Demitri Muna, Andrea Muñoz-Gutiérrez, Adam D. Myers, Seshadri Nadathur, Preethi Nair, Kirpal Nandra, Janaina Correa do Nascimento, Rebecca Jean Nevin, Jeffrey A. Newman, David L. Nidever, Christian Nitschelm, Pasquier Noterdaeme, Julia E. O’Connell, Matthew D. Olmstead, Daniel Oravetz, Audrey Oravetz, Yeisson Osorio, Zachary J. Pace, Nelson Padilla, Nathalie Palanque-Delabrouille, Pedro A. Palicio, Hsi-An Pan, Kaike Pan, James Parker, Romain Paviot, Sebastien Peirani, Karla Peña Ramŕez, Samantha Penny, Will J. Percival, Ismael Perez-Fournon, Ignasi Pérez-Ràfols, Patrick Petitjean, Matthew M. Pieri, Marc Pinsonneault, Vijith Jacob Poovelil, Joshua Tyler Povick, Abhishek Prakash, Adrian M. Price-Whelan, M. Jordan Raddick, Anand Raichoor, Amy Ray, Sandro Barboza Rembold, Mehdi Rezaie, Rogemar A. Riffel, Rogério Riffel, Hans-Walter Rix, Annie C. Robin, A. Roman-Lopes, Carlos Román-Zúñiga, Benjamin Rose, Ashley J. Ross, Graziano Rossi, Kate Rowlands, Kate H. R. Rubin, Mara Salvato, Ariel G. Sánchez, Laura Sánchez-Menguiano, José R. Sánchez-Gallego, Conor Sayres, Adam Schaefer, Ricardo P. Schiavon, Jaderson S. Schimoia, Edward Schlafly, David Schlegel, Donald P. Schneider, Mathias Schultheis, Axel Schwope, Hee-Jong Seo, Aldo Serenelli, Arman Shafieloo, Shoaib Jamal Shamsi, Zhengyi Shao, Shiyin Shen, Matthew Shetrone, Raphael Shirley, Víctor Silva Aguirre, Joshua D. Simon, M. F. Skrutskie, Anže Slosar, Rebecca Smethurst, Jennifer Sobeck, Bernardo Cervantes Sodi, Diogo Souto, David V. Stark, Keivan G. Stassun, Matthias Steinmetz, Dennis Stello, Julianna Stermer, Thaisa Storchi-Bergmann, Alina Streblyanska, Guy S. Stringfellow, Amelia Stutz, Genaro Suárez, Jing Sun, Manuchehr Taghizadeh-Popp, Michael S. Talbot, Jamie Tayar, Aniruddha R. Thakar, Riley Theriault, Daniel Thomas, Zak C. Thomas, Jeremy Tinker, Rita Tojeiro, Hector Hernandez Toledo, Christy A. Tremonti, Nicholas W. Troup, Sarah Tuttle, Eduardo Unda-Sanzana, Marica Valentini, Jaime Vargas-González, Mariana Vargas-Magaña, Jose Antonio Vázquez-Mata, M. Vivek, David Wake, Yuting Wang, Benjamin Alan Weaver, Anne-Marie Weijmans, Vivienne Wild, John C. Wilson, Robert F. Wilson, Nathan Wolthuis, W. M. Wood-Vasey, Renbin Yan, Meng Yang, Christophe Yèche, Olga Zamora, Pauline Zarrouk, Gail Zasowski, Kai Zhang, Cheng Zhao, Gongbo Zhao, Zheng Zheng, Guangtun Zhu, Hu Zou, Department of Physics, Joseph Louis LAGRANGE (LAGRANGE), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Instituto de Astrofisica de Canarias (IAC), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México (UNAM), Department of Astrophysical Sciences [Princeton], Princeton University, Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Department of Astronomy, Yale University [New Haven], University of Notre Dame [Indiana] (UND), Department of Physics and Astronomy [Philadelphia], University of Pennsylvania [Philadelphia], University of Wisconsin-Madison, Texas Tech University Health Sciences Center, Texas Tech University [Lubbock] (TTU), Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), California Institute of Technology (CALTECH), Sub-department of Astrophysics [Oxford], Department of Physics [Oxford], University of Oxford [Oxford]-University of Oxford [Oxford], Center for Astrophysics and Space Sciences [La Jolla] (CASS), University of California [San Diego] (UC San Diego), University of California-University of California, Department of Psychology, St John's University, Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Departamento de FisicaTeorica e IFT-UAM/CSIC, Universidad Autonoma de Madrid (UAM), Lowell Observatory [Flagstaff], Observatorio Nacional [Rio de Janeiro], Vernalis (R&D) Ltd, Special Care Dentistry, UCLH Eastman Dental Hospital, University of Utah, Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - 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CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), New York University [New York] (NYU), NYU System (NYU), Research Institute of Forest Resource Information Techniques, Chinese Academy of Forestry, New Mexico State University, Pennsylvania State University (Penn State), Penn State System, Princess Margaret Hospital, University of Toronto, Cognition, Langues, Langage, Ergonomie (CLLE-ERSS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Toulouse - Jean Jaurès (UT2J)-Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS), J. A. Baker Institute, Cornell University [New York], Institute of Infection, Immunity & Inflammation, University of Glasgow, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Carnegie Observatories, Carnegie Institution for Science [Washington], Institute of Science and Technology [Austria] (IST Austria), Universidad de Atacama, Department of Chemical and Biomolecular Engineering, Universidad de Antofagasta, Harvard-Smithsonian Center for Astrophysics (CfA), Smithsonian Institution-Harvard University [Cambridge], Institute of cosmology and gravitation, University of Portsmouth, Institut d'Astronomie et d'Astrophysique [Bruxelles] (IAA), Université libre de Bruxelles (ULB), Département d'Astrophysique, de physique des Particules, de physique Nucléaire et de l'Instrumentation Associée (DAPNIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Max-Planck-Institut für Astrophysik (MPA), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Département des Sciences et Gestion de l'Environnement/Océanologie [Liège], Université de Liège, Universidad Andrés Bello [Santiago] (UNAB), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Montana State University (MSU), Institut d'Astrophysique de Paris (IAP), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Astronomy (Ohio State University), Ohio State University [Columbus] (OSU), Institut Lagrange de Paris, Sorbonne Université (SU), The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], Liverpool John Moores University (LJMU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Space Sciences [Barcelona] (ICE-CSIC), Spanish National Research Council [Madrid] (CSIC), Chinese Academy of Sciences [Beijing] (CAS), McDonald Observatory, University of Texas at Austin [Austin], Astronomy Centre, University of Sussex, Department of Physics and Astronomy [Aarhus], Aarhus University [Aarhus], University of Washington [Seattle], Vanderbilt University [Nashville], Stellar Astrophysics Centre [Aarhus] (SAC), University of Colorado [Boulder], Laboratoire de Biochimie Médicale (LBM), CHU Rouen, Normandie Université (NU)-Normandie Université (NU), University of St Andrews [Scotland], Instituto de Astronomıa, universidad catolica del Norte, Institut d'Astrophysique et de Géophysique [Liège], Laboratoire de Physique des Solides (LPS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Department of Computer Science and Engineering [Minneapolis], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Dunlap Institute for Astronomy and Astrophysics [Toronto], World Bank, State Key Laboratory in Computer Science [Beijing] (SKLCS), Institute of Software Chinese Academy of Sciences [Beijing], Nanjing University of Information Science and Technology (NUIST), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Johns Hopkins University (JHU), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of Oxford-University of Oxford, University of California (UC)-University of California (UC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universidad Autónoma de Madrid (UAM), University of Virginia, Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), University of California [Irvine] (UC Irvine), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS), Carnegie Institution for Science, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Harvard University-Smithsonian Institution, Laboratoire d'études spatiales et d'instrumentation en astrophysique = Laboratory of Space Studies and Instrumentation in Astrophysics (LESIA), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Oxford, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-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), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Centre National d'Études Spatiales [Toulouse] (CNES), Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Ahumada R., Prieto C.A., Almeida A., Anders F., Anderson S.F., Andrews B.H., Anguiano B., Arcodia R., Armengaud E., Aubert M., Avila S., Avila-Reese V., Badenes C., Balland C., Barger K., Barrera-Ballesteros J.K., Basu S., Bautista J., Beaton R.L., Beers T.C., Benavides B.I.T., Bender C.F., Bernardi M., Bershady M., Beutler F., Bidin C.M., Bird J., Bizyaev D., Blanc G.A., Blanton M.R., Boquien M., Borissova J., Bovy J., Brandt W.N., Brinkmann J., Brownstein J.R., Bundy K., Bureau M., Burgasser A., Burtin E., Cano-Diaz M., Capasso R., Cappellari M., Carrera R., Chabanier S., Chaplin W., Chapman M., Cherinka B., Chiappini C., Doohyun Choi P., Chojnowski S.D., Chung H., Clerc N., Coffey D., Comerford J.M., Comparat J., Da Costa L., Cousinou M.-C., Covey K., Crane J.D., Cunha K., Ilha G.D.S., Dai Y.S., Damsted S.B., Darling J., Davidson J.W., Davies R., Dawson K., De N., De La Macorra A., De Lee N., Queiroz A.B.D.A., Deconto Machado A., De La Torre S., Dell'Agli F., Du Mas Des Bourboux H., Diamond-Stanic A.M., Dillon S., Donor J., Drory N., Duckworth C., Dwelly T., Ebelke G., Eftekharzadeh S., Davis Eigenbrot A., Elsworth Y.P., Eracleous M., Erfanianfar G., Escoffier S., Fan X., Farr E., Fernandez-Trincado J.G., Feuillet D., Finoguenov A., Fofie P., Fraser-Mckelvie A., Frinchaboy P.M., Fromenteau S., Fu H., Galbany L., Garcia R.A., Garcia-Hernandez D.A., Oehmichen L.A.G., Ge J., Maia M.A.G., Geisler D., Gelfand J., Goddy J., Gonzalez-Perez V., Grabowski K., Green P., Grier C.J., Guo H., Guy J., Harding P., Hasselquist S., Hawken A.J., Hayes C.R., Hearty F., Hekker S., Hogg D.W., Holtzman J.A., Horta D., Hou J., Hsieh B.-C., Huber D., Hunt J.A.S., Chitham J.I., Imig J., Jaber M., Angel C.E.J., Johnson J.A., Jones A.M., Jonsson H., Jullo E., Kim Y., Kinemuchi K., Kirkpatrick Iv C.C., Kite G.W., Klaene M., Kneib J.-P., Kollmeier J.A., Kong H., Kounkel M., Krishnarao D., Lacerna I., Lan T.-W., Lane R.R., Law D.R., Le Goff J.-M., Leung H.W., Lewis H., Li C., Lian J., Lin L., Long D., Longa-Peña P., Lundgren B., Lyke B.W., Ted Mackereth J., Macleod C.L., Majewski S.R., Manchado A., Maraston C., Martini P., Masseron T., Masters K.L., Mathur S., McDermid R.M., Merloni A., Merrifield M., Meszaros S., Miglio A., Minniti D., Minsley R., Miyaji T., Mohammad F.G., Mosser B., Mueller E.-M., Muna D., Muñoz-Gutierrez A., Myers A.D., Nadathur S., Nair P., Nandra K., Do Nascimento J.C., Nevin R.J., Newman J.A., Nidever D.L., Nitschelm C., Noterdaeme P., O'Connell J.E., Olmstead M.D., Oravetz D., Oravetz A., Osorio Y., Pace Z.J., Padilla N., Palanque-Delabrouille N., Palicio P.A., Pan H.-A., Pan K., Parker J., Paviot R., Peirani S., Ramrez K.P., Penny S., Percival W.J., Perez-Fournon I., Perez-Rafols I., Petitjean P., Pieri M.M., Pinsonneault M., Poovelil V.J., Povick J.T., Prakash A., Price-Whelan A.M., Raddick M.J., Raichoor A., Ray A., Rembold S.B., Rezaie M., Riffel R.A., Riffel R., Rix H.-W., Robin A.C., Roman-Lopes A., Roman-Zuñiga C., Rose B., Ross A.J., Rossi G., Rowlands K., Rubin K.H.R., Salvato M., Sanchez A.G., Sanchez-Menguiano L., Sanchez-Gallego J.R., Sayres C., Schaefer A., Schiavon R.P., Schimoia J.S., Schlafly E., Schlegel D., Schneider D.P., Schultheis M., Schwope A., Seo H.-J., Serenelli A., Shafieloo A., Shamsi S.J., Shao Z., Shen S., Shetrone M., Shirley R., Aguirre V.S., Simon J.D., Skrutskie M.F., Slosar A., Smethurst R., Sobeck J., Sodi B.C., Souto D., Stark D.V., Stassun K.G., Steinmetz M., Stello D., Stermer J., Storchi-Bergmann T., Streblyanska A., Stringfellow G.S., Stutz A., Suarez G., Sun J., Taghizadeh-Popp M., Talbot M.S., Tayar J., Thakar A.R., Theriault R., Thomas D., Thomas Z.C., Tinker J., Tojeiro R., Toledo H.H., Tremonti C.A., Troup N.W., Tuttle S., Unda-Sanzana E., Valentini M., Vargas-Gonzalez J., Vargas-Magaña M., Vazquez-Mata J.A., Vivek M., Wake D., Wang Y., Weaver B.A., Weijmans A.-M., Wild V., Wilson J.C., Wilson R.F., Wolthuis N., Wood-Vasey W.M., Yan R., Yang M., Yeche C., Zamora O., Zarrouk P., Zasowski G., Zhang K., Zhao C., Zhao G., Zheng Z., Zhu G., Zou H., Alfred P. Sloan Foundation, and Department of Energy (US)
Subjects: Optical telescopes, SAMPLE, Astrophysics, 01 natural sciences, Astronomi, astrofysik och kosmologi, Infrared astronomy, Observatory, Astronomy, Astrophysics and Cosmology, Astrophysics::Solar and Stellar Astrophysics, REDSHIFT 0.8, redshift surveys, stellar spectral lines, 010303 astronomy & astrophysics, ComputingMilieux_MISCELLANEOUS, media_common, Astronomy databases, Redshift surveys, Physics, Astrophysics::Instrumentation and Methods for Astrophysics, stellar properties, CATALOG, astro-ph.CO, astronomy databases, Data release, [PHYS.ASTR.IM]Physics [physics]/Astrophysics [astro-ph]/Instrumentation and Methods for Astrophysic [astro-ph.IM], infrared astonomy, TELESCOPE, astro-ph.GA, media_common.quotation_subject, Astrophysics::Cosmology and Extragalactic Astrophysics, MASS, [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Galactic abundances, Stellar properties, 0103 physical sciences, Astrophysics::Galaxy Astrophysics, DISTANCES, Stellar spectral lines, 010308 nuclear & particles physics, Astronomy and Astrophysics, optical telescopes, 115 Astronomy, Space science, Galaxy, GALAXY, [PHYS.ASTR.GA]Physics [physics]/Astrophysics [astro-ph]/Galactic Astrophysics [astro-ph.GA], STELLAR, 13. Climate action, Space and Planetary Science, Sky, [SDU]Sciences of the Universe [physics], galactic abundances, MILKY, astro-ph.IM, SDSS-IV MANGA
Abstract: This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)., Funding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High-Performance Computing at the University of Utah. The SDSS website is www.sdss.org.
Published: 2020

35. Extending Drawings of Graphs to Arrangements of Pseudolines

Author: Arroyo, Alan, Bensmail, Julien, Richter, R. Bruce, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Combinatorics, Optimization and Algorithms for Telecommunications (COATI), 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)-COMmunications, Réseaux, systèmes Embarqués et Distribués (Laboratoire I3S - COMRED), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Waterloo [Waterloo], Institute of Science and Technology [Austria] (IST Austria), COMmunications, Réseaux, systèmes Embarqués et Distribués (Laboratoire I3S - COMRED), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: graphs, 050101 languages & linguistics, crossing numbers, 05 social sciences, 02 engineering and technology, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], arrangements of pseudolines, FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, Mathematics - Combinatorics, 020201 artificial intelligence & image processing, 0501 psychology and cognitive sciences, graph drawings, Combinatorics (math.CO), stretchability, 05C10, 05C85, 52C40, 52C30, geometric graph drawings
Abstract: In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of $K_n$ was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible., Journal of Computational Geometry, Vol. 12 No. 2 (2021)
Published: 2020

36. Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport

Author: Alexander W. Johnson, Marco Marconi, Alain Gojon, Eléonore Bouguyon, Andrea Vega, Jiri Friml, Krisztina Ötvös, Juan Carlos Montesinos, Rodrigo A. Gutiérrez, Candela Cuesta, Krzysztof Wabnik, Christina Artner, Shutang Tan, Eva Benková, Yuzhou Zhang, Rashed Abualia, Livio Antonielli, Jose O' Brien, Institute of Science and Technology [Austria] (IST Austria), AIT Austrian Inst Technol GmbH, Ctr Hlth & Bioresources, Bioresources Unit, Partenaires INRAE, Centro de Biotecnologia y Genomica de Plantas (CBGP), Pontificia Universidad Católica de Chile (UC), Pontifical Catholic University of Chile, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Biotecnologıa y genomica de plantas UPM-INIA and ETSI agronomos, and Universidad Politécnica de Madrid (UPM)
Subjects: 2. Zero hunger, 0106 biological sciences, chemistry.chemical_classification, 0303 health sciences, Fine-tuning, Cell division, Chemistry, [SDV]Life Sciences [q-bio], 15. Life on land, 01 natural sciences, 03 medical and health sciences, Nutrient, Auxin, Modulation, Biophysics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Polar auxin transport, Adaptation, Flux (metabolism), 030304 developmental biology, 010606 plant biology & botany
Abstract: Nitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, live in vivo high- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth, i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.
Published: 2020

37. DILS: Demographic Inferences with Linked Selection by using ABC

Author: Alexis Simon, Nicolas Bierne, Nicolas Galtier, Camille Roux, Christelle Fraïsse, Stéphane Delmotte, Xavier Vekemans, Jonathan Romiguier, Etienne Loire, Iva Popovic, Laurent Duret, Clément Mazoyer, Bruno Spataro, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), School of Biological Sciences [Brisbane], University of Queensland [Brisbane], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), We would like to acknowledge the support of the I‐Site ULNE Foundation for this work., Institute of Science and Technology [Austria] (IST Austria), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: Gene Flow, 0301 basic medicine, 0106 biological sciences, Genetic Speciation, Computer science, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Population, Locus (genetics), Genomics, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Gene flow, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetic algorithm, Genetics, Selection, Genetic, education, Divergence (statistics), Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), 030304 developmental biology, media_common, Population Density, 0303 health sciences, education.field_of_study, [SHS.STAT]Humanities and Social Sciences/Methods and statistics, Models, Genetic, Population size, Bayes Theorem, Speciation, Genetics, Population, 030104 developmental biology, Approximate Bayesian computation, Biotechnology
Abstract: We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective sizeNeand migration rateN.mare heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also availableviaa web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs ofMytilusmussel populations/species.
Published: 2020

38. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion

Author: Georgi Dimchev, Michael Sixt, Matthias Schaks, Joern Linkner, Stefan Bruehmann, Laurent Blanchoin, Maria Nemethova, Klemens Rottner, Laetitia Kurzawa, Jan Mueller, Thomas Pokrant, Julia Damiano-Guercio, Jan Faix, Institute for Biophysical Chemistry, Hannover Medical School [Hannover] (MHH), CytoMorphoLab, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Science and Technology [Austria] (IST Austria), Technical University Braunschweig, Helmholtz Centre for Infection Research, Deutsche Forschungsgemeinschaft (DFG), grants FA330/11-1 and RO2414/5-1, PROCOMPAS graduate program GRK2223/1, European Project: 741773,AAA, European Project: CoG 724373,GRADIENTSENSING, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), and HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Subjects: Integrins, cell migration, Melanoma, Experimental, Polymerization, Gene Knockout Techniques, Mice, 0302 clinical medicine, Cell Movement, cell biology, microspikes, Pseudopodia, Biology (General), Cytoskeleton, 0303 health sciences, biology, Chemistry, General Neuroscience, cytoskeleton, Cell migration, General Medicine, Recombinant Proteins, Cell biology, DNA-Binding Proteins, Actin Cytoskeleton, Medicine, Lamellipodium, Filopodia, Research Article, QH301-705.5, Science, Actin Capping Proteins, Integrin, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, macromolecular substances, Actin-Related Protein 2-3 Complex, General Biochemistry, Genetics and Molecular Biology, Focal adhesion, 03 medical and health sciences, filopodia, Cell Line, Tumor, Animals, Cell adhesion, mouse, Actin, 030304 developmental biology, Focal Adhesions, General Immunology and Microbiology, Ena/VASP proteins, cell adhesion, Fibroblasts, Actins, lamellipodia, NIH 3T3 Cells, biology.protein, CRISPR-Cas Systems, Actin filaments, 030217 neurology & neurosurgery
Abstract: International audience; Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.
Published: 2020

39. Broad spectral tuning of ultra-low-loss polaritons in a van der Waals crystal by intercalation

Author: Qiaoliang Bao, Ion Errea, Jiahua Duan, Kyle Crowley, Javier Martín-Sánchez, Weiliang Ma, Halyna Volkova, Marta Autore, Ivan Prieto, Alexey Y. Nikitin, Javier Taboada-Gutiérrez, Andrei Bylinkin, Pablo Alonso-González, Rainer Hillenbrand, Kenta Kimura, Gonzalo Álvarez-Pérez, Shaojuan Li, Marie-Hélène Berger, Xuan P. A. Gao, Tsuyoshi Kimura, Principado de Asturias, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Air Force Office of Scientific Research (US), Ministerio de Economía y Competitividad (España), Eusko Jaurlaritza, Australian Research Council, Ministerio de Economía, Industria y Competitividad (España), European Research Council, Institute of Science and Technology [Austria] (IST Austria), Centre des Matériaux (MAT), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Graduate School of Engineering, Osaka University, Osaka University [Osaka], Donostia International Physics Center - DIPC (SPAIN), Donostia International Physics Center (DIPC), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)-University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), CIC nanoGUNE Consolider, and Donostia International Physcis Center
Subjects: Materials science, Phonon, Intercalation (chemistry), Nanophotonics, Physics::Optics, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, 7. Clean energy, Molecular physics, Crystal, symbols.namesake, Condensed Matter::Materials Science, Condensed Matter::Superconductivity, Polariton, General Materials Science, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], business.industry, Mechanical Engineering, General Chemistry, Spectral bands, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 0104 chemical sciences, Semiconductor, Mechanics of Materials, symbols, van der Waals force, 0210 nano-technology, business
Abstract: Phonon polaritons—light coupled to lattice vibrations—in polar van der Waals crystals are promising candidates for controlling the flow of energy on the nanoscale due to their strong field confinement, anisotropic propagation and ultra-long lifetime in the picosecond range1,2,3,4,5. However, the lack of tunability of their narrow and material-specific spectral range—the Reststrahlen band—severely limits their technological implementation. Here, we demonstrate that intercalation of Na atoms in the van der Waals semiconductor α-V2O5 enables a broad spectral shift of Reststrahlen bands, and that the phonon polaritons excited show ultra-low losses (lifetime of 4 ± 1 ps), similar to phonon polaritons in a non-intercalated crystal (lifetime of 6 ± 1 ps). We expect our intercalation method to be applicable to other van der Waals crystals, opening the door for the use of phonon polaritons in broad spectral bands in the mid-infrared domain., J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the Government of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA-20-PF-BP19-053, respectively). J.M.-S. acknowledges finantial support from the Clarín Programme from the Government of the Principality of Asturias and a Marie Curie-COFUND grant (PA-18-ACB17-29) and the Ramón y Cajal Program from the Government of Spain (RYC2018-026196-I). K.C., X.P.A.G., H.V. and M.H.B. acknowledge the Air Force Office of Scientific Research (AFOSR) grant no. FA 9550-18-1-0030 for funding support. I.E. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness (grant no. FIS2016-76617-P). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT2017-88358-C3-3-R) and the Basque Government (grant no. IT1164-19). Q.B. acknowledges the support from Australian Research Council (grant nos. FT150100450, IH150100006 and CE170100039). R.H. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (national project RTI2018-094830-B-100 and the Project MDM-2016-0618 of the María de Maeztu Units of Excellence Program) and the Basque Goverment (grant no. IT1164-19). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA.
Published: 2020

40. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate

Author: Eva Benková, Alain Gojon, Carine Alcon, Amel Maghiaoui, Candela Cuesta, Lien Bach, Gabriel Krouk, Francine Perrine-Walker, Eleonore Bouguyon, Philippe Nacry, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de La Réunion - UFR Santé (UR UFRS), Université de La Réunion (UR), Institute of Science and Technology [Austria] (IST Austria), School of Life and Environmental Sciences A08 [Australia) (University of Sydney), The University of Sydney, Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-16-CE20-0022,NitraSense,Intégration des réponses physiologiques et développementales de la plante au nitrate: rôle de la signalisation dépendante de NRT1.1 (NPF6.3/CHL1) dans l'efficience d'utilisation de l'azote(2016)
Subjects: 0106 biological sciences, Auxin influx, Cell signaling, Physiology, [SDV]Life Sciences [q-bio], lateral root primordia, Plant Science, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, transceptor, Auxin, nitrate, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Primordium, development, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Lateral root, fungi, food and beverages, biology.organism_classification, Cell biology, chemistry, Stele, NRT1.1, 010606 plant biology & botany, auxin signaling
Abstract: International audience; In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.
Published: 2020

41. LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia

Author: Thomas P. Jensen, James P. Reynolds, Olga Kopach, Sylvain Rama, Christian Henneberger, Erlend A. Nagelhus, Michel K. Herde, Daniel Minge, Aude Panatier, Inmaculada Sanchez-Romero, Michael G. Stewart, Colin J. Jackson, Dmitri A. Rusakov, U. Valentin Nägerl, Stéphane H. R. Oliet, Nikolay I. Medvedev, Lucie Bard, Kaiyu Zheng, Ole Petter Ottersen, Stefanie Anders, Janosch P. Heller, Harald Janovjak, Igor Kraev, INSERM, Neurocentre Magendie, U1215, Physiopathologie de la Plasticité Neuronale, F-33000 Bordeaux, France, Interdisciplinary Institute for Neuroscience [Bordeaux] (IINS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB), German Research Center for Neurodegenerative Diseases - Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University College of London [London] (UCL), Neurocentre Magendie : Physiopathologie de la Plasticité Neuronale (U1215 Inserm - UB), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM), The Open University [Milton Keynes] (OU), University of Bonn, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Australian National University (ANU), Monash University [Melbourne], University of Oslo (UiO), Oliet, Stephane, Physiopathologie de la Plasticité Neuronale (Neurocentre Magendie - U1215 Inserm), and Institute of Science and Technology [Austria] (IST Austria)
Subjects: 0301 basic medicine, Male, hippocampus, [SDV]Life Sciences [q-bio], [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, astrocyte plasticity, Synapse, Rats, Sprague-Dawley, Mice, 0302 clinical medicine, super-resolution microscopy, LTP induction, whisker stimulation, ComputingMilieux_MISCELLANEOUS, glutamate sensor imaging, Mice, Knockout, metabolism [Astrocytes], Chemistry, General Neuroscience, Glutamate receptor, Long-term potentiation, Cofilin, 3. Good health, [SDV] Life Sciences [q-bio], Excitatory postsynaptic potential, barrel cortex, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Female, methods [Imaging, Three-Dimensional], Glutamic Acid, Mice, Transgenic, Article, 03 medical and health sciences, Excitatory synapse, Imaging, Three-Dimensional, Organ Culture Techniques, Animals, ddc:610, Rats, Wistar, long-term potentiation, metabolism [Glutamic Acid], metabolism [Synapses], Barrel cortex, glutamate spillover, Rats, Mice, Inbred C57BL, 030104 developmental biology, Astrocytes, ultrastructure [Synapses], Synapses, ultrastructure [Astrocytes], physiology [Long-Term Potentiation], Neuroscience, 030217 neurology & neurosurgery, perisynaptic astroglial processes
Abstract: Summary Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections., Highlights • Induction of synaptic LTP prompts withdrawal of perisynaptic astroglia • The underlying mechanisms involve NKCC1 transporter and cofilin • Reduced synaptic astroglial coverage boosts extrasynaptic glutamate escape • LTP induction thus enhances NMDAR-dependent inter-synaptic cross-talk, Central synapses are often surrounded by thin astroglial processes that confine chemical neurotransmission to the synaptic cleft. Henneberger et al. find that memory trace formation at synaptic connections prompts withdrawal of these processes, thus boosting extrasynaptic neurotransmitter actions. Such actions can alter signal integration rules among neighboring synapses.
Published: 2020
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42. Inductive Reachability Witnesses

Author: Asadi, Ali, Chatterjee, Krishnendu, Fu, Hongfei, Goharshady, Amir Kafshdar, Mahdavi, Mohammad, Sharif University of Technology [Tehran] (SUT), Institute of Science and Technology [Austria] (IST Austria), and Shanghai Jiao Tong University [Shanghai]
Subjects: Software Engineering (cs.SE), FOS: Computer and information sciences, Computer Science - Logic in Computer Science, Computer Science - Software Engineering, Computer Science - Programming Languages, [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL], [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Programming Languages (cs.PL), Logic in Computer Science (cs.LO)
Abstract: In this work, we consider the fundamental problem of reachability analysis over imperative programs with real variables. The reachability property requires that a program can reach certain target states during its execution. Previous works that tackle reachability analysis are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic/reverse Hoare logic). In contrast, we propose a novel approach for reachability analysis that can handle general programs, is (semi-)complete, and can be entirely automated for a wide family of programs. Our approach extends techniques from both invariant generation and ranking-function synthesis to reachability analysis through the notion of (Universal) Inductive Reachability Witnesses (IRWs/UIRWs). While traditional invariant generation uses over-approximations of reachable states, we consider the natural dual problem of under-approximating the set of program states that can reach a target state. We then apply an argument similar to ranking functions to ensure that all states in our under-approximation can indeed reach the target set in finitely many steps. On the theoretical level, we first show that our IRW/UIRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs/UIRWs. In the linear case, our techniques are based on Farkas' lemma. For the polynomial case, our approach utilizes three classical theorems in polyhedral geometry and real algebraic geometry, namely Handelman's Theorem, Hilbert's Nullstellensatz and Putinar's Positivstellensatz. To the best of our knowledge, such a combination of these theorems to obtain algorithms for reachability analysis in programs is a novel contribution. On the practical side, our experimental results show that our automated approaches can efficiently prove complex reachability objectives over various benchmarks.
Published: 2020
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43. enGeneralizing CGAL Periodic Delaunay Triangulations

Author: Osang, Georg, Rouxel-Labbé, Mael, Teillaud, Monique, Fabrizio Grandoni, Grzegorz Herman, Peter Sanders, Institute of Science and Technology [Austria] (IST Austria), GeometryFactory, Geometric Algorithms and Models Beyond the Linear and Euclidean realm (GAMBLE ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Georg Osang: This author is partially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183. Monique Teillaud: This author is partially supported by the grants ANR-17-CE40-0033 of the French National Research Agency ANR (project SoS) and INTER/ANR/16/11554412/SoS of the Luxembourg National Research fund FNR (https://members.loria.fr/Monique.Teillaud/collab/SoS/)., ANR-17-CE40-0033,SoS,Structures sur des surfaces(2017), European Project: 788183,Alpha, and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: algorithm, software, TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY, Theory of computation → Computational geometry, Delaunay triangulation, experiments, Computer Science::Computational Geometry, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], ComputingMethodologies_COMPUTERGRAPHICS, lattice
Abstract: Best Paper Award (Track B: Engineering and Applications); International audience; Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity.
Published: 2020

44. Action at a distance in transcriptional regulation

Author: Bialek, William, Gregor, Thomas, Tkačik, Gašper, City University of New York [New York] (CUNY), Department of Physics, Princeton University (DPPU), Princeton University, Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute of Science and Technology [Austria] (IST Austria), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Quantitative Biology - Subcellular Processes, Statistical Mechanics (cond-mat.stat-mech), Biological Physics (physics.bio-ph), FOS: Biological sciences, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, Physics - Biological Physics, Subcellular Processes (q-bio.SC), [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Condensed Matter - Statistical Mechanics
Abstract: There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests.
Published: 2019

45. Transcultural adaptation and French validation of the Pain Sensitivity Questionnaire

Author: Sylvie Eschalier, Ruth Ruscheweyh, Vedat Eljezi, Claude Dubray, Christian Dualé, Candy Guiguet-Auclair, Ulrich Bauer, Brigitte Storme, CHU Gabriel Montpied (CHU), CHU Clermont-Ferrand, CIC Clermont Ferrand, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Pharmacologie Clinique-CHU Gabriel-Montpied, Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pôle Cardiologie médicale et chirurgicale, Centre Hospitalier Universitaire Gabriel Montpied, Centre d’Investigation Clinique (CIC), PEPRADE, Centre Hospitalier Universitaire de Clermont-Ferrand, and Institute of Science and Technology [Austria] (IST Austria)
Subjects: medicine.medical_specialty, Psychometrics, Intraclass correlation, [SDV]Life Sciences [q-bio], Pain medicine, Concurrent validity, 03 medical and health sciences, 0302 clinical medicine, Cronbach's alpha, [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication, 030202 anesthesiology, medicine, ComputingMilieux_MISCELLANEOUS, business.industry, Cold pressor test, General Medicine, Anesthesiology and Pain Medicine, Convergent validity, Anesthesia, Physical therapy, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Anxiety, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], medicine.symptom, business, 030217 neurology & neurosurgery
Abstract: To validate a French translation of the Pain Sensitivity Questionnaire (PSQ), which is a valuable tool to predict an individual’s natural disposition to feel pain that could be used after surgery. We studied content validity, internal consistency, convergent validity (anxiety, depression and catastrophism) and test-retest reliability of the French version of the PSQ (PSQ-F) in 146 patients either before scheduled surgery or during pregnancy; then, convergent and concurrent validity in 85 healthy volunteers submitted to nociceptive tests. Internal consistency of the PSQ-F was found to be excellent, with Cronbach’s α at 0.866, 0.886, and 0.927, respectively for its “minor”, “moderate” and “total” scores. Test-retest reliability was significant, with intraclass correlation coefficients at 0.629, 0.629, and 0.635, respectively for the above- mentioned scores. These three scores correlated with anxiety, depression and catastrophizing scores in patients, but not in healthy volunteers, possibly because of low and few variant psychometric scores in this group. They were inversely correlated to the temperature needed to evoke heat pain rated 6 out of 10, but not to the mechanical pain threshold (electronic von Frey), nor to the heat pain threshold. Finally, they directly correlated to the pain induced by the cold pressor test (minor and total scores only). This validated version can now be used by French-speaking researchers and physicians. www.ClinicalTrials.gov (NCT03113903); 14 April, 2017.
Published: 2019

46. Effect of the Anomalous Diffusion of Fluctuating Cooper Pairs in the Density of States of Superconducting NbN Thin Films

Author: Brigitte Leridon, Pietro Brighi, Marco Grilli, Sergio Caprara, Institute of Science and Technology [Austria] (IST Austria), Istituto Sistemi Complessi [ROME] (ISC), Consiglio Nazionale delle Ricerche [Roma] (CNR), Dipartimento di Fisica [Roma La Sapienza], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Laboratoire de Physique et d'Etude des Matériaux (UMR 8213) (LPEM), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et d'Etude des Matériaux (LPEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: disordered superconducting films, Anomalous diffusion, FOS: Physical sciences, 02 engineering and technology, 01 natural sciences, law.invention, Superconductivity (cond-mat.supr-con), Diffusion, anomalous diffusion, law, Condensed Matter::Superconductivity, 0103 physical sciences, 010306 general physics, Scanning tunneling microscopy, ComputingMilieux_MISCELLANEOUS, Quantum tunnelling, Superconducting films, Physics, Superconductivity, Condensed matter physics, Condensed Matter - Superconductivity, 021001 nanoscience & nanotechnology, Niobium compounds, [PHYS.COND.CM-S]Physics [physics]/Condensed Matter [cond-mat]/Superconductivity [cond-mat.supr-con], Unpaired electron, Density of states, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Scanning tunneling microscope, Cooper pair, [PHYS.COND.CM-SCE]Physics [physics]/Condensed Matter [cond-mat]/Strongly Correlated Electrons [cond-mat.str-el], 0210 nano-technology, Pseudogap
Abstract: Recent scanning tunnelling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature $T_c$. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs, that display a {\em quasi-confinement} (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunnelling experiments. Here we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above $T_c$. We find that the density of states is substantially suppressed up to temperatures well above $T_c$. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely the localisation of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario)., 6 pages 7 figures
Published: 2019

47. Molecular noise of innate immunity shapes bacteria-phage ecologies

Author: Călin C. Guet, Gašper Tkačik, Jakob Ruess, Maroš Pleška, Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), InBio - Méthodes Expérimentales et Computationnelles pour la Modélisation des Processus Cellulaires / Experimental and Computational Methods for Modeling Cellular Processes, Institut Pasteur [Paris] (IP)-Inria de Paris, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Rockefeller University [New York], ANR-18-CE91-0002,CyberCircuits,Circuits cybergénétiques pour tester la composabilité des réseaux génétiques(2018), ANR-16-CE33-0018,MEMIP,Modèles à effets mixtes de processus intracellulaires: méthodes, outils et applications(2016), Méthodes Expérimentales et Computationnelles pour la Modélisation des Processus Cellulaires / Experimental and Computational Methods for Modeling Cellular Processes (InBio ), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Inria de Paris, and Institute of Science and Technology [Austria] (IST Austria)
Subjects: [SDV]Life Sciences [q-bio], Theoretical Ecology, Medicine and Health Sciences, Bacteriophages, Biology (General), [MATH]Mathematics [math], Innate Immune System, 0303 health sciences, education.field_of_study, Ecology, biology, Population size, Chemical Reactions, Chemistry, Viruses, Physical Sciences, Single-Cell Analysis, Research Article, Evolutionary Immunology, QH301-705.5, Ecology (disciplines), Microbial Consortia, Immunology, Population, Models, Biological, Methylation, Microbiology, Microbial Ecology, 03 medical and health sciences, DNA Restriction-Modification Enzymes, education, Ecosystem, 030304 developmental biology, Stochastic Processes, Evolutionary Biology, Bacterial Evolution, Innate immune system, Bacteria, Population Biology, 030306 microbiology, Ecology and Environmental Sciences, Models, Immunological, Organisms, Computational Biology, Biology and Life Sciences, Bacteriology, biology.organism_classification, Immunity, Innate, Organismal Evolution, 13. Climate action, Evolutionary biology, Immune System, Microbial Evolution, Population Ecology, Bacterial virus
Abstract: Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems., Author summary Mathematical understanding of how randomness at the molecular scale, also known as molecular noise, ultimately affects the fate of organisms and whole populations is widely recognized as a challenging problem in multi-scale modeling. Here, we develop an analytical framework for analyzing how the randomness of individual reaction events in single cells propagates to higher levels of biological organization and affects population and ecology scale dynamics. We deploy our mathematical results to study an example from the ecology of bacteria and bacteriophage viruses. Bacteria defend themselves against viruses by a simple innate immune system composed of a pair of enzymes. Due to molecular noise, however, viruses sometimes escape this immunity, causing bacterial populations to plummet. Noise can also cause the immune system to turn against its own host. By analyzing how such costs and benefits of bacterial immunity balance at the ecological level, we predict the optimal parameters for bacterial innate immune systems. While the focus of this work is on bacteria-phage ecologies, we expect that our results will generally help to better understand population and ecology scale consequences of stochastic cell fate decisions in diverse biological domains ranging from cell differentiation in developmental biology to studies of the microbiome and consequences of stochasticity in apoptotic responses for anti-cancer therapies.
Published: 2019

48. Local conditions for triangulating submanifolds of Euclidean space

Author: André Lieutier, Ramsay Dyer, Jean-Daniel Boissonnat, Arijit Ghosh, Mathijs Wintraecken, 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), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Advanced Computing and Microelectronics Unit [Kolkata] (ACMU), Indian Statistical Institute [Kolkata], Dassault Systèmes, Institute of Science and Technology [Austria] (IST Austria), 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 Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Vertex (graph theory), Computational Topology, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Boundary (topology), Computational Geometry, 0102 computer and information sciences, Pseudo-manifolds, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], 01 natural sciences, Theoretical Computer Science, Combinatorics, Triangulation criteria, [MATH.MATH-GT]Mathematics [math]/Geometric Topology [math.GT], Tangent space, Discrete Mathematics and Combinatorics, 0101 mathematics, Whitney, Mathematics, Triangulation (topology), Euclidean space, 010102 general mathematics, Submanifolds of Euclidean space, Computational geometry, Mathematics::Geometric Topology, Manifold, Projection (relational algebra), Computational Theory and Mathematics, 010201 computation theory & mathematics, [MATH.MATH-DG]Mathematics [math]/Differential Geometry [math.DG], [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], Triangulation of Submanifolds, Geometry and Topology, Mathematics::Differential Geometry
Abstract: We consider the following setting: suppose that we are given a manifold M in $${\mathbb {R}}^d$$ R d with positive reach. Moreover assume that we have an embedded simplical complex $${\mathcal {A}}$$ A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in $${\mathcal {A}}$$ A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then $${\mathcal {A}}$$ A is a triangulation of the manifold, that is, they are homeomorphic.
Published: 2019

49. On quantum cohomology of Grassmannians of isotropic lines, unfoldings of An-singularities, and Lefschetz exceptional collections

Author: Morales, John Alexander Cruz, Kuznetsov, Alexander, Mellit, Anton, Perrin, Nicolas, Smirnov, Maxim, National University of Colombia, Steklov Mathematical Institute (SMI), Russian Academy of Sciences [Moscow] (RAS), Institute of Science and Technology [Austria] (IST Austria), Laboratoire de Mathématiques de Versailles (LMV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universität Augsburg [Augsburg], and Steklov Mathematical Institute [Moscow] (SMI)
Subjects: Mathematics - Algebraic Geometry, Mathematics - Symplectic Geometry, Rings and Algebras (math.RA), FOS: Mathematics, Symplectic Geometry (math.SG), Mathematics - Rings and Algebras, [MATH]Mathematics [math], Algebraic Geometry (math.AG)
Abstract: The subject of this paper is the big quantum cohomology rings of symplectic isotropic Grassmannians $\text{IG}(2, 2n)$. We show that these rings are regular. In particular, by "generic smoothness", we obtain a conceptual proof of generic semisimplicity of the big quantum cohomology for $\text{IG}(2, 2n)$. Further, by a general result of Claus Hertling, the regularity of these rings implies that they have a description in terms of isolated hypersurface singularities, which we show in this case to be of type $A_{n-1}$. By the homological mirror symmetry conjecture, these results suggest the existence of a very special full exceptional collection in the derived category of coherent sheaves on $\text{IG}(2, 2n)$. Such a collection is constructed in the appendix by Alexander Kuznetsov., Comment: Appendix by Alexander Kuznetsov. The paper incorporates the results of the earlier preprint arXiv:1510.07903. Comments are welcome
Published: 2019

50. Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks with Guarantees

Author: Vyacheslav Kungurtsev, Malcolm Egan, Bapi Chatterjee, Dan Alistarh, Department of Computer Science, Czech Technical University in Prague (CTU), Modèle et algorithmes pour des systèmes de communication fiables (MARACAS), CITI Centre of Innovation in Telecommunications and Integration of services (CITI), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria), Institute of Science and Technology [Austria] (IST Austria), Vyacheslav Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16 019/0000765 'Research Center for Informatics.' Bapi Chatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement N° 754411 (ISTPlus). Dan Alistarh has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement N° 805223 ScaleML)., European Project: 754411,ISTplus(2017), European Project: 805223,ScaleML(2019), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-CITI Centre of Innovation in Telecommunications and Integration of services (CITI), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)
Subjects: Optimization and Control (math.OC), FOS: Mathematics, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], General Medicine, Mathematics - Optimization and Control
Abstract: Asynchronous distributed algorithms are a popular way to reduce synchronization costs in large-scale optimization, and in particular for neural network training. However, for nonsmooth and nonconvex objectives, few convergence guarantees exist beyond cases where closed-form proximal operator solutions are available. As most popular contemporary deep neural networks lead to nonsmooth and nonconvex objectives, there is now a pressing need for such convergence guarantees. In this paper, we analyze for the first time the convergence of stochastic asynchronous optimization for this general class of objectives. In particular, we focus on stochastic subgradient methods allowing for block variable partitioning, where the shared-memory-based model is asynchronously updated by concurrent processes. To this end, we first introduce a probabilistic model which captures key features of real asynchronous scheduling between concurrent processes; under this model, we establish convergence with probability one to an invariant set for stochastic subgradient methods with momentum. From the practical perspective, one issue with the family of methods we consider is that it is not efficiently supported by machine learning frameworks, as they mostly focus on distributed data-parallel strategies. To address this, we propose a new implementation strategy for shared-memory based training of deep neural networks, whereby concurrent parameter servers are utilized to train a partitioned but shared model in single- and multi-GPU settings. Based on this implementation, we achieve on average 1.2x speed-up in comparison to state-of-the-art training methods for popular image classification tasks without compromising accuracy.
Published: 2019

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