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627 results on '"FWF"'

151. Forecasting of a complex microbial community using meta-omics

Author: F. Delogu, B. J. Kunath, P. M. Queirós, R. Halder, L. A. Lebrun, P. B. Pope, P. May, S. Widder, E. E. L. Muller, P. Wilmes, The project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research. This work was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 863664). The work of P.M. was funded by the ‘Plan Technologies de la Santé du Gouvernement du Grand-Duché de Luxembourg’ through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. S.W. was supported by the Austrian Science Fund (FWF) Elise Richter V585- B31. P.B.P is grateful for support from The Research Council of Norway (FRIPRO program: 250479) and The Novo Nordisk Foundation (Project no. 0054575). [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], and University of Luxembourg: High Performance Computing - ULHPC [research center]
Subjects: Environmental sciences & ecology [F08] [Life sciences], Sciences de l'environnement & écologie [F08] [Sciences du vivant], Microbiologie [F11] [Sciences du vivant], microbial communities, time-series analysis, forecasting, Microbiology [F11] [Life sciences], prediction, Genetics & genetic processes [F10] [Life sciences], multi-omics, Génétique & processus génétiques [F10] [Sciences du vivant], wastewater treatment plant
Abstract: Microbial communities are complex assemblages whose dynamics are shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in the future. In this context, communities in biological wastewater treatment plants (BWWTPs) represent excellent model systems, because forecasting them is required to ultimately control and operate the plants in a sustainable manner. Here, we forecast the microbial community from the water-air interface of the anaerobic tank of a BWWTP via longitudinal meta-omics (metagenomics, metatranscriptomics and metaproteomics) data covering 14 months at weekly intervals. We extracted all the available time-dependent information, summarised it in 17 temporal signals (explaining 91.1% of the temporal variance) and linked them over time to rebuild the sequence of ecological phenomena behind the community dynamics. We forecasted the signals over the following five years and tested the predictions with 21 extra samples. We were able to correctly forecast five signals accounting for 22.5% of the time-dependent information in the system and generate mechanistic predictions on the ecological events in the community (e.g. a predation cycle involving bacteria, viruses and amoebas). Through the forecasting of the 17 signals and the environmental variables readings we reconstructed the gene abundance and expression for the following 5 years, showing a nearly perfect trend prediction (coefficient of determination ≥ 0.97) for the first 2 years. The study demonstrates the maturity of microbial ecology to forecast composition and gene expression of open microbial ecosystems using year-spanning interactions between community cycles and environmental parameters.
Published: 2022
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152. Effects of snow cover change on freezing induced xylem dysfunctions in subalpine woody species

Author: Ganthaler, Andrea, Charra-Vaskou, Katline, Ameglio, Thierry, Charrier, Guillaume, Mayr, Stefan, Institute of Botany [Innsbruck], Leopold Franzens Universität Innsbruck - University of Innsbruck, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Austrian Science Fund (FWF) I4918-B.ANR Acoufollow (ANR-20-CE91-0008), ANR-20-CE91-0008,ACOUFOLLOW,ANALYSES DU DYSFONCTIONNEMENT ET DE LA REPARATION DU XYLÈME INDUIT PAR LE GEL CHEZ LES ARBUSTES, LES CONIFÈRES ET LES ARBRES À FEUILLES CADUQUES :(2020), Charrier, Guillaume, and ANALYSES DU DYSFONCTIONNEMENT ET DE LA REPARATION DU XYLÈME INDUIT PAR LE GEL CHEZ LES ARBUSTES, LES CONIFÈRES ET LES ARBRES À FEUILLES CADUQUES : - - ACOUFOLLOW2020 - ANR-20-CE91-0008 - AAPG2020 - VALID
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE.BIO] Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, [SDV.SA.SF] Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: International audience
Published: 2022

153. A splitting method for SDEs with locally Lipschitz drift : illustration on the FitzHugh-Nagumo model

Author: Evelyn Buckwar, Adeline Samson, Massimiliano Tamborrino, Irene Tubikanec, Johannes Kepler Universität Linz (JKU), Statistique pour le Vivant et l’Homme (SVH), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Department of Mathematics, University of Warwick, Warwick Mathematics Institute (WMI), University of Warwick [Coventry]-University of Warwick [Coventry], Their support is highly appreciated. E.B. was supported by the COMET-K2 Center of the Linz Center of Mechatronics (LCM) funded by the Austrian federal government and the federal state of Upper Austria, number 37920770. A.S. was supported by MIAI@Grenoble Alpes, (ANR-19-P3IA-0003). E.B., M.T. and I.T. were supported by the Austrian Science Fund (FWF): W1214-N15, project DK14. All authors were supported by the Austrian Exchange Service (OeAD), bilateral project FR 03/2017., and ANR-19-P3IA-0003,MIAI,MIAI @ Grenoble Alpes(2019)
Subjects: Numerical Analysis, Applied Mathematics, Ergodicity, Probability (math.PR), Splitting methods, Numerical Analysis (math.NA), Dynamical Systems (math.DS), 60H10, 60H35, 65C20, 65C30, Locally Lipschitz drift, Computational Mathematics, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Hypoellipticity, FitzHugh-Nagumo model, Mean-square convergence AMS subject classifications 60H10, Stochastic differential equations, FOS: Mathematics, Mathematics - Numerical Analysis, Mathematics - Dynamical Systems, QA, Mathematics - Probability
Abstract: In this article, we construct and analyse an explicit numerical splitting method for a class of semi-linear stochastic differential equations (SDEs) with additive noise, where the drift is allowed to grow polynomially and satisfies a global one-sided Lipschitz condition. The method is proved to be mean-square convergent of order 1 and to preserve important structural properties of the SDE. First, it is hypoelliptic in every iteration step. Second, it is geometrically ergodic and has an asymptotically bounded second moment. Third, it preserves oscillatory dynamics, such as amplitudes, frequencies and phases of oscillations, even for large time steps. Our results are illustrated on the stochastic FitzHugh-Nagumo model and compared with known mean-square convergent tamed/truncated variants of the Euler-Maruyama method. The capability of the proposed splitting method to preserve the aforementioned properties may make it applicable within different statistical inference procedures. In contrast, known Euler-Maruyama type methods commonly fail in preserving such properties, yielding ill-conditioned likelihood-based estimation tools or computationally infeasible simulation-based inference algorithms., 38 pages, 10 figures
Published: 2022
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154. The fungal expel of 5-fluorocytosine derived fluoropyrimidines mitigates its antifungal activity and generates a cytotoxic environment

Author: Luis Enrique Sastré-Velásquez, Alex Dallemulle, Alexander Kühbacher, Clara Baldin, Laura Alcazar-Fuoli, Anna Niedrig, Christoph Müller, Fabio Gsaller, and FWF Austrian Science Fund
Subjects: Mammals, Antifungal Agents, Antimetabolites, Aspergillus fumigatus, Immunology, Flucytosine, Antineoplastic Agents, Microbiology, Drug Resistance, Fungal, Virology, Genetics, Aspergillosis, Animals, Humans, Parasitology, Fluorouracil, Molecular Biology
Abstract: Invasive aspergillosis remains one of the most devastating fungal diseases and is predominantly linked to infections caused by the opportunistic human mold pathogen Aspergillus fumigatus. Major treatment regimens for the disease comprise the administration of antifungals belonging to the azole, polyene and echinocandin drug class. The prodrug 5-fluorocytosine (5FC), which is the only representative of a fourth class, the nucleobase analogs, shows unsatisfactory in vitro activities and is barely used for the treatment of aspergillosis. The main route of 5FC activation in A. fumigatus comprises its deamination into 5-fluorouracil (5FU) by FcyA, which is followed by Uprt-mediated 5FU phosphoribosylation into 5-fluorouridine monophosphate (5FUMP). In this study, we characterized and examined the role of a metabolic bypass that generates this nucleotide via 5-fluorouridine (5FUR) through uridine phosphorylase and uridine kinase activities. Resistance profiling of mutants lacking distinct pyrimidine salvage activities suggested a minor contribution of the alternative route in 5FUMP formation. We further analyzed the contribution of drug efflux in 5FC tolerance and found that A. fumigatus cells exposed to 5FC reduce intracellular fluoropyrimidine levels through their export into the environment. This release, which was particularly high in mutants lacking Uprt, generates a toxic environment for cytosine deaminase lacking mutants as well as mammalian cells. Employing the broad-spectrum fungal efflux pump inhibitor clorgyline, we demonstrate synergistic properties of this compound in combination with 5FC, 5FU as well as 5FUR. This research was funded by the Austrian Science Fund (FWF), grant P31093 to F.G. and M2867 to C.B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Sí
Published: 2022
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155. Mapping land-use fluxes for 2001–2020 from global models to national inventories

Author: Giacomo Grassi, Clemens Schwingshackl, Thomas Gasser, Richard A. Houghton, Stephen Sitch, Josep G. Canadell, Alessandro Cescatti, Philippe Ciais, Sandro Federici, Pierre Friedlingstein, Werner A. Kurz, Maria J. Sanz Sanchez, Raúl Abad Viñas, Ramdane Alkama, Guido Ceccherini, Etsushi Kato, Daniel Kennedy, Jürgen Knauer, Anu Korosuo, Matthew J. McGrath, Julia Nabel, Benjamin Poulter, Simone Rossi, Anthony P. Walker, Wenping Yuan, Xu Yue, Julia Pongratz, and G.G. acknowledges funding from the EU’s Horizon 2020 VERIFY project (no. 776810). J.G.C. acknowledges the support of the Australian National Environmental Science Program - Climate Systems Hub. T.G. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under grant agreement #101003536 (ESM2025 project), and by the Austrian Science Fund (FWF) under grant agreement P31796-N29 (ERM project). The authors thank Peter Anthoni and Almut Arneth (LPJ-GUESS model) and Sebastian Lienert (LPX model)
Abstract: With the focus of climate policy shifting from pledges to implementation, there is an increasing need to track progress on climate change mitigation at country level, especially for the land-use sector. Despite new tools and models offering unprecedented monitoring opportunities, striking differences remain in estimations of anthropogenic land-use CO2 fluxes between the national greenhouse gas inventories (NGHGIs) used to assess compliance with the Paris Agreement, and the Global Carbon Budget and IPCC assessment reports, both based on global bookkeeping models (BMs). Recent evidence showed that these differences are mainly due to inconsistent definitions of anthropogenic forest CO2 fluxes. In particular, the part of the land sink that is caused by the indirect effects of human-induced environmental change (e.g., fertilization effect on vegetation growth due to increase atmospheric CO2 concentration, climate change) on managed lands is treated as non-anthropogenic by BMs, while in most cases is considered anthropogenic in NGHGIs. In addition, countries use a broader definition of managed land than BMs. Building on previous studies, we implement an approach that adds the CO2 sink due to environmental change from countries’ managed forest area (estimated by Dynamic Global Vegetation Models, DGVMs) to the original land-use flux from BMs. This sum is expected to be conceptually more comparable to NGHGIs. Our analysis uses updated and more comprehensive data from NGHGIs than previous studies and provides model results at a greater level of disaggregation in terms of land categories (i.e., forest land, deforestation, organic soils, other land uses) and countries. Our results confirm a large difference in land use CO2 fluxes between the ensemble mean of the BMs, estimating a source of 4.3 GtCO2 yr-1 globally for the period 2001–2020, and NGHGIs, which estimate a sink of -1.7 GtCO2 yr-1. Most of this 6.0 GtCO2 yr-1 gap is found on forest land (3.8 GtCO2 yr-1), with differences also for deforestation (1.1 GtCO2 yr-1), other land uses (1.0 GtCO2 yr-1), and to a lesser extent for organic soils (0.1 GtCO2 yr-1). By adding the DGVM ensemble mean sink arising from environmental change in managed forests (-5.1 GtCO2 yr-1) to BMs estimates, the gap between BMs and NGHGIs becomes significantly smaller both globally (residual gap: 0.9 GtCO2 yr-1) and in most regions and countries. The remaining differences mostly reflect smaller net emissions from deforestation and agricultural land in the NGHGIs of developing countries than in the BMs. By reconciling most of the differences between NGHGIs and global models (BMs and DGVMs), offering a blueprint for operationalizing future comparisons, and identifying areas to be further investigated, this study represents an important step forward for increasing transparency and confidence in land-use CO2 flux estimates at the country level. This is crucial to support land-based mitigation investments and assess the countries’ collective progress under the Paris Agreement’s Global Stocktake.
Published: 2022

156. Pareto rationalizability by two single-peaked preferences

Author: Arlegi Pérez, Ricardo, Teschl, Miriam, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Institute for Advanced Research in Business and Economics (INARBE), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Austrian Science Fund (FWF T366-G14), Universidad Pública de Navarra. Departamento de Economía, Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa. Inarbe - Institute for Advanced Research in Business and Economics, and Nafarroako Unibertsitate Publikoa. Ekonomia Saila
Subjects: Sociology and Political Science, Single-peaked preferences, General Social Sciences, Statistics, Probability and Uncertainty, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, General Psychology, Pareto rationalizability
Abstract: We study, in a finite setting, the problem of Pareto rationalizability of choice functions by means of a preference profile that is single-peaked with respect to an exogenously given linear order over the alternatives. This problem requires a new condition to be added to those that characterize Pareto rationalizability in the general domain of orders (Moulin (1985)). This new condition appeals to the existence of a central range of options such that the choice function excludes alternatives which are distant from that range. We acknowledge financial support from the Spanish Ministry of Science and Technology (Project ECO2015-65031-R MINECO/FEDER, UE) and the Austrian Science Fund (FWF T366-G14).
Published: 2022
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157. Premature Ovarian Insufficiency in CLPB Deficiency: Transcriptomic, Proteomic and Phenotypic Insights

Author: Elena J Tucker, Megan J Baker, Daniella H Hock, Julia T Warren, Sylvie Jaillard, Katrina M Bell, Rajini Sreenivasan, Shabnam Bakhshalizadeh, Chloe A Hanna, Nikeisha J Caruana, Saskia B Wortmann, Shamima Rahman, Robert D S Pitceathly, Jean Donadieu, Aurelia Alimi, Vincent Launay, Paul Coppo, Sophie Christin-Maitre, Gorjana Robevska, Jocelyn van den Bergen, Brianna L Kline, Katie L Ayers, Phoebe N Stewart, David A Stroud, Diana Stojanovski, Andrew H Sinclair, University of Melbourne, Murdoch Children's Research Institute (MCRI), Durham University, Washington University School of Medicine [Saint Louis, MO], Service de Cytogénétique et de Biologie Cellulaire, Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Royal Children's Hospital Melbourne, Victoria University [Melbourne], Paracelsus Medizinische Privatuniversität = Paracelsus Medical University (PMU), Amalia Children’s Hospital [Nijmegen, The Netherlands], Great Ormond Street Hospital for Children NHS Foundation Trust [London, UK] (GOSHC), UCL Institute of Neurology, Queen Square [London], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU de Saint-Brieuc, CHU Saint-Antoine [AP-HP], Sorbonne Université (SU), Royal Hobart Hospital, and This work was supported by an National Health and Medical Research Council (NHMRC) program grant (1074258 toA.H.S.), NHMRC grant (1140906 to D.A.S.), NHMRC fellowships (1054432 to E.J.T., 1126995 to R.S., 2009732 to D.A.S., 1062854 to A.H.S.), a Suzi Carp postdoctoral scholarship (to E.J.T.), a CHU Rennes grant (Appel à Projets Innovations 2019 to S.J.), an Australian Government Research Training Program scholarship (to M.J.B.), the Australian Mito Foundation for provision of instrumentation, incubator grants (to E.J.T. and D.S.), a Booster grant (to D.S.) and PhD Top-up scholarships (to M.J.B. and D.H.H.), and a Medical Research Council (UK) Clinician Scientist Fellowship (MR/S002065/1 to R.D.S.P.). S.B.W. was funded by ERAPERMED2019-310—Personalized Mitochondrial Medicine (PerMiM): Optimizing diagnostics and treatment for patients with mitochondrial diseases (FWF 4704-B).
Subjects: Proteomics, premature ovarian insufficiency, Neutropenia, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, primary mitochondrial disease, Biochemistry (medical), Clinical Biochemistry, Menopause, Premature, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Endopeptidase Clp, Primary Ovarian Insufficiency, Biochemistry, Cataract, mitochondria, Endocrinology, Phenotype, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, CLPB, Humans, genetics, Female, infertility, Transcriptome
Abstract: Context Premature ovarian insufficiency (POI) is a common form of female infertility that usually presents as an isolated condition but can be part of various genetic syndromes. Early diagnosis and treatment of POI can minimize comorbidity and improve health outcomes. Objective We aimed to determine the genetic cause of syndromic POI, intellectual disability, neutropenia, and cataracts. Methods We performed whole-exome sequencing (WES) followed by functional validation via RT-PCR, RNAseq, and quantitative proteomics, as well as clinical update of previously reported patients with variants in the caseinolytic peptidase B (CLPB) gene. Results We identified causative variants in CLPB, encoding a mitochondrial disaggregase. Variants in this gene are known to cause an autosomal recessive syndrome involving 3-methylglutaconic aciduria, neurological dysfunction, cataracts, and neutropenia that is often fatal in childhood; however, there is likely a reporting bias toward severe cases. Using RNAseq and quantitative proteomics we validated causation and gained insight into genotype:phenotype correlation. Clinical follow-up of patients with CLPB deficiency who survived to adulthood identified POI and infertility as a common postpubertal ailment. Conclusion A novel splicing variant is associated with CLPB deficiency in an individual who survived to adulthood. POI is a common feature of postpubertal female individuals with CLPB deficiency. Patients with CLPB deficiency should be referred to pediatric gynecologists/endocrinologists for prompt POI diagnosis and hormone replacement therapy to minimize associated comorbidities.
Published: 2022
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158. How the Glasgow Declaration on Forests can help keep alive the 1.5 °C target

Author: Gasser, Thomas, Ciais, Philippe, Lewis, Simon L., International Institute for Applied Systems Analysis [Laxenburg] (IIASA), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), School of Geography [Leeds], University of Leeds, University College of London [London] (UCL), and We thank R. A. Houghton and A. D. de Almeida Castanho for sharing their FRA2020-based land use and land cover change drivers. T.G. acknowledges support from the EU H2020 'CONSTRAIN' project (Grant No. 820829) and the FWF 'ERM' project (grant P31796-N29).
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Multidisciplinary, biomass, soil fertility, air pollution, environmental risk, greenhouse effect, hydroponics, heavy metal removal, Forests, MESH: Forests, Note, Global Warming, United Kingdom, carbon dioxide emission, forest, environmental policy, atmosphere, deforestation, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, biodiversity
Abstract: International audience; At last year's 26th UN Climate Change Conference of the Parties (COP26) in Glasgow, 141 countries committed to halt and reverse forest loss and land degradation by 2030 (1). It was part of one of several side deals designed to keep the objectives of the Paris agreement within reach. The UK government boasted that these nations had made a landmark pledge to end deforestation (2). Yet, one crucial detail was left out: whether that deforestation will be gross or net. The distinction matters, because differing interpretations of how countries can "end deforestation" significantly impact future carbon dioxide emissions. Put simply, ending gross deforestation would be a major step forward for the climate. But considering only net deforestation could be anecdotal and even be detrimental to biodiversity. Overall, human activities related to land use emit 4 gigatonnes (Gt) of carbon dioxide (CO 2) per year to the atmosphere (3). These are net emissions, comprising both carbon losses and carbon gains. On the loss side, the destruction of tree biomass during deforestation, for large-scale agriculture, cattle ranching, or shifting cultivation (cycles of cutting forest for agriculture, then abandoning to recover soil fertility, then returning), and the legacy emissions from harvested wood products, form the bulk of gross emissions, totaling 14 Gt CO 2 per year (3). On the gain side, secondary forest regrowth after reforestation, agricultural abandonment, or during shifting cultivation form the bulk of the gross carbon Differing interpretations as to how countries can "end deforestation" will have significant impacts on future carbon dioxide emissions. Only ending gross deforestation would be a major step forward for the climate. Image credit: Shutterstock/guentermanaus.
Published: 2022
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159. Convergence and quasi-optimal cost of adaptive algorithms for nonlinear operators including iterative linearization and algebraic solver

Author: Alexander Haberl, Martin Vohralík, Stefan Schimanko, Dirk Praetorius, Institute for Analysis and Scientific Computing [Wien], Vienna University of Technology (TU Wien), Simulation for the Environment: Reliable and Efficient Numerical Algorithms (SERENA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), The authors thankfully acknowledge support by the Austrian Science Fund(FWF) through the research projects Computational nonlinear PDEs (grant P33216),Optimal isogeometric boundary element method (grant P29096), as well as Taming complexity in partial differential systems(grant SFB F65). This project has also received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No647134 GATIPOR)., and European Project: 647134,H2020 ERC,ERC-2014-CoG,GATIPOR(2015)
Subjects: Finite element method, Discretization, 65N12, 65N15, 65N30, 65N50, 68Q25, 010103 numerical & computational mathematics, 01 natural sciences, 2010 Mathematics Subject Classification: 65N12, 65N15, 65N30, 65N50, 68Q25, Quasi-optimal computational cost, Linearization, 65N12, 65N15, 65N30, 65N50, 68Q25 [2010 Mathematics Subject Classification], FOS: Mathematics, Monotone nonlinearity, Mathematics - Numerical Analysis, 0101 mathematics, Algebraic number, Banach–Picard linearization, Mathematics, Contraction, Adaptive algorithm, Adaptive mesh refinement, Adaptive mesh-refinement, Error decay, Applied Mathematics, Numerical analysis, Numerical Analysis (math.NA), Solver, Inexact solver, 010101 applied mathematics, Computational Mathematics, Rate of convergence, Algebraic resolution, A posteriori error estimate, Algorithm, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract: We consider a second-order elliptic boundary value problem with strongly monotone and Lipschitz-continuous nonlinearity. We design and study its adaptive numerical approximation interconnecting a finite element discretization, the Banach–Picard linearization, and a contractive linear algebraic solver. In particular, we identify stopping criteria for the algebraic solver that on the one hand do not request an overly tight tolerance but on the other hand are sufficient for the inexact (perturbed) Banach–Picard linearization to remain contractive. Similarly, we identify suitable stopping criteria for the Banach–Picard iteration that leave an amount of linearization error that is not harmful for the residual a posteriori error estimate to steer reliably the adaptive mesh-refinement. For the resulting algorithm, we prove a contraction of the (doubly) inexact iterates after some amount of steps of mesh-refinement/linearization/algebraic solver, leading to its linear convergence. Moreover, for usual mesh-refinement rules, we also prove that the overall error decays at the optimal rate with respect to the number of elements (degrees of freedom) added with respect to the initial mesh. Finally, we prove that our fully adaptive algorithm drives the overall error down with the same optimal rate also with respect to the overall algorithmic cost expressed as the cumulated sum of the number of mesh elements over all mesh-refinement, linearization, and algebraic solver steps. Numerical experiments support these theoretical findings and illustrate the optimal overall algorithmic cost of the fully adaptive algorithm on several test cases.
Published: 2021
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160. Endothelial sprouting, proliferation, or senescence: tipping the balance from physiology to pathology

Author: Mühleder, Severin, Fernández-Chacón, Macarena, Garcia-Gonzalez, Irene, Benedito, Rui, FWF Austrian Science Fund, Fundación La Caixa, European Research Council, Centro Nacional de Investigaciones Cardiovasculares Carlos III (España), Ministerio de Economía, Industria y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), and Fundación ProCNIC
Subjects: Senescence, Aging, Cell cycle checkpoint, Vascular differentiation, Angiogenesis, Endothelial cells, medicine.medical_treatment, Neovascularization, Physiologic, Review, Disease, Biology, Cell-cycle arrest, Regenerative medicine, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Cell Movement, Neoplasms, medicine, Humans, Molecular Biology, Cell Proliferation, 030304 developmental biology, Feedback, Physiological, Pharmacology, 0303 health sciences, Neovascularization, Pathologic, Cell growth, Growth factor, Endothelial Cells, Cell Biology, Cell biology, Cardiovascular Diseases, 030220 oncology & carcinogenesis, Malformations, Molecular Medicine, Signal transduction, Sprouting, Signal Transduction
Abstract: Therapeutic modulation of vascular cell proliferation and migration is essential for the effective inhibition of angiogenesis in cancer or its induction in cardiovascular disease. The general view is that an increase in vascular growth factor levels or mitogenic stimulation is beneficial for angiogenesis, since it leads to an increase in both endothelial proliferation and sprouting. However, several recent studies showed that an increase in mitogenic stimuli can also lead to the arrest of angiogenesis. This is due to the existence of intrinsic signaling feedback loops and cell cycle checkpoints that work in synchrony to maintain a balance between endothelial proliferation and sprouting. This balance is tightly and effectively regulated during tissue growth and is often deregulated or impaired in disease. Most therapeutic strategies used so far to promote vascular growth simply increase mitogenic stimuli, without taking into account its deleterious effects on this balance and on vascular cells. Here, we review the main findings on the mechanisms controlling physiological vascular sprouting, proliferation, and senescence and how those mechanisms are often deregulated in acquired or congenital cardiovascular disease leading to a diverse range of pathologies. We also discuss alternative approaches to increase the effectiveness of pro-angiogenic therapies in cardiovascular regenerative medicine. Severin Mühleder was funded by the Austrian Science Fund (FWF) project J4358. Macarena Fernández-Chacón and Irene Garcia-Gonzalez were supported by PhD fellowships from Fundación La Caixa (CX_E-2015-01 and CX-SO-16-1, respectively). Rui Benedito was funded by the European Research Council (ERC-2014-StG—638028), the Centro Nacional de Investigaciones Cardiovasculares (CNIC), and by the Ministerio de Economia, Industria y Competitividad (MEIC: SAF2013-44329-P, SAF2017-89299-P, and RYC-2013-13209). The CNIC is supported by the Ministerio de Ciencia, Innovación y Universidades (MCNU) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505). Sí
Published: 2020
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161. The RALph miner for automated discovery and verification of resource-aware process models

Author: Christian Sturm, Jan Mendling, Cristina Cabanillas, Stefan Schönig, Lars Ackermann, Universidad de Sevilla. Departamento de Lenguajes y Sistemas Informáticos, Austrian Science Found (FWF), and Ministerio de Ciencia, Innovación y Universidades (MICINN). España
Subjects: Model checking, Process modeling, Process (engineering), Computer science, 02 engineering and technology, Organisational mining, Notation, Task (project management), Business process discovery, Resource (project management), 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, 102015 Information systems, Process mining, RALph, resource assignment, 102015 Informationssysteme, 102022 Softwareentwicklung, business.industry, Event (computing), 102022 Software development, Process verification, Modeling and Simulation, 020201 artificial intelligence & image processing, Timestamp, Resource mining, Software engineering, business, Software
Abstract: Automated process discovery is a technique that extractsmodels of executed processes from event logs. Logs typically include information about the activities performed, their timestamps and the resources that were involved in their execution. Recent approaches to process discovery put a special emphasis on (human) resources, aiming at constructing resource-aware process models that contain the inferred resource assignment constraints. Such constraints can be complex and process discovery approaches so far have missed the opportunity to represent expressive resource assignments graphically together with process models. A subsequent verification of the extracted resource-aware process models is required in order to check the proper utilisation of resources according to the resource assignments. So far, research on discovering resource-aware process models has assumed that models can be put into operation without modification and checking. Integrating resource mining and resource-aware process model verification faces the challenge that different types of resource assignment languages are used for each task. In this paper, we present an integrated solution that comprises (i) a resource mining technique that builds upon a highly expressive graphical notation for defining resource assignments; and (ii) automated model-checking support to validate the discovered resource-aware process models. All the concepts reported in this paper have been implemented and evaluated in terms of feasibility and performance. Austrian Science Found (FWF)—Grant V 569-N31 (PRAIS) Ministerio de Ciencia, Innovación y Universidade RTI2018-100763-J-100 (CONFLEX)
Published: 2020
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162. Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery

Author: Marie-Christine Vaney, Mariano Dellarole, Stéphane Duquerroy, Iris Medits, Georgios Tsouchnikas, Alexander Rouvinski, Patrick England, Karin Stiasny, Franz X. Heinz, Félix A. Rey, Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris-Saclay, Institute of Virology (Vienna), Medizinische Universität Wien = Medical University of Vienna, Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), This work was supported by the French ANR (Agence Nationale de la Recherche), grants ANR-13-ISV8-0002-01, ANR-10-LABX-62-10 IBEID, Wellcome Trust collaborative grant (UNS22082) to FAR, as well as by Institut Pasteur and CNRS. K.S and F.X.H acknowledge support from the Austrian Science Fund FWF (I1378-B13 and P27501-B21)., ANR-13-ISV8-0002,flavistem,La protéine E des flavivirus : interactions et fusion membranaire(2013), and ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
Subjects: Furin, Multidisciplinary, Viral Envelope Proteins, [SDV]Life Sciences [q-bio], Virion, General Physics and Astronomy, General Chemistry, Membrane Fusion, General Biochemistry, Genetics and Molecular Biology, Encephalitis Viruses, Tick-Borne
Abstract: We thank the staff at beamlines PX1 and PX2 at SOLEIL synchrotron (St. Aubin, France) and at PX beamlines at the ESRF (Grenoble, France); A. Haouz and the staff at the crystallographic facility at Institut Pasteur; F. Agou from the Chemogenomic and Biological Screening platform at Institut Pasteur; P. Guardado Calvo and I. Fernandez for helping for the MALS experiments.; International audience; The flavivirus envelope glycoproteins prM and E drive the assembly of icosahedral, spiky immature particles that bud across the membrane of the endoplasmic reticulum. Maturation into infectious virions in the trans-Golgi network involves an acid-pH-driven rearrangement into smooth particles made of (prM/E)2 dimers exposing a furin site for prM cleavage into "pr" and "M". Here we show that the prM "pr" moiety derives from an HSP40 cellular chaperonin. Furthermore, the X-ray structure of the tick-borne encephalitis virus (pr/E)2 dimer at acidic pH revealed the E 150-loop as a hinged-lid that opens at low pH to expose a positively-charged prbinding pocket at the E dimer interface, inducing (prM/E)2 dimer formation to generate smooth particles in the Golgi. Furin cleavage is followed by lid-closure upon deprotonation in the neutral-pH extracellular environment, expelling pr while the 150-loop takes the relay in fusion loop protection, thus revealing the elusive flavivirus mechanism of fusion activation.
Published: 2022
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163. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Author: Andrea Fulgione, Célia Neto, Ahmed F. Elfarargi, Emmanuel Tergemina, Shifa Ansari, Mehmet Göktay, Herculano Dinis, Nina Döring, Pádraic J. Flood, Sofia Rodriguez-Pacheco, Nora Walden, Marcus A. Koch, Fabrice Roux, Joachim Hermisson, Angela M. Hancock, Max Planck Society (GERMANY), University of Vienna [Vienna], Max F. Perutz Laboratories, Vienna Grad Sch Populat Genet, Parque Nat Fogo, Associação Projecto Vitó, Universität Heidelberg [Heidelberg] = Heidelberg University, Biosystematics Group, Wageningen University and Research, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathematics and BioSciences Group, Faculty of Mathematics [Vienna], University of Vienna [Vienna]-University of Vienna [Vienna], Marie Curie CIG : 304301, National Science Foundation (NSF) 1064766, Max Planck Society Funding, Austrian Science Fund (FWF) : DK W1225-B20, German Research Foundation (DFG)European CommissionFOR 1078, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and European Project: 638810,H2020,ERC-2014-STG,CVI_ADAPT(2015)
Subjects: Multidisciplinary, Arabidopsis Proteins, Arabidopsis, General Physics and Astronomy, MADS Domain Proteins, Flowers, General Chemistry, Biosystematiek, General Biochemistry, Genetics and Molecular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Mutation, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biosystematics
Abstract: Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue.
Published: 2022
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164. TactJam: An End-to-End Prototyping Suite for Collaborative Design of On-Body Vibrotactile Feedback

Author: Dennis Wittchen, Katta Spiel, Bruno Fruchard, Donald Degraen, Oliver Schneider, Georg Freitag, Paul Strohmeier, Dresden University of Applied Sciences, Vienna University of Technology (TU Wien), Technology and knowledge for interaction (LOKI), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Saarland University [Saarbrücken], Deutsches Forschungszentrum für Künstliche Intelligenz GmbH = German Research Center for Artificial Intelligence (DFKI), University of Waterloo [Waterloo], Max Planck Institute for Informatics [Saarbrücken], This project received funding from the European Research Council (ERC StG Interactive Skin 714797) and the Hertha-Firnberg Grant T 1146-G by the Austrian Science Fund (FWF)., and European Project: 714797,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),InteractiveSkin(2017)
Subjects: [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC]
Abstract: International audience; We present TactJam, an end-to-end suite for creating and sharing low fidelity prototypes of on-body vibrotactile feedback. With Tac-tJam, designers can create, record and share vibrotactile patterns online. This opens up new ways of collaboratively designing vibrotactile patterns both in collocated as well as in remote settings. We evaluate TactJam in a two-part distributed online workshop, exploring the design of on-body tactons. Participants were able to successfully use TactJam to learn about tacton design. We present an overview of mappings between tactons and their associated concepts before comparing the results of tactons created using solely a GUI and tactons created through experimenting with placements directly on the body. Conducting both parts of the workshop separately highlighted the importance of designing directly with bodies: less implicit assumptions were made, and designs were guided by personal experience. We reflect on these results and close on deliberations for the future development of TactJam.
Published: 2022
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165. Effect of growth rate and pH on Li isotope fractionation during its incorporation in calcite

Author: Füger, A., Kuessner, M., Rollion-Bard, C., Leis, A., Magna, T., Dietzel, M., Mavromatis, Vasileios, Institute of Applied Geosciences [Graz] (IAG), Graz University of Technology [Graz] (TU Graz), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Czech Geological Survey [Praha], Institute of Applied Geosciences [Darmstadt] (IAG), Darmstadt University of Technology [Darmstadt], Géosciences Environnement Toulouse (GET), 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)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut 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), This project has received funding by Marie Skłodowska-Curie Horizon 2020 Project BASE-LiNE Earth (H2020-MSCA-INT-2014- 643084) and by the FWF-DFG project Charon II (FWF-I3028-N29)., and European Project: 643084,H2020,H2020-MSCA-ITN-2014,BASE-LiNE Earth(2015)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Growth rate, Geochemistry and Petrology, 550 Earth sciences & geology, Calcite, PH effect, Li isotopes, Fractionation, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment
Abstract: International audience; Lithium isotope compositions were determined for synthetic calcite and fluid, reported in Füger et al. (2019). Calcite was precipitated at 25°C, and mineral growth rate and pH varied within the range of 10$^{−8.1}$≤ r$_p$ (mol m$^{−2}$ s$^{−1}$) ≤ 10$^{−7.2}$ and 6.3 ≤ pH ≤ 9.5, respectively. At pH = 8.25±0.15, the Δ$^7$Li$_{calcite-fluid}$ = δ$^7$Li$_{calcite}$ - δ$^7$Li$_{fluid}$ value of −2.76 ± 0.22 ‰ (n=4) was yielded when calcite growth rate was lower than ∼10$^{−7.7}$ (mol m$^{−2}$ s$^{−1}$). As calcite growth rate increased, Δ$^7$Li$_{calcite-fluid}$ values progressively decreased to about −4.5 ‰. The dependence of Li isotope fractionation on calcite growth rate is described by the surface reaction kinetic model developed by DePaolo (2011). In this model the equilibrium and kinetic isotope fractionation factors obtain values of -2.7 ± 0.1 ‰ and -8.8 ± 0.1 ‰, respectively. In addition, for experiments performed under similar surface-normalized growth rate of 10$^{−7.7}$±0.2 (mol m$^{−2}$ s$^{−1}$) a significant decrease in Δ$^7$Li$_{calcite-fluid}$ from pH 9.5 to 6.3 was observed. These variations of Δ$^7$Li$_{calcite-fluid}$ as a function of pH for experiments performed under low degrees of solution saturation with respect to calcite point towards the incorporation of two or more Li-bearing species in the solid phase. Thus, the Li isotope composition of the solid reflects the abundance of these species, which depends on solution pH and fluid composition.Overall the results of this study suggest that both calcite growth rate and pH are parameters that can significantly affect the measured Li isotope fractionation between calcite and fluid. The high sensitivity of Δ$^7$Li$_{calcite-fluid}$ to calcite growth rate observed in this study suggests that a high variability of δ$^7$Li$_{calcite}$ in natural samples, such as foraminifera, brachiopods, and speleothems can be expected in natural environments. The implications for the potential use of elemental and isotope fractionation of Li during calcite formation are discussed in the light of reconstruction of paleo-environmental conditions.
Published: 2022
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166. The hare and the tortoise: stomatal kinetics under light change in Poaceae crops

Author: Guillaume Charrier, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Pack Ambition Recherche program 'Doux-Glace' from the Auvergne-Rhone Alpes regionAustrian Science Fund (FWF), and ANR-20-CE91-0008,ACOUFOLLOW,ANALYSES DU DYSFONCTIONNEMENT ET DE LA REPARATION DU XYLÈME INDUIT PAR LE GEL CHEZ LES ARBUSTES, LES CONIFÈRES ET LES ARBRES À FEUILLES CADUQUES :(2020)
Subjects: Crops, Agricultural, Kinetics, Physiology, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, Plant Science, Hares, Poaceae, News and Views, ComputingMilieux_MISCELLANEOUS, Turtles
Abstract: International audience
Published: 2022
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167. Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments

Author: Barata C, Carolin Kosiol, Rui Borges, BBSRC, Vienna Science and Technology Fund, The Royal Society, Carnegie Trust, The Wellcome Trust, Austrian Science Fund FWF, University of St Andrews. Centre for Biological Diversity, and University of St Andrews. School of Biology
Subjects: QA75, Pool-seq, Computer science, QA75 Electronic computers. Computer science, QH301 Biology, Bayesian inference, Bayesian probability, QH426 Genetics, computer.software_genre, QH301, Targets of selection, Feature (machine learning), Null distribution, Allele, Adaptation (computer science), Moran model, QH426, Selection (genetic algorithm), Ecology, Evolution, Behavior and Systematics, MCC, Experimental evolution, Selection coefficients, 3rd-DAS, E&R, Data mining, computer
Abstract: funding: This research was funded in part, by the Vienna Science and Technology Fund (WWTF) [MA16-061], the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/W000768/1], and the Austrian Science Fund (FWF) [P34524-B]. CK received funding from the Royal Society (RG170315) and Carnegie Trust (RIG007474). The computational results presented have been partly achieved using the St Andrews Bioinformatics Unit (StABU), which is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z). For over a decade, experimental evolution has been combined with high-throughput sequencing techniques. In so-called Evolve-and-Resequence (E&R) experiments, populations are kept in the laboratory under controlled experimental conditions where their genomes are sampled and allele frequencies monitored. However, identifying signatures of adaptation in E&R datasets is far from trivial, and it is still necessary to develop more efficient and statistically sound methods for detecting selection in genome-wide data. Here, we present Bait-ER – a fully Bayesian approach based on the Moran model of allele evolution to estimate selection coefficients from E&R experiments. The model has overlapping generations, a feature that describes several experimental designs found in the literature. We tested our method under several different demographic and experimental conditions to assess its accuracy and precision, and it performs well in most scenarios. Nevertheless, some care must be taken when analysing trajectories where drift largely dominates and starting frequencies are low. We compare our method with other available software and report that ours has generally high accuracy even for trajectories whose complexity goes beyond a classical sweep model. Furthermore, our approach avoids the computational burden of simulating an empirical null distribution, outperforming available software in terms of computational time and facilitating its use on genome-wide data. We implemented and released our method in a new open-source software package that can be accessed at https://doi.org/10.5281/zenodo.7351736. Publisher PDF
Published: 2022
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168. The C-terminal tail of ribosomal protein Rps15 is engaged in cytoplasmic pre-40S maturation

Author: Ingrid Rössler, Sarah Weigl, José Fernández-Fernández, Sara Martín-Villanueva, Daniela Strauss, Ed Hurt, Jesús de la Cruz, Brigitte Pertschy, Universidad de Sevilla. Departamento de Genética, Austrian science fund (FWF), Ministerio de Ciencia e Innovación (MICIN). España, Agencia Estatal de Investigación. España, Junta de Andalucía, Austrian Science Fund, BioTechMed-Graz, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación Española para la Ciencia y la Tecnología, Rössler, Ingrid 0000-0003-4573-6903`], Martín-Villanueva, Sara, Cruz, Jesús de la, and Pertschy, Brigitte
Subjects: Ribosomal Proteins, Ribosome Subunits, Small, Eukaryotic, Chronic lymphocytic leukaemia, Saccharomyces cerevisiae Proteins, Cell Biology, yeast, Ribosomal protein, Yeast, ribosomal protein, rps15/uS19, Ribosome biogenesis, Protein Biosynthesis, RNA Precursors, Humans, rps15/ uS19, 40S ribosomal subunit, Molecular Biology, Ribosomes, CLL, chronic lymphocytic leukaemia
Abstract: The small ribosomal subunit protein Rps15/uS19 is involved in early nucleolar ribosome biogenesis and subsequent nuclear export of pre-40S particles to the cytoplasm. In addition, the C-terminal tail of Rps15 was suggested to play a role in mature ribosomes, namely during translation elongation. Here, we show that Rps15 not only functions in nucleolar ribosome assembly but also in cytoplasmic pre-40S maturation, which is indicated by a strong genetic interaction between Rps15 and the 40S assembly factor Ltv1. Specifically, mutations either in the globular or C-terminal domain of Rps15 when combined with the non-essential ltv1 null allele are lethal or display a strong growth defect. However, not only rps15 ltv1 double mutants but also single rps15 C-terminal deletion mutants exhibit an accumulation of the 20S pre-rRNA in the cytoplasm, indicative of a cytoplasmic pre-40S maturation defect. Since in pre-40S particles, the C-terminal tail of Rps15 is positioned between assembly factors Rio2 and Tsr1, we further tested whether Tsr1 is genetically linked to Rps15, which indeed could be demonstrated. Thus, the integrity of the Rps15 C-terminal tail plays an important role during late pre-40S maturation, perhaps in a quality control step to ensure that only 40S ribosomal subunits with functional Rps15 C-terminal tail can efficiently enter translation. As mutations in the C-terminal tail of human RPS15 have been observed in connection with chronic lymphocytic leukaemia, it is possible that apart from defects in translation, an impaired late pre-40S maturation step in the cytoplasm could also be a reason for this disease., This work was funded by Austrian science fund (FWF) grant P27996-B21, Austrian science fund P28874-B21, and doc.fund 50 ‘Molecular Metabolism’ to B.P. Additionally, B.P. was supported by the BioTechMed-Graz Flagship project DYNIMO, the ‘Land Steiermark’ and ‘Stadt Graz’. Work in the J.d.l.C. lab was supported by the Spanish Ministry of Science and Innovation (PID2019–103850-GB-I00/Agencia Estatal de Investigación agencia estatal de investigación AEI/10.13039/501100011033) and the Andalusian regional government (Andalusian regional government P20_00581 and BIO-271). S.M.-V. is an academic research staff of the Andalusian Research, Development, and Innovation Plan by the Andalusian regional government (PAIDI 2020). J.F.-F. acknowledges an FPI fellowship from the Spanish Ministry of Science and Innovation (BFundación Española para la Ciencia y la Tecnología ES-2017-080876).
Published: 2022
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169. How environment affects active particle swarms: a case study

Author: Pierre Degond, Angelika Manhart, Sara Merino-Aceituno, Diane Peurichard, Lorenzo Sala, Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University College of London [London] (UCL), University of Vienna [Vienna], Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), SImulations en Médecine, BIOtechnologie et ToXicologie de systèmes multicellulaires (SIMBIOTX ), 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), and SMA was supported by the Vienna Science and Technology Fund (WWTF) with a Vienna Research Groups for Young Investigators, grant VRG17-014. The research by SMA was partially supported by the Austrian Science Fund (FWF) through the project F65.
Subjects: Multidisciplinary, 37N25 (primary), 70F40, 35Q70, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], FOS: Physical sciences, Mathematical Physics (math-ph), [MATH]Mathematics [math], Mathematical Physics
Abstract: We investigate the collective motion of self-propelled agents in an environment filled with obstacles that are tethered to fixed positions via springs. The active particles are able to modify the environment by moving the obstacles through repulsion forces. This creates feedback interactions between the particles and the obstacles from which a breadth of patterns emerges (trails, band, clusters, honey-comb structures,...). We will focus on a discrete model first introduced in [Aceves2020] and derived into a continuum PDE model. As a first major novelty, we perform an in-depth investigation of pattern formation of the discrete and continuum models in 2D: we provide phase-diagrams and determine the key mechanisms for bifurcations to happen using linear stability analysis. As a result, we discover that the agent-agent repulsion, the agent-obstacle repulsion and the obstacle's spring stiffness are the key forces in the appearance of patterns, while alignment forces between the particles play a secondary role. The second major novelty lies in the development of an innovative methodology to compare discrete and continuum models that we apply here to perform an in-depth analysis of the agreement between the discrete and continuum models., Comment: 39 pages, 14 figures
Published: 2022

170. Global modelling of soil carbonyl sulfide exchanges

Author: Abadie, Camille, Maignan, Fabienne, Remaud, Marine, Ogée, Jérôme, Campbell, J. Elliott, Whelan, Mary E., Kitz, Florian, Spielmann, Felix M., Wohlfahrt, Georg, Wehr, Richard, Sun, Wu, Raoult, Nina, Seibt, Ulli, Hauglustaine, Didier, Lennartz, Sinikka T., Belviso, Sauveur, Montagne, David, Peylin, Philippe, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sierra Nevada Research Institute, University of California (UC), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), Leopold Franzens Universität Innsbruck - University of Innsbruck, Center for Atmospheric and Environmental Chemistry [Billerica], Aerodyne Research Inc., Carnegie Institution for Science, Department of Atmospheric and Oceanic Sciences [Los Angeles] (AOS), University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Modelling the Earth Response to Multiple Anthropogenic Interactions and Dynamics (MERMAID), University of Oldenburg, Massachusetts Institute of Technology (MIT), ICOS-RAMCES (ICOS-RAMCES), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Financial support. This research has been mainly supported by the 4C project of the European Commission’s Horizon 2020 framework programme (grant no. 821003) and to a small extent by VERIFY (grant no. 776810). Florian Kitz, Felix M. Spielmann, and Georg Wohlfahrt were supported by the Austrian Science Fund (FWF) (contract nos. P26931, P27176, P31669, and I03859) and the University of Innsbruck., and The authors thank the reviewers for their insightful and useful comments which helped to improve this study. The authors are very grateful to everyone who participated in field data collection used in this study. We thank Vladislav Bastrikov for providing the ORCHIDAS code. We also acknowledge Nicolas Vuichard for providing the soil bulk density map used in ORCHIDEE simulations. Operation of the US-HA site is supported by the AmeriFlux Management Project with funding by the US Department of Energy’s Office of Science (contract no. DE-AC02- 05CH11231), and additionally it is a part of the Harvard Forest Long Term Ecological Research (LTER) site supported by the National Science Foundation (grant no. DEB-1832210). The field campaign at DK-SOR was supported by the Danish ICOS contribution (ICOS/DK) and by the Independent Research Fund Denmark (grant no. DFF-1323-00182).
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Sulfure de carbonyle, MathematicsofComputing_NUMERICALANALYSIS, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, GeneralLiterature_MISCELLANEOUS, Earth-Surface Processes
Abstract: Carbonyl sulfide (COS) is an atmospheric trace gas of interest for C cycle research because COS uptake by continental vegetation is strongly related to terrestrial gross primary productivity (GPP), the largest and most uncertain flux in atmospheric CO2 budgets. However, to use atmospheric COS as an additional tracer of GPP, an accurate quantification of COS exchange by soils is also needed. At present, the atmospheric COS budget is unbalanced globally, with total COS flux estimates from oxic and anoxic soils that vary between −409 and −89 GgS yr−1. This uncertainty hampers the use of atmospheric COS concentrations to constrain GPP estimates through atmospheric transport inversions. In this study we implemented a mechanistic soil COS model in the ORCHIDEE (Organising Carbon and Hydrology In Dynamic Ecosystems) land surface model to simulate COS fluxes in oxic and anoxic soils. Evaluation of the model against flux measurements at seven sites yields a mean root mean square deviation of 1.6 pmol m−2 s−1, instead of 2 pmol m−2 s−1 when using a previous empirical approach that links soil COS uptake to soil heterotrophic respiration. However, soil COS model evaluation is still limited by the scarcity of observation sites and long-term measurement periods, with all sites located in a latitudinal band between 39 and 62∘ N and no observations during wintertime in this study. The new model predicts that, globally and over the 2009–2016 period, oxic soils act as a net uptake of −126 GgS yr−1 and anoxic soils are a source of +96 GgS yr−1, leading to a global net soil sink of only −30 GgS yr−1, i.e. much smaller than previous estimates. The small magnitude of the soil fluxes suggests that the error in the COS budget is dominated by the much larger fluxes from plants, oceans, and industrial activities. The predicted spatial distribution of soil COS fluxes, with large emissions from oxic (up to 68.2 pmol COS m−2 s−1) and anoxic (up to 36.8 pmol COS m−2 s−1) soils in the tropics, especially in India and in the Sahel region, marginally improves the latitudinal gradient of atmospheric COS concentrations, after transport by the LMDZ (Laboratoire de Météorologie Dynamique) atmospheric transport model. The impact of different soil COS flux representations on the latitudinal gradient of the atmospheric COS concentrations is strongest in the Northern Hemisphere. We also implemented spatiotemporal variations in near-ground atmospheric COS concentrations in the modelling of biospheric COS fluxes, which helped reduce the imbalance of the atmospheric COS budget by lowering soil COS uptake by 10 % and plant COS uptake by 8 % globally (with a revised mean vegetation budget of −576 GgS yr−1 over 2009–2016). Sensitivity analyses highlighted the different parameters to which each soil COS flux model is the most responsive, selected in a parameter optimization framework. Having both vegetation and soil COS fluxes modelled within ORCHIDEE opens the way for using observed ecosystem COS fluxes and larger-scale atmospheric COS mixing ratios to improve the simulated GPP, through data assimilation techniques.
Published: 2022
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171. A two phase escarpment evolution of the Red Sea margin of southwestern Saudi Arabia. Insights from low-temperature apatite thermochronology

Author: Syed Ali Turab, Kurt Stüwe, Finlay M. Stuart, Nathan Cogne, David M. Chew, Jörg Robl, Karl-Franzens-Universität Graz, University of Peshawar (UOP), Scottish Universities Environmental Research Centre (SUERC), University of Glasgow-University of Edinburgh, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Trinity College Dublin, University of Salzburg, Higher Education Commission (HEC) of Pakistan, FWF Project (P22351-N22), Saudi Geological Survey, and Science Foundation Ireland (SFI) under grant numbers 13/RC/2092_P2 and 13/RC/2092_P2 (iCRAG - the SFI Research Centre in Applied Geosciences)
Subjects: Geophysics, escarpment evolution, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Space and Planetary Science, Geochemistry and Petrology, orographic precipitation, Saudi Arabia, geomorphic analysis, Earth and Planetary Sciences (miscellaneous), low-temperature thermochronology, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology
Abstract: International audience; Rifting of the Red Sea resulted in the formation of one of the highest escarpments on our planet: the Great Escarpment of southwestern Saudi Arabia. Published low-temperature geochronology ages are around the Paleogene-Neogene transition, but geomorphic features like the height, the steepness and the preservation of the escarpment may indicate a younger aspect to the exhumation history. Here we use apatite fission track (AFT) and (U-Th-Sm)/He (AHe) cooling ages in combination with a geomorphic analysis of the region from Jeddah to Jizan to test this idea. Pooled AFT ages range from to Ma (1σ). The base of the AFT partial annealing zone prior to rock uplift is at ∼200 m elevation in most of the studied area, but track length data show that the amount of exhumation is insufficient to affect all coastal plain samples. Consistent with earlier estimates in the literature, the total amount of rock uplift is estimated to be ∼4 km. Single grain AHe ages range from to Ma (1σ) and do not have a clear trend with distance from the escarpment. Overall, the distribution of data appears to indicate widespread downwearing of the elevated topography around the rift flank. In contrast, geomorphic analysis that indicates escarpment retreat including a flexural uplift response. We suggest that the conflict between geomorphological and geochronological data can be resolved by invoking a two-stage erosion model. The first stage involved dome-shaped rift flank uplift since initiation of the Afar plume, downwearing of this topography and cooling recorded by the AFT ages. The second stage involved the massive erosion that excavated the present day Saudi escarpment and reset the AHe ages. We suggest that this second stage is related to the formation of oceanic lithosphere since 13 Ma in the Red Sea, associated downwarping of the margin and flexural updoming of the eastern rift flank. The consequential orographic precipitation initiated asymmetric erosion and formation of a retreating escarpment. This model is consistent with the large age difference between Miocene AFT and Pliocene AHe ages and the geomorphic metrics.
Published: 2023
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172. Efficient computation of modal Green's kernels for vectorial equations in helioseismology under spherical symmetry

Author: Barucq, Hélène, Faucher, Florian, Fournier, Damien, Gizon, Laurent, Pham, Ha, Modélisation et simulation de la propagation des ondes fondées sur des mesures expérimentales pour caractériser des milieux géophysiques et héliophysiques et concevoir des objets complexes (MAKUTU), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Polytechnique de Bordeaux (Bordeaux INP), E2S UPPA, Faculty of Mathematics [Vienna], University of Vienna [Vienna], Max Planck Institute for Solar System Research (MPS), Max-Planck-Gesellschaft, Inria -- MPS -- FWF, Inria Bordeaux - Sud Ouest, Associated-team Ants (Advanced Numerical meThods for helioSeismology)., and Max-Planck-Institut für Sonnensystemforschung = Max Planck Institute for Solar System Research (MPS)
Subjects: Galbrun's equation, Vector spherical harmonics, Modal Green's kernels, Hybridizable discontinuous Galerkin method, Helioseismology, Wave equation, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Radiation boundary conditions, [PHYS.ASTR.SR]Physics [physics]/Astrophysics [astro-ph]/Solar and Stellar Astrophysics [astro-ph.SR], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
Abstract: We investigate the numerical computation of physical modal Green's kernels for the time-harmonic Galbrun's equation in helioseismology under spherical symmetry. These kernels are the coefficients of the 3D Green's kernels in the vector spherical harmonic expansion. In a previous work, we have characterized the physical kernels for the isothermal radial solar background model S-AtmoI and provide their well-posedness results. Here, we provide an algorithm to compute efficiently these kernels for all receiver and source positions in a region of interest and develop the technical ingredients for its implementation. The kernels are built from the solution of a scalar wave equation for the radial displacement. The solution and its derivative which are both necessary to assemble the Green's kernel are obtained by solving a first-order system using the HDG method. This approach extends previous works considering a scalar wave equation and allows to model not only the pressure modes but also the surface and internal gravity waves. While being physically more interesting, this problem raises additional numerical difficulties. In particular, the solution of the Schrodinger equation for the radial displacement is singular without attenuation and it is thus preferable to solve the original equation. Moreover, for low frequencies and high-modes, the potential switches sign in the atmosphere which requires the position of the artificial boundary to be further away from the solar surface in order to capture the correct physical solution.; Dans ce travail, nous étudions et calculons les noyaux de Green modaux pour l’équation de Galbrun pour les ondes harmoniques dans un problème d’héliosismologie avec symétrie sphérique. Ces noyaux sont les coefficients des noyaux de Green 3D décomposés en harmoniques sphériques vectorielles. Dans nos travaux précédents, nous avons caractérisé les noyaux physiques pour le milieu solaire isothermal S-AtmoI, en donnant les résultats sur le caractère bien-posé du problème. Dans ce travail, nous définissons un algorithme pour calculer de manière efficace et précise ces noyaux, pour tous les récepteurs et les sources, et développons tous les ingrédients techniques à sa mise en place. Les noyaux sont construits à partir de la solution de l’équation d’onde pour le déplacement radial. Plus précisément, la solution et sa dérivée sont toutes les deux nécessaires pour assembler les noyaux de Green et sont obtenues à partir du système du premier-ordre en utilisant la méthode de discrétisation de Galerkin discontinue hybride. Cette approche étend nos travaux précédents sur l’équation d’onde scalaire, et nous permet de modéliser non seulement les modes acoustiques du soleil, mais également les ondes de gravité de surface et internes. Ce problème vectoriel révèle aussi des difficultés numériques additionnelles. En particulier, la solution de l’équation de Schrödinger pour le déplacement radial est singulière dans le cas sans atténuation, et il est ainsi préférable de résoudre l’équation originale à la place. De plus, à fréquences basses et modes de hauts degrés, le potentiel change de signe dans l’atmosphère, ce qui implique que la condition de radiation pour la troncature du domaine numérique doit être placée bien plus loin que la surface solaire afin d’obtenir la solution correcte.
Published: 2021

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

Author: Johann Valentin Pototschnig, Kenneth G. Dyall, Lucas Visscher, André Severo Pereira Gomes, Theoretical Chemistry, AIMMS, Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Dirac Solutions, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), French Ministry of Higher Education and Research, Austrian Science Fund(FWF):J 4177- N36, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, French national supercomputing facilities (grants DARI A0070801859 and A0090801859), MESONM International Associated Laboratory (LAI) (ANR-16-IDEX-0004)., ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-16-IDEX-0004,ULNE,ULNE(2016), Vrije Universiteit Amsterdam [Amsterdam] (VU), and VU University Amsterdam
Subjects: General Physics and Astronomy, FOS: Physical sciences, Electron, Electronic structure, 01 natural sciences, Fock space, symbols.namesake, Physics - Chemical Physics, 0103 physical sciences, SDG 7 - Affordable and Clean Energy, Physical and Theoretical Chemistry, 010306 general physics, Physics, Chemical Physics (physics.chem-ph), 010304 chemical physics, Configuration interaction, 3. Good health, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Dipole, Chemistry, Coupled cluster, Excited state, symbols, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Atomic physics, Hamiltonian (quantum mechanics)
Abstract: We report an investigation of the low-lying excited states of the YbF molecule--a candidate molecule for experimental measurements of the electron electric dipole moment--with 2-component based multi-reference configuration interaction (MRCI), equation of motion coupled cluster (EOM-CCSD) and the extrapolated intermediate Hamiltonian Fock-space coupled cluster (XIHFS-CCSD). Specifically, we address the question of the nature of these low-lying states in terms of configurations containing filled or partially-filled Yb $4f$ shells. We show that while it does not appear possible to carry out calculations with both kinds of configurations contained in the same active space, reliable information can be extracted from different sectors of Fock space--that is, by performing electron attachment and detachment IHFS-CCSD and EOM-CCSD calculation on the closed-shell YbF$^+$ and YbF$^-$ species, respectively. From these we observe $\Omega = 1/2, 3/2$ states that arise from the $4f^{13}\sigma_{6s}^2$, $4f^{14}5d$/$6p$, and $4f^{13}5d\sigma_{6s}$ configurations appear in the same energy range around the ground-state equilibrium geometry and they are therefore able to interact. As these states are generated from different sectors of Fock space, they are almost orthogonal and provide complementary descriptions of parts of the excited state manifold. To obtain a comprehensive picture, we introduce a simple adiabatization model to extract energies of interacting $\Omega = 1/2, 3/2$ states that can be compared to experimental observations., Comment: 28+57 pages, 8+18 tables, 5+34 figures
Published: 2021
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174. In-Situ Transmission Electron Microscopy Imaging of Aluminum Diffusion in Germanium Nanowires for the Fabrication of Sub-10 nm Ge Quantum Disks

Author: Alois Lugstein, Masiar Sistani, Pascal Gentile, Minh Anh Luong, Eric Robin, B. Fernandez, M. den Hertog, N. Pauc, Maria Spies, Laboratoire d'Etude des Matériaux par Microscopie Avancée (LEMMA ), Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Silicon Nanoelectronics Photonics and Structures (SiNaps), PHotonique, ELectronique et Ingénierie QuantiqueS (PHELIQS), Institute of Applied Physics [Vienna] (TU Wien), Vienna University of Technology (TU Wien), Matériaux, Rayonnements, Structure (NEEL - MRS), Institut Néel (NEEL), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Nanofabrication (NEEL - Nanofab), Austrian Science Fund (FWF): project no. P28175-N27, ANR-10-LABX-0051,LANEF,Laboratory of Alliances on Nanosciences - Energy for the Future(2010), and European Project: 758385,e-See - H2020-EU.1.1.
Subjects: In situ, Materials science, in-situ transmission electron microscopy, Nanowire, chemistry.chemical_element, Germanium, 02 engineering and technology, rapid thermal annealing, 01 natural sciences, 7. Clean energy, Condensed Matter::Materials Science, Aluminium, 0103 physical sciences, Thermal, General Materials Science, solid state exchanged reaction, Nuclear Experiment, 010302 applied physics, business.industry, Heterojunction, Condensed Matter::Mesoscopic Systems and Quantum Hall Effect, 021001 nanoscience & nanotechnology, Atomic diffusion, chemistry, Quantum dot, aluminum, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Optoelectronics, 0210 nano-technology, business
Abstract: International audience; The thermal activated solid state reaction forming aluminum–germanium nanowire (NW) heterostructures is a promising system as very sharp and well-defined one-dimensional contacts can be created between a metal and a semiconductor, that can become a quantum dot if the size becomes sufficiently small. In the search for high performance devices without variability, it is of high interest to allow deterministic fabrication of nanowire quantum dots, avoiding sample variability and obtaining atomic scale precision on the fabricated dot size. In this paper, we present a proof of principle experiment to produce sub-10 nm Ge quantum disks (QDs), using a combination of ex-situ thermal annealing via rapid thermal annealing (RTA) and in-situ Joule heating technique in a transmission electron microscope (TEM). First we present in-situ direct joule heating experiments showing how the heating electrode could be damaged due to the formation of Al crystals and voids at the vicinity of the metal/NW contact, likely related with electro-migration phenomena. We show that the contact quality can be preserved by including an additional ex-situ RTA step prior to the in-situ heating. The in-situ observations also show in real-time how the exchange reaction initiates simultaneously from several locations underneath the Al contact pad, and the Al crystal grows gradually inside the initial Ge NW with the growth interface along a Ge {111} lattice plane. Once the reaction front moves out from underneath the contact metal, two factors jeopardize an atomically accurate control of the Al/Ge reaction interface. We observed a local acceleration of the reaction interface due to the electron beam irradiation in the transmission electron microscope as well as the appearance of large jumps of the interface in unpassivated Ge wires, whereas a smooth advancement of the reaction interface was observed in wires with an Al$_2$O$_3$ passivation shell on the surface. Carefully controlling all aspects of the exchange reaction, we demonstrate a proof of principle experiment combining ex-situ and in-situ heating techniques to precisely control and produce axial Al/Ge/Al NW heterostructures with an ultrashort Ge segment down to 7 nm. Practically, the scaling down of the Ge segment length is only limited by the microscope resolution.
Published: 2020
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175. Data-driven estimates of global nitrous oxide emissions from croplands

Author: Francesco N. Tubiello, Qihui Wang, Feng Zhou, Shilong Piao, Robert B. Jackson, Philippe Ciais, Wilfried Winiwarter, Greet Janssens-Maenhout, Josep G. Canadell, Ziyin Shang, Xiaoqing Cui, Hanqin Tian, Shu Tao, Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University [Beijing], Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ICOS-ATC (ICOS-ATC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), International Institute for Applied Systems Analysis [Laxenburg] (IIASA), University of Zielona Góra, Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), European Commission - Joint Research Centre [Ispra] (JRC), Auburn University (AU), Global Carbon Project (GCP), CSIRO Marine and Atmospheric Research (CSIRO-MAR), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), the National Natural Science Foundation of China (41671464, 7181101181), the National Key Research and Development Program of China (2016YFD0800501, 2018YFC0213304) and the 111 Project (B14001), the Austrian Science Fund (FWF) (P 29130-G27), ANR-16-CONV-0003,CLAND,CLAND : Changement climatique et usage des terres(2016), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: emission factor, 010504 meteorology & atmospheric sciences, AcademicSubjects/SCI00010, temporal trend, Climate change, 010501 environmental sciences, Atmospheric sciences, Spatial distribution, 01 natural sciences, chemistry.chemical_compound, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Multidisciplinary, nitrous oxide, flux upscaling, Nitrous oxide, emission inventories, Tier 1 network, chemistry, 13. Climate action, Earth Sciences, Environmental science, agricultural soils, AcademicSubjects/MED00010, Research Article
Abstract: Croplands are the single largest anthropogenic source of nitrous oxide (N2O) globally, yet their estimates remain difficult to verify when using Tier 1 and 3 methods of the Intergovernmental Panel on Climate Change (IPCC). Here, we re-evaluate global cropland-N2O emissions in 1961–2014, using N-rate-dependent emission factors (EFs) upscaled from 1206 field observations in 180 global distributed sites and high-resolution N inputs disaggregated from sub-national surveys covering 15593 administrative units. Our results confirm IPCC Tier 1 default EFs for upland crops in 1990–2014, but give a ∼15% lower EF in 1961–1989 and a ∼67% larger EF for paddy rice over the full period. Associated emissions (0.82 ± 0.34 Tg N yr–1) are probably one-quarter lower than IPCC Tier 1 global inventories but close to Tier 3 estimates. The use of survey-based gridded N-input data contributes 58% of this emission reduction, the rest being explained by the use of observation-based non-linear EFs. We conclude that upscaling N2O emissions from site-level observations to global croplands provides a new benchmark for constraining IPCC Tier 1 and 3 methods. The detailed spatial distribution of emission data is expected to inform advancement towards more realistic and effective mitigation pathways.
Published: 2019
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176. The metabolomic signature of extreme longevity: naked mole rats versus mice

Author: Frank Madeo, Sylvère Durand, Deborah Lefevre, Mélanie Viltard, Christine Leroy, Maria Perez-Lanzon, Guido Kroemer, Gérard Friedlander, Fanny Aprahamian, Gestionnaire, Hal Sorbonne Université, Fondation pour la Recherche en Physiologie [Brussels, Belgium], Institut Gustave Roussy (IGR), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Université Paris Cité (UPCité), Université Paris-Saclay, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Karl-Franzens-Universität Graz, Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), University of Science & Technology of China [Suzhou], Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], Plateforme de métabolomique, Direction de la recherche [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), GK is supported by the Ligue contre le Cancer (équipe labellisée), Agence National de la Recherche (ANR) – Projets blancs, ANR under the frame of E-Rare-2, the ERA-Net for Research on Rare Diseases, Association pour la Recherche sur le Cancer (ARC), Cancéropôle Ile-de-France, Chancelerie des universités de Paris (Legs Poix), Fondation pour la Recherche Médicale (FRM), a donation by Elior, European Research Area Network on Cardiovascular Diseases (ERA-CVD, MINOTAUR), Gustave Roussy Odyssea, the European Union Horizon 2020 Project Oncobiome, Fondation Carrefour, High-end Foreign Expert Program in China (GDW20171100085 and GDW20181100051), Institut National du Cancer (INCa), Inserm (HTE), Institut Universitaire de France, LeDucq Foundation, the LabEx Immuno-Oncology (ANR-18-IDEX-0001), the RHU Torino Lumière, the Seerave Foundation, the SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE), and the SIRIC Cancer Research and Personalized Medicine (CARPEM). F.M. is grateful to the Austrian Science Fund FWF (SFB LIPOTOX F3007 & F3012, W1226, P29203, P29262, P27893, P 31727 and the Austrian Federal Ministry of Education, Science and Research and the University of Graz for grants 'Unkonventionelle Forschung-InterFast' and 'flysleep' (BMWFW 80.109/0001-WF/V/3b/2015) as well as the field of excellence program BioHealth. We acknowledge support from NAWI Graz and the BioTechMed-Graz flagship project 'EPIAge'. M.V. is grateful to the Ecole Nationale Vétérinaire d’Alfort (EnvA) and the Association De Prévoyance Santé (ADPS) partners of Allianz, for their invaluable help in establishing and funding the animal facility. M.P.L. is supported by Fondation pour la Recherche Médicale (FRM FDT201904008383)., Université de Paris (UP), and Karl-Franzens-Universität [Graz, Autriche]
Subjects: autophagy, Aging, Rodent, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], medicine.medical_treatment, media_common.quotation_subject, Longevity, 03 medical and health sciences, chemistry.chemical_compound, Mice, 0302 clinical medicine, Metabolomics, Species Specificity, biology.animal, spermidine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], medicine, Metabolome, microbiota, Animals, 030304 developmental biology, media_common, meta-organism, 0303 health sciences, biology, Vitamin E, Mole Rats, catabolism, Laboratory mouse, Cell Biology, Rats, Spermidine, Metabolic pathway, antioxidants, Biochemistry, chemistry, 030220 oncology & carcinogenesis, Priority Research Paper
Abstract: International audience; The naked mole-rat (Heterocephalus glaber) is characterized by a more than tenfold higher life expectancy compared to another rodent species of the same size, namely, the laboratory mouse (Mus musculus). We used mass spectrometric metabolomics to analyze circulating plasma metabolites in both species at different ages. Interspecies differences were much more pronounced than age-associated alterations in the metabolome. Such interspecies divergences affected multiple metabolic pathways involving amino, bile and fatty acids as well as monosaccharides and nucleotides. The most intriguing metabolites were those that had previously been linked to pro-health and antiaging effects in mice and that were significantly increased in the long-lived rodent compared to its short-lived counterpart. This pattern applies to α-tocopherol (also known as vitamin E) and polyamines (in particular cadaverine, N8-acetylspermidine and N1,N8-diacetylspermidine), all of which were more abundant in naked mole-rats than in mice. Moreover, the age-associated decline in spermidine and N1-acetylspermidine levels observed in mice did not occur, or is even reversed (in the case of N1-acetylspermidine) in naked mole-rats. In short, the present metabolomics analysis provides a series of testable hypotheses to explain the exceptional longevity of naked mole-rats.
Published: 2019
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177. Multidomain spectral method for the Gauss hypergeometric function

Author: Marco Fasondini, Nikola Stoilov, Christian Klein, Siegfried Crespo, Corentin Vallée, Institut de Mathématiques de Bourgogne [Dijon] (IMB), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB), University of Kent [Canterbury], Vision, Action et Gestion d'informations en Santé (VisAGeS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), université de Bourgogne, IMB, Approches analytiques, numériques et des systèmes intégrables pour les équations aux dérivées partielles dispersives nonlinéaires - - ANuI2017 - ANR-17-CE40-0035 - AAPG2017 - VALID, Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Institute of Mathematics (University of Kent), Neuroimagerie: méthodes et applications (Empenn), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), This work was partially supported by the PARI and FEDER programs in 2016 and 2017, by the ANR-FWF project ANuI by the isite BFC via the project NAANoD and by the Marie-Curie RISE network IPaDEGAN. M. Fasondini acknowledges financial support from the EPSRC grant EP/P026532/1., ANR-17-CE40-0035,ANuI,Approches analytiques, numériques et des systèmes intégrables pour les équations aux dérivées partielles dispersives nonlinéaires(2017), Vallée, Corentin, Empenn, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: Singular differential equations, Mathematics::Classical Analysis and ODEs, Riemann sphere, [MATH] Mathematics [math], 010103 numerical & computational mathematics, 01 natural sciences, symbols.namesake, FOS: Mathematics, Hypergeometric function, Mathematics - Numerical Analysis, [MATH]Mathematics [math], 0101 mathematics, QA, Mathematics, Laplace's equation, Applied Mathematics, Riemann surface, Mathematical analysis, Numerical Analysis (math.NA), [MATH.MATH-NA] Mathematics [math]/Numerical Analysis [math.NA], Hypergeometric distribution, 010101 applied mathematics, Spectral methods, Harmonic function, Ordinary differential equation, symbols, Spectral method, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract: International audience; We present a multidomain spectral approach for Fuchsian ordinary differential equations in the particular case of the hypergeometric equation. Our hybrid approach uses Frobenius’ method and Moebius transformations in the vicinity of each of the singular points of the hypergeometric equation, which leads to a natural decomposition of the real axis into domains. In each domain, solutions to the hypergeometric equation are constructed via the well-conditioned ultraspherical spectral method. The solutions are matched at the domain boundaries to lead to a solution which is analytic on the whole compactified real line R∪∞, except for the singular points and cuts of the Riemann surface on which the solution is defined. The solution is further extended to the whole Riemann sphere by using the same approach for ellipses enclosing the singularities. The hypergeometric equation is solved on the ellipses with the boundary data from the real axis. This solution is continued as a harmonic function to the interior of the disk by solving the Laplace equation in polar coordinates with an optimal complexity Fourier–ultraspherical spectral method. In cases where logarithms appear in the solution, a hybrid approach involving an analytical treatment of the logarithmic terms is applied. We show for several examples that machine precision can be reached for a wide class of parameters, but also discuss almost degenerate cases where this is not possible.
Published: 2019
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178. Molecular analysis indicates high levels of carabid weed seed consumption in cereal fields across Central Europe

Author: Frei, Britta, Guenay, Yasemin, Bohan, David A., Traugott, Michael, Wallinger, Corinna, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, University of Innsbruck, Austrian Academy of Sciences (OeAW), and Austrian Science Fund FWF [P28578-B25]
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, food and beverages, Pest regulation, Carabidae, Granivory, Seed predation, Rapid Communication
Abstract: International audience; Carabid beetles are abundant in temperate agroecosystems and can play a pivotal role as biocontrol agents. While there is good knowledge regarding their effects on invertebrate pests in some systems, comparably little is known on the rate of seed feeding under field conditions. Molecular approaches are ideally suited for investigating carabid feeding interactions; to date, however, they have only been applied to animal prey. We sampled adult carabid beetles in organic cereal fields in three regions along a Central European transect. Regurgitates from populations of the three most common species, Poecilus cupreus, Pseudoophonus rufipes and Pterostichus melanarius, were screened for plant DNA, cereal aphids, collembolans and earthworms. The frequency of carabid individuals positive for plant DNA was high (>70%) and independent of carabid species, sex, region and the time point of sampling. Detections for non-pest and pest prey were comparably lower, with 21.6% for collembolans, 18.1% for earthworms and 4.2% for aphids, respectively. Despite the prolonged detection period of plant DNA in carabid guts, as compared to animal prey, these first results suggest that weed seeds form an important part of the adult carabid diet. It would also lend support to the hypothesis that seed-feeding carabids are biocontrol agents of weeds, with effects of regulation on the weed seedbank that depend on behavioural and contextual factors including carabid species preferences for weed seed species, their life stage and tillage practices.
Published: 2019
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179. Buoyancy versus shear forces in building orogenic wedges

Author: Lorenzo G. Candioti, Thibault Duretz, Evangelos Moulas, Stefan M. Schmalholz, Institut des sciences de la terre [Lausanne] (ISTE), Université de Lausanne (UNIL), Géosciences Rennes (GR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Johannes Gutenberg - Universität Mainz (JGU), Austrian Science Fund (FWF) (grant 200020 163169), Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU)
Subjects: [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, Paleontology, Stratigraphy, Earth-Surface Processes, Geochemistry and Petrology, Geology, Geophysics, Soil Science
Abstract: The dynamics of growing collisional orogens are mainly controlled by buoyancy and shear forces. However, the relative importance of these forces, their temporal evolution and their impact on the tectonic style of orogenic wedges remain elusive. Here, we quantify buoyancy and shear forces during collisional orogeny and investigate their impact on orogenic wedge formation and exhumation of crustal rocks. We leverage two-dimensional petrological–thermomechanical numerical simulations of a long-term (ca. 170 Myr) lithosphere deformation cycle involving subsequent hyperextension, cooling, convergence, subduction and collision. Hyperextension generates a basin with exhumed continental mantle bounded by asymmetric passive margins. Before convergence, we replace the top few kilometres of the exhumed mantle with serpentinite to investigate its role during subduction and collision. We study the impact of three parameters: (1) shear resistance, or strength, of serpentinites, controlling the strength of the evolving subduction interface; (2) strength of the continental upper crust; and (3) density structure of the subducted material. Densities are determined by linearized equations of state or by petrological-phase equilibria calculations. The three parameters control the evolution of the ratio of upward-directed buoyancy force to horizontal driving force, FB/FD=ArF, which controls the mode of orogenic wedge formation: ArF≈0.5 causes thrust-sheet-dominated wedges, ArF≈0.75 causes minor wedge formation due to relamination of subducted crust below the upper plate, and ArF≈1 causes buoyancy-flow- or diapir-dominated wedges involving exhumation of crustal material from great depth (>80 km). Furthermore, employing phase equilibria density models reduces the average topography of wedges by several kilometres. We suggest that during the formation of the Pyrenees ArF⪅0.5 due to the absence of high-grade metamorphic rocks, whereas for the Alps ArF≈1 during exhumation of high-grade rocks and ArF⪅0.5 during the post-collisional stage. In the models, FD increases during wedge growth and subduction and eventually reaches magnitudes (≈18 TN m−1) which are required to initiate subduction. Such an increase in the horizontal force, required to continue driving subduction, might have “choked” the subduction of the European plate below the Adriatic one between 35 and 25 Ma and could have caused the reorganization of plate motion and subduction initiation of the Adriatic plate.
Published: 2021
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180. Implementation of relativistic coupled cluster theory for massively parallel GPU-accelerated computing architectures

Author: Loïc Halbert, Michal Repisky, Hans Jørgen Aa. Jensen, Lucas Visscher, Anastasios Papadopoulos, Dmitry I. Lyakh, André Severo Pereira Gomes, Johann V. Pototschnig, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam [Amsterdam] (VU), National Center for Computational Sciences, Oak Ridge National Laboratory, Hylleraas Centre for Quantum Molecular Sciences (Hylleraas), Department of Chemistry [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark, Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under ContractDE-AC05-00OR22725, French Ministry of Higher Education and Research, region Hauts de France council and European Regional Development Fund (ERDF) project CPER CLIMIBIO, French national supercomputing facilities (grants DARI A0070801859 and Joliot Curie grands challenges 2019 gch0417)., MESONM International Associated Laboratory (LAI) (ANR-16-IDEX-0004), Austrian Science Fund(FWF):J 4177-N36, Research Council of Norway through a Center of Excellence Grant (Grant No. 262695), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-16-IDEX-0004,ULNE,ULNE(2016), University of Southern Denmark (SDU), Theoretical Chemistry, and AIMMS
Subjects: Computer science, Dirac (software), FOS: Physical sciences, 010402 general chemistry, 01 natural sciences, Article, Field (computer science), Computational science, Set (abstract data type), Software, Physics - Chemical Physics, 0103 physical sciences, Point (geometry), SDG 7 - Affordable and Clean Energy, Physical and Theoretical Chemistry, Massively parallel, Chemical Physics (physics.chem-ph), 010304 chemical physics, business.industry, 0104 chemical sciences, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Coupled cluster, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Relativistic quantum chemistry, business
Abstract: International audience; In this paper, we report a reimplementation of the core algorithms of relativistic coupled cluster theory aimed at modern heterogeneous high-performance computational infrastructures. The code is designed for efficient parallel execution on many compute nodes with optional GPU coprocessing, accomplished via the new ExaTENSOR back end. The resulting ExaCorr module is primarily intended for calculations of molecules with one or more heavy elements, as relativistic effects on electronic structure are included from the outset. In the current work, we thereby focus on exact 2-component methods and demonstrate the accuracy and performance of the software. The module can be used as a stand-alone program requiring a set of molecular orbital coefficients as starting point, but is also interfaced to the DIRAC program that can be used to generate these. We therefore also briefly discuss an improvement of the parallel computing aspects of the relativistic self-consistent field algorithm of the DIRAC program.
Published: 2021
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181. Perceiving neighbors to anticipate the struggle for light

Author: Guillaume Charrier, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Austrian Science Fund (FWF)Pack Ambition Recherche program 'Doux-Glace' from the Auvergne-Rhone Alpes region, and ANR-20-CE91-0008,ACOUFOLLOW,ANALYSES DU DYSFONCTIONNEMENT ET DE LA REPARATION DU XYLÈME INDUIT PAR LE GEL CHEZ LES ARBUSTES, LES CONIFÈRES ET LES ARBRES À FEUILLES CADUQUES :(2020)
Subjects: 0106 biological sciences, Physiology, Plant Development, Plant Science, Plant, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 010603 evolutionary biology, 01 natural sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Genetics, Environmental science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Photosynthesis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, light, News and Views, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract: International audience
Published: 2021
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182. Multiplicative chaos of the Brownian loop soup

Author: Aïdekon, Elie, Berestycki, Nathanaël, Jego, Antoine, Lupu, Titus, Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Sorbonne Université (SU), University of Vienna [Vienna], University of Cambridge [UK] (CAM), Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Mathématiques et de leurs Interactions (INSMI), DOC Fellowship of the Austrian Academy of Sciences at the Faculty of Mathematics of the University of Vienna, EPSRC grant EP/L016516/1 for the University of Cambridge Centre for Doctoral Training, the Cambridge Centre for Analysis, University of Vienna start-up grant, FWF grant P33083 on 'Scaling limits in random conformal geometry', and ANR-16-CE93-0003,MALIN,Marches aléatoires en interaction(2016)
Subjects: convergence, Thick points, MSC2020: 60G15, 60G55, 60J55, 60J65, 81T27, General Mathematics, Probability (math.PR), FOS: Physical sciences, Mathematical Physics (math-ph), Brownian multiplicative chaos, field, Brownian loop soup, Gaussian multiplicative chaos, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], local time, motion, FOS: Mathematics, Mathematics - Probability, Mathematical Physics, Gaussian free field, Isomorphism theorems
Abstract: We construct a measure on the thick points of a Brownian loop soup in a bounded domain D of the plane with given intensity $\theta>0$, which is formally obtained by exponentiating the square root of its occupation field. The measure is constructed via a regularisation procedure, in which loops are killed at a fix rate, allowing us to make use of the Brownian multiplicative chaos measures previously considered in [BBK94, AHS20, Jeg20a], or via a discrete loop soup approximation. At the critical intensity $\theta = 1/2$, it is shown that this measure coincides with the hyperbolic cosine of the Gaussian free field, which is closely related to Liouville measure. This allows us to draw several conclusions which elucidate connections between Brownian multiplicative chaos, Gaussian free field and Liouville measure. For instance, it is shown that Liouville-typical points are of infinite loop multiplicity, with the relative contribution of each loop to the overall thickness of the point being described by the Poisson--Dirichlet distribution with parameter $\theta = 1/2$. Conversely, the Brownian chaos associated to each loop describes its microscopic contribution to Liouville measure. Along the way, our proof reveals a surprising exact integrability of the multiplicative chaos associated to a killed Brownian loop soup. We also obtain some estimates on the discrete and continuous loop soups which may be of independent interest., Comment: 107 pages, 3 figures; to appear in Proceedings of the London Mathematical Society
Published: 2021

183. Using electrical resistivity tomography to detect wetwood and estimate moisture content in silver fir (Abies alba Mill.)

Author: L. Martin, Stefan Mayr, Eric Badel, Hervé Cochard, Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Leopold Franzens Universität Innsbruck - University of Innsbruck, Austrian Science Fund (FWF)P32203, European Project: ERDF, and University of Innsbruck
Subjects: Moisture content, 040101 forestry, 0106 biological sciences, Ecology, biology, Forestry, Soil science, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, 01 natural sciences, Wetwood, Abies alba, Electrical resistivity and conductivity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 0401 agriculture, forestry, and fisheries, Environmental science, Electrical resistivity tomography, Nondestructive testing, Water content, 010606 plant biology & botany
Abstract: International audience; Key message: Using several experimental approaches, we have demonstrated that electrical resistivity tomography (ERT) is a reliable nondestructive tool for estimating the moisture content of heartwood in situ. ERT measurements show that water pockets in heartwood (wetwood) are present in a large majority (90%) of silver fir (Abies alba Mill.) trunks. Context: For wood professionals, the presence of wetwood in wood logs leads to an increase in costs, especially during the drying process. Assessing these internal properties in situ with a nondestructive method will provide reliable information for improved management of respective forests. Aims: The objective of this study was to evaluate the efficiency of the electrical resistivity tomography (ERT) tool to detect wetwood in standing trees and to estimate the mean moisture content (MC) of silver fir trunks. Methods: The study was carried out in 3 forests located in the region "Massif Central" in France. We selected 58 silver fir trees, visually healthy and without visible default. Each tree has been subject to regular ERT measurements for more than a year. At the same time, one to three cores were taken from each tree in order to measure the actual MC of the wood. Results: 90% of the silver fir trees showed the presence of wetwood in their heartwood. Our results showed a significant correlation between the mean heartwood MC measured on cores and the mean electrical resistivity (ER) obtained with ERT. Conclusion: (i) The presence of wetwood occurs in a high proportion of the silver fir trees studied, and (ii) ERT can be used to estimate the average MC of the heartwood of standing trees. However, the data provided by ERT vary seasonally and do not allow the precise location of wetwood.
Published: 2021
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184. On FGLM Algorithms with Tate Algebras

Author: Xavier Caruso, Tristan Vaccon, Thibaut Verron, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Lithe and fast algorithmic number theory (LFANT), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Johannes Kepler Universität Linz (JKU), This work was supported by the ANR project CLap–CLap (ANR-18-CE40-0026-01). T. Verron was supported by the Austrian FWF grant P31571-N32., Frédéric Chyzak, George Labahn and Marc Mezzarobba, ANR-18-CE40-0026,CLap-CLap,Correspondance de Langlands p-adique : une approche constructive et algorithmique(2018), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), and Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest
Subjects: Computer Science - Symbolic Computation, FOS: Computer and information sciences, Polynomial, GeneralLiterature_INTRODUCTORYANDSURVEY, Formalism (philosophy), Mathematics::Number Theory, p-adic precision, Context (language use), 0102 computer and information sciences, Algebraic geometry, Symbolic Computation (cs.SC), 01 natural sciences, Gröbner basis, Analytic geometry, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, Convergence (routing), 0101 mathematics, Tate algebra, Mathematics, [INFO.INFO-SC]Computer Science [cs]/Symbolic Computation [cs.SC], 010102 general mathematics, FGLM algorithm, 010201 computation theory & mathematics, Gröbner bases, Signature (topology), Algorithm, Algorithms
Abstract: International audience; Tate introduced in [Ta71] the notion of Tate algebras to serve, in the context of analytic geometry over the-adics, as a counterpart of polynomial algebras in classical algebraic geometry. In [CVV19, CVV20] the formalism of Gröbner bases over Tate algebras has been introduced and advanced signature-based algorithms have been proposed. In the present article, we extend the FGLM algorithm of [FGLM93] to Tate algebras. Beyond allowing for fast change of ordering, this strategy has two other important benefits. First, it provides an efficient algorithm for changing the radii of convergence which, in particular, makes effective the bridge between the polynomial setting and the Tate setting and may help in speeding up the computation of Gröbner basis over Tate algebras. Second, it gives the foundations for designing a fast algorithm for interreduction, which could serve as basic primitive in our previous algorithms and accelerate them significantly.
Published: 2021
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185. Existence of traveling wave solutions for the Diffusion Poisson Coupled Model: a computer-assisted proof

Author: Maxime Breden, Antoine Zurek, Claire Chainais-Hillairet, Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Reliable numerical approximations of dissipative systems (RAPSODI ), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Institute for Analysis and Scientific Computing [Wien], Vienna University of Technology (TU Wien), Maxime Breden and Claire Chainais-Hillairet have been supported by the program NEEDS, via the project POCO., Antoine Zurek has been partially supported by the Austrian Science Fund (FWF), grants P30000, P33010, F65, and W1245, and by the multilateralproject of the Austrian Agency for International Co-operation in Education and Research (OeAD), grant MULT 11/2020., Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Technical University of Vienna [Vienna] (TU WIEN)
Subjects: Surface (mathematics), 010103 numerical & computational mathematics, 01 natural sciences, Domain (mathematical analysis), Computer-assisted proof, Position (vector), spectral methods, 35C07, 35Q92, 47H10, 65G20, 65N35, Free boundary problem, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], corrosion model, 0101 mathematics, Diffusion (business), Mathematics, Numerical Analysis, Applied Mathematics, 010102 general mathematics, Mathematical analysis, Rigorous numerics, Computational Mathematics, Modeling and Simulation, fixed-point argument, traveling wave solutions, Poisson's equation, Spectral method, Analysis, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], [MATH.MATH-SP]Mathematics [math]/Spectral Theory [math.SP]
Abstract: International audience; The Diffusion Poisson Coupled Model describes the evolution of a dense oxide layer appearing at the surface of carbon steel canisters in contact with a claystone formation. This model is a one dimensional free boundary problem involving drift-diffusion equations on the density of species (electrons, ferric cations and oxygen vacancies), coupled with a Poisson equation on the electrostatic potential and with moving boundary equations, which describe the evolution of the position of each unknown interfaces of the spatial domain. Numerical simulations suggest the existence of traveling wave solutions for this model. These solutions are defined by stationary profiles on a fixed size domain with interfaces moving both at the same velocity. In this paper, we present and apply a computer-assisted method in order to prove the existence of these traveling wave solutions. We also establish a precise and certified description of the solutions.
Published: 2021
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186. Separation of the Ca V 1.2‐Ca V 1.3 calcium channel duo prevents type 2 allergic airway inflammation

Author: Joerg Striessnig, Marion Mars, Brice Ronsin, Magali Savignac, Marc Moreau, Jean-Charles Guéry, Lucette Pelletier, Marine Michelet, Nicolas Giang, Antoine Magnan, Geoffrey G. Murphy, José E. Mejía, Grégory Bouchaud, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan (CPTP), Centre de biologie du développement (CBD), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du thorax, Université de Nantes (UN)-IFR26-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Toulouse, Hôpital des Enfants, Unité de Gastroentérologie, Hépatologie et Nutrition, Département de Pédiatrie, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Eastern Michigan University, Universität Innsbruck [Innsbruck], Leopold Franzens Universität Innsbruck - University of Innsbruck, Austrian Science Fund (FWF) : P27809, Foundation for Medical Research : DEQ20180339187, and French Society of Allergology : A11013BS.
Subjects: Calcium metabolism, Th2 lymphocytes, Voltage-dependent calcium channel, Calcium channel, T cell, Immunology, chemistry.chemical_element, Tyrosine phosphorylation, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Calcium, asthma, Ca(v)1, cytokines, Cell biology, chemistry.chemical_compound, Calcium imaging, medicine.anatomical_structure, chemistry, Transcription (biology), calcium channels, cardiovascular system, medicine, Immunology and Allergy, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, signaling
Abstract: International audience; Background Voltage-gated calcium (Ca(v)1) channels contribute to T-lymphocyte activation. Ca(v)1.2 and Ca(v)1.3 channels are expressed in Th2 cells but their respective roles are unknown, which is investigated herein. Methods We generated mice deleted for Ca(v)1.2 in T cells or Ca(v)1.3 and analyzed TCR-driven signaling. In this line, we developed original fast calcium imaging to measure early elementary calcium events (ECE). We also tested the impact of Ca(v)1.2 or Ca(v)1.3 deletion in models of type 2 airway inflammation. Finally, we checked whether the expression of both Ca(v)1.2 and Ca(v)1.3 in T cells from asthmatic children correlates with Th2-cytokine expression. Results We demonstrated non-redundant and synergistic functions of Ca(v)1.2 and Ca(v)1.3 in Th2 cells. Indeed, the deficiency of only one channel in Th2 cells triggers TCR-driven hyporesponsiveness with weakened tyrosine phosphorylation profile, a strong decrease in initial ECE and subsequent reduction in the global calcium response. Moreover, Ca(v)1.3 has a particular role in calcium homeostasis. In accordance with the singular roles of Ca(v)1.2 and Ca(v)1.3 in Th2 cells, deficiency in either one of these channels was sufficient to inhibit cardinal features of type 2 airway inflammation. Furthermore, Ca(v)1.2 and Ca(v)1.3 must be co-expressed within the same CD4(+) T cell to trigger allergic airway inflammation. Accordingly with the concerted roles of Ca(v)1.2 and Ca(v)1.3, the expression of both channels by activated CD4(+) T cells from asthmatic children was associated with increased Th2-cytokine transcription. Conclusions Thus, Ca(v)1.2 and Ca(v)1.3 act as a duo, and targeting only one of these channels would be efficient in allergy treatment.
Published: 2021
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187. Correlated electronic structure and optical response of rare-earth based semiconductors

Author: Leonid Pourovskii, Silke Biermann, Alain Demourgues, James Boust, Anna Galler, Institute of Solid State Physics, Technical University of Vienna (TUW), Vienna University of Technology (TU Wien), Centre de Physique Théorique [Palaiseau] (CPHT), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Mathematical Physics [Lund], Lund University [Lund], European Theoretical Spectroscopy Facility, Chaire Physique de la matière condensée (A. Georges), Collège de France (CdF (institution)), and This work was supported by the Austrian Science Fund (FWF), Schrödinger fellowship J-4267, the European Research Council (Project No. 617196 CORRELMAT) and IDRIS-GENCI Orsay under Project No. t2020091393. We thank the computer team at CPHT for support.
Subjects: Physics, Condensed Matter - Materials Science, Valence (chemistry), Strongly Correlated Electrons (cond-mat.str-el), Condensed matter physics, Band gap, business.industry, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, [CHIM.MATE]Chemical Sciences/Material chemistry, 02 engineering and technology, Electronic structure, 021001 nanoscience & nanotechnology, Thermal conduction, 01 natural sciences, Optical conductivity, Condensed Matter - Strongly Correlated Electrons, Semiconductor, Absorption edge, 0103 physical sciences, 010306 general physics, 0210 nano-technology, Anisotropy, business
Abstract: The coexistence of Mott localized $f$ states with wide conduction and valence bands in $f$-electron semiconductors results, quite generically, in a complex optical response with the nature of the absorption edge difficult to resolve both experimentally and theoretically. Here, we combine a dynamical mean-field theory approach to localized $4f$ shells with an improved description of band gaps by a semilocal exchange-correlation potential to calculate the optical properties of the light rare-earth fluorosulfides $Ln\mathrm{SF}$ ($Ln=\mathrm{Pr}$, Nd, Sm, Gd) from first principles. In agreement with experiment, we find the absorption edge in SmSF to stem from $\mathrm{S}\text{\ensuremath{-}}3p$ to $\mathrm{Sm}\text{\ensuremath{-}}4f$ transitions, while the Gd compound behaves as an ordinary $p\text{\ensuremath{-}}d$ gap semiconductor. In the unexplored PrSF and NdSF systems we predict a rather unique occurrence of strongly hybridized $4f\text{\ensuremath{-}}5d$ states at the bottom of the conduction band. The nature of the absorption edge results in a characteristic anisotropy of the optical conductivity in each system, which may be used as a fingerprint of the relative energetic positions of different states.
Published: 2021
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188. Account of the baryonic feedback effect in gamma-ray measurements of intergalactic magnetic fields

Author: K. Bondarenko, A. Boyarsky, A. Korochkin, A. Neronov, D. Semikoz, A. Sokolenko, AstroParticule et Cosmologie (APC (UMR_7164)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Work of D.S. and A.N. has been supported in part by the French National Research Agency (ANR) grant ANR-19-CE31-0020, work of A.K. was supported in part by Russian Science Foundation grant 20-42-09010. A.K.’s stay in the APC laboratory was provided by the 'Vernadsky' scholarship of the French embassy in Russia. K.B. and A.B. are supported by the European ResearchCouncil (ERC) Advanced Grant 'NuBSM' (694896). A.S. is supported by the FWF Research Group grant FG1., ANR-19-CE31-0020,MMUniverse,Nouvelles fenêtres sur l'Univers par l'astronomie multi-messenger(2019), European Project: 694896,H2020,ERC-2015-AdG,NuBSM(2016), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: extragalactic background light, Astrophysics and Astronomy, Cosmology and Nongalactic Astrophysics (astro-ph.CO), Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, magnetic fields, magnetohydrodynamics (MHD), illustristng simulations, Astrophysics::Galaxy Astrophysics, High Energy Astrophysical Phenomena (astro-ph.HE), astro-ph.HE, Computer Science::Information Retrieval, simulating galaxy formation, Astronomy and Astrophysics, gamma rays: general, jets and outflows, gamma rays, ISM: jets and outflows, Space and Planetary Science, general, astro-ph.CO, intergalactic medium, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - High Energy Astrophysical Phenomena, ism, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: Intergalactic magnetic fields in the voids of the large-scale structure can be probed via measurements of secondary gamma-ray emission from gamma-ray interactions with extragalactic background light. Lower bounds on the magnetic field in the voids were derived from the non-detection of this emission. It is not clear a priori what kind of magnetic field is responsible for the suppression of the secondary gamma-ray flux: a cosmological magnetic field that might be filling the voids or the field spread by galactic winds driven by star formation and active galactic nuclei. We used IllustrisTNG cosmological simulations to study the effect of magnetized galactic wind bubbles on the secondary gamma-ray flux. We show that within the IllustrisTNG model of baryonic feedback, the galactic wind bubbles typically provide energy-independent secondary flux suppression at the level of about 10%. The observed flux suppression effect has to be due to the cosmological magnetic field in the voids. This might not be the case for a special case when the primary gamma-ray source has a hard intrinsic gamma-ray spectrum that peaks in the energy range above 50 TeV. In this case, the observational data may be strongly affected by the magnetized bubble that is blown by the source host galaxy., V2: 8 pages, 7 figures, minor changes in the text. Version accepted for publication in A&A
Published: 2021
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189. Effects of doping substitutions on the thermal conductivity of half-Heusler compounds

Author: Mauro Fava, Bonny Dongre, Natalio Mingo, Ambroise van Roekeghem, Georg K. H. Madsen, Jesús Carrete, Département de l'électricité et de l'hydrogène dans les transports (DEHT), Laboratoire d'Innovation pour les Technologies des Energies Nouvelles et les nanomatériaux (LITEN), Institut National de L'Energie Solaire (INES), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de L'Energie Solaire (INES), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Vienna University of Technology (TU Wien), Austrian Science Funds (FWF) Grant No. FWF-I-3576-N36), and ANR-17-CE08-0044,CODIS,Calcul haut-débit des défauts dans les semiconducteurs(2017)
Subjects: Condensed Matter::Materials Science, Materials science, Thermal conductivity, Condensed matter physics, Dopant, Phonon scattering, Impurity, Doping, Condensed Matter::Strongly Correlated Electrons, Electronic density of states, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Thermoelectric materials, Volume concentration
Abstract: The promise posed by half-Heusler compounds as thermoelectric materials depends on their thermal conductivity, which is strongly affected by doping. Here we elucidate the effect of $p$ dopants on the lattice thermal conductivity (${\ensuremath{\kappa}}_{\text{ph}}$) of seven selected half-Heusler compounds and for twelve different substitutional defects. We unveil a strong reduction in ${\ensuremath{\kappa}}_{\text{ph}}$ even for low concentrations of transition-metal substitutional atoms. Furthermore, we quantify the strength of the bond perturbation induced by substitutional impurities and interpret it in terms of the changes in the local electronic density of states. In several cases we find a significant destructive interference between the mass difference and bond perturbations which reduces the phonon scattering rates below the value expected if the two effects were treated independently. We compare our first-principles calculations with the available experimental measurements on the thermal conductivity of (${\mathrm{Zr},\mathrm{Hf})}_{\text{Nb}}$-doped NbFeSb and ${\mathrm{Sn}}_{\text{Sb}}$-doped ZrCoSb. For the latter, including the effect of independent Co vacancies and interstitials yields an almost perfect agreement with experiment.
Published: 2021
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190. La juste mesure dans les livres de cuisine de l’Occident islamique médiéval

Author: Brisville, Marianne, Histoire, Archéologie et Littératures des mondes chrétiens et musulmans médiévaux (CIHAM), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-École des hautes études en sciences sociales (EHESS)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Université de Tours, CoReMA (Corpus des Recettes culinaires du Moyen Âge), Micrologus Society, FWF Der Wissenschaftsfonds, École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-École des hautes études en sciences sociales (EHESS)-Université Jean Moulin - Lyon 3 (UJML), Thème 1 - Territoires, Économie, Environnement (CIHAM - TerEcoEnv), and Université de Lyon-Université de Lyon-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-École des hautes études en sciences sociales (EHESS)-Université Jean Moulin - Lyon 3 (UJML)
Subjects: [SHS.HIST]Humanities and Social Sciences/History, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

191. WKB-method for the 1D Schrödinger equation in the semi-classical limit: enhanced phase treatment

Author: Bernhard Ujvari, Anton Arnold, Christian Klein, Institut für Analysis und Scientific Computing, Vienna University of Technology (TU Wien), Institut de Mathématiques de Bourgogne [Dijon] (IMB), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB), Austrian Science Fund (FWF)bi-national FWFI3538-N32Clear Sky VenturesFrench National Research Agency (ANR)isite BFC project NAANoDANR-17-EURE-0002 EIPHIEuropean Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie RISE 2017 Grant778010, and ANR-17-EURE-0002,EIPHI,Ingénierie et Innovation par les sciences physiques, les savoir-faire technologiques et l'interdisciplinarité(2017)
Subjects: Computer Networks and Communications, Computation, Phase (waves), Semiclassical physics, Schrödinger equation, 010103 numerical & computational mathematics, 01 natural sciences, Classical limit, WKB approximation, symbols.namesake, Higher order WKB-approximation, Applied mathematics, [INFO]Computer Science [cs], Limit (mathematics), 0101 mathematics, [MATH]Mathematics [math], Physics, Uniformly accurate scheme, Applied Mathematics, 010101 applied mathematics, Computational Mathematics, Spectral methods, Highly oscillating wave functions, Asymptotically correct finite difference scheme, symbols, Spectral method, Software
Abstract: International audience; This paper is concerned with the efficient numerical computation of solutions to the 1D stationary Schrödinger equation in the semiclassical limit in the highly oscillatory regime. A previous approach to this problem based on explicitly incorporating the leading terms of the WKB approximation is enhanced in two ways: first a refined error analysis for the method is presented for a not explicitly known WKB phase, and secondly the phase and its derivatives will be computed with spectral methods. The efficiency of the approach is illustrated for several examples.
Published: 2021
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192. 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
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193. Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort

Author: Raphaël Vernet, Valérie Siroux, Florence Demenais, Jean Bousquet, Christian Lupinek, Hubert Gheerbrant, Christophe Pison, Winfried F. Pickl, Alicia Guillien, Rachel Nadif, Emmanuelle Bouzigon, Rudolf Valenta, Isabelle Pin, Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Service de pneumologie [Grenoble], Centre Hospitalier Universitaire [Grenoble] (CHU), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Medizinische Universität Wien = Medical University of Vienna, Laboratory of Fundamental and Applied Bioenergetics = Laboratoire de bioénergétique fondamentale et appliquée (LBFA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of Vienna [Vienna], NRC Institute of immunology FMBA, Moscow Russian federation, Sechenov First Moscow State Medical University, The study was supported in part by ANR-19-CE36-0005-01 NIRVANA, Inserm Aviesan Itmo santé publique, the Scientific committee 'AGIR for chronic diseases,' grant F4605 of the Austrian Science Fund (FWF), by a grant from the Country of Lower Austria and by the Megagrant of the Government of the Russian Federation, grant number 14.W03.31.0024 to RV, and by the European Commission's Seventh Framework Program MeDALL under grant agreement no. 261357. Genotyping was supported grant from the European Commission (No. LSHB-CT-2006-018996-GABRIEL)., ANR-19-CE36-0005,NIRVANA,Facteurs génomiques impliqués dans l'effet des allergènes et virus respiratoires sur l'asthme(2019), European Project: 261357, BARBAGALLO, Maïlys, Facteurs génomiques impliqués dans l'effet des allergènes et virus respiratoires sur l'asthme - - NIRVANA2019 - ANR-19-CE36-0005 - AAPG2019 - VALID, the European Commission's Seventh Framework Program MeDALL under grant agreement no. - 261357 - INCOMING, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon (MACVIA-LR), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-European Innovation Partnership on Active and Healthy Ageing Reference Site (EIP on AHA), and Commission Européenne-Commission Européenne-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: Allergy, genetic epidemiology, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immunology, Population, [SDV.GEN] Life Sciences [q-bio]/Genetics, Human leukocyte antigen, Biology, medicine.disease_cause, Immunoglobulin E, specific IgE, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 03 medical and health sciences, 0302 clinical medicine, Allergen, Hypersensitivity, medicine, Humans, Immunology and Allergy, education, Alleles, Sensitization, 030304 developmental biology, 0303 health sciences, education.field_of_study, Timothy-grass, [SDV.GEN]Life Sciences [q-bio]/Genetics, HLA class-II genes, Allergens, medicine.disease, biology.organism_classification, 3. Good health, medicine.anatomical_structure, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Phleum, MeDALL allergen-chip, respiratory allergen, biology.protein, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Population study, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 030215 immunology
Abstract: International audience; Background: Allergy, the most frequent immune disorder affecting 30% of the world's population, is the consequence of immunoglobin E (IgE) sensitization to allergens. Among the genetic factors suspected to be involved in allergy, the HLA class-II genomic region is a strong candidate.Objective: To assess the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules.Methods: The analysis relied on 927 participants of the EGEA cohort, including 497 asthmatics. The study focuses on 26 aeroallergens recognized by sIgE in at least 5% of the study population (determined with the MEDALL chip with sIgE ≥ 0.3 ISU) and 23 imputed HLA class-II alleles. For each sIgE sensitization and HLA class-II allele, we fitted a logistic regression model accounting for familial dependence and adjusted for gender, age, and genetic principal components. p-values were corrected for multiple comparisons (False Discovery Rate).Results: Most of the 19 statistically significant associations observed regard pollen allergens (mugwort Art v 1, olive tree Ole e 1, timothy grass Phl p 2, Phl p 5 and plantain Pla l 1), three were mold allergen (Alternaria Alt a 1), and a single one regards house dust mite allergen (Der p 7). No association was observed with pet allergens. The strongest associations were found with mugwort Art v 1 (OR = 5.42 (95%CI, 3.30; 8.88), 4.14 (2.65; 6.47), 3.16 (1.88; 5.31) with DQB1*05:01, DQA1*01:01 and DRB1*01:01, respectively).Conclusion: Our results support the important role of HLA class-II alleles as immune response genes predisposing their carriers for sensitization to various major pollen allergens.
Published: 2021
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194. Global economic costs of aquatic invasive alien species

Author: Ryan J. Wasserman, Andrew M. Kramer, Jane A. Catford, Christophe Diagne, Melina Kourantidou, Ross N. Cuthbert, Boris Leroy, Phillip J. Haubrock, Zarah Pattison, Tatenda Dalu, Elena Angulo, Rodolphe E. Gozlan, César Capinha, Franck Courchamp, Laura N. H. Verbrugge, Nigel G. Taylor, Franz Essl, Danish A. Ahmed, David Renault, Elizabeta Briski, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Newcastle University [Newcastle], Institut de recherche de la Tour du Valat, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Aalto University, Université Paris-Saclay, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Gulf University for Science and Technology (GUST), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Universidade de Lisboa = University of Lisbon (ULISBOA), King‘s College London, University of Melbourne, South African Institute for Aquatic Biodiversity (SAIAB), National Research Foundation [South Africa] (NRF), University of Vienna [Vienna], 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), University of South Bohemia, Senckenberg Research Institute and Natural History Museum [Frankfurt], Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Woods Hole Oceanographic Institution (WHOI), University of Southern Denmark (SDU), University of South Florida [Tampa] (USF), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Rhodes University, Grahamstown, The authors acknowledge the French National Research Agency (ANR-14-CE02-0021) and the BNP-Paribas Foundation Climate Initiative for funding the InvaCost project that allowed the construction of the InvaCost database. The present work was conducted following a workshop funded by the AXA Research Fund Chair of Invasion Biology and is part of the AlienScenarios project funded by BiodivERsA and Belmont-Forum call 2018 on biodiversity scenarios. RNC is funded through a Humboldt Research Fellowship from the Alexander von Humboldt Foundation. DAA is funded by the Kuwait Foundation for the Advancement of Sciences (KFAS) (PR1914SM-01) and the Gulf University for Science and Technology (GUST) internal seed fund (187092). CD was funded by the BiodivERsA-Belmont Forum Project AlienScenarios (BMBF/PT DLR 01LC1807C). EA was funded by the AXA Research Fund Chair of Invasion Biology of University Paris Saclay. CC was supported by Portuguese National Funds through Fundação para a Ciência e a Tecnologia (CEECIND/02037/2017, UIDB/00295/2020 and UIDP/00295/2020). TD acknowledges funding from National Research Foundation (NRF_ZA) (Grant Number: 117700). FE appreciates funding by the Austrian Science Foundation (FWF project no I 4011-B32). AMK was supported by the NSF Macrosystems Biology program under grant 1834548. DR thanks InEE-CNRS who supports the French national network Biological Invasions (Groupement de Recherche InvaBio, 2014–2022)., ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014), Helsinki Institute of Sustainability Science (HELSUS), Department of Forest Sciences, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), 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, University of Helsinki, Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Universidade de Lisboa (ULISBOA), South African Institute for Aquatic Biodiversity, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Repositório da Universidade de Lisboa, Helmholtz-Zentrum für Ozeanforschung Kiel, Newcastle University, Research Institute for the Conservation of Mediterranean Wetlands, Water and Environmental Eng., Gulf University for Science and Technology, Muséum national d'histoire naturelle, Universidade de Lisboa, King’s College London, University of Mpumalanga, University of Vienna, Université de Montpellier, Senckenberg Gesellschaft für Naturforschung, Woods Hole Oceanographic Institution, University of South Florida, Universite de Rennes, Rhodes University, Department of Built Environment, and Aalto-yliopisto
Subjects: 010504 meteorology & atmospheric sciences, Natural resource economics, ERADICATION, Biodiversity, Distribution (economics), Introduced species, ECOSYSTEM SERVICES, 010501 environmental sciences, 01 natural sciences, THREATS, Ecosystem services, Economic cost, DRIVERS, freshwater, Waste Management and Disposal, RISK, SCIENCE, Pollution, Monetary impact, Geography, 1181 Ecology, evolutionary biology, brackish, 511 Economics, Brackish, monetary impact, InvaCost, Environmental Engineering, Resource (biology), Asia, Freshwater, Environmental Chemistry, Animals, Ecosystem, LAKE VICTORIA, 14. Life underwater, habitat biases, 0105 earth and related environmental sciences, Marine, business.industry, marine, 15. Life on land, ECOLOGICAL IMPACTS, PREVENTION, 13. Climate action, Habitat biases, Africa, North America, Damages, BIODIVERSITY, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Introduced Species
Abstract: Much research effort has been invested in understanding ecological impacts of invasive alien species (IAS) across ecosystems and taxonomic groups, but empirical studies about economic effects lack synthesis. Using a comprehensive global database, we determine patterns and trends in economic costs of aquatic IAS by examining: (i) the distribution of these costs across taxa, geographic regions and cost types; (ii) the temporal dynamics of global costs; and (iii) knowledge gaps, especially compared to terrestrial IAS. Based on the costs recorded from the existing literature, the global cost of aquatic IAS conservatively summed to US$345 billion, with the majority attributed to invertebrates (62%), followed by vertebrates (28%), then plants (6%). The largest costs were reported in North America (48%) and Asia (13%), and were principally a result of resource damages (74%); only 6% of recorded costs were from management. The magnitude and number of reported costs were highest in the United States of America and for semi-aquatic taxa. Many countries and known aquatic alien species had no reported costs, especially in Africa and Asia. Accordingly, a network analysis revealed limited connectivity among countries, indicating disparate cost reporting. Aquatic IAS costs have increased in recent decades by several orders of magnitude, reaching at least US$23 billion in 2020. Costs are likely considerably underrepresented compared to terrestrial IAS; only 5% of reported costs were from aquatic species, despite 26% of known invaders being aquatic. Additionally, only 1% of aquatic invasion costs were from marine species. Costs of aquatic IAS are thus substantial, but likely underreported. Costs have increased over time and are expected to continue rising with future invasions. We urge increased and improved cost reporting by managers, practitioners and researchers to reduce knowledge gaps. Few costs are proactive investments; increased management spending is urgently needed to prevent and limit current and future aquatic IAS damages.
Published: 2021
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195. Basal oxidation of conserved cysteines modulates cardiac titin stiffness and dynamics

Author: Elías Herrero-Galán, Inés Martínez-Martín, Cristina Sánchez-González, Natalia Vicente, Elena Bonzón-Kulichenko, Enrique Calvo, Carmen Suay-Corredera, Maria Rosaria Pricolo, Ángel Fernández-Trasancos, Diana Velázquez-Carreras, Claudio Badía Careaga, Mahmoud Abdellatif, Simon Sedej, Peter P. Rainer, David Giganti, Raúl Pérez-Jiménez, Jesús Vázquez, Jorge Alegre-Cebollada, Ministerio de Ciencia e Innovación (España), Comunidad de Madrid (España), European Research Council, European Science Foundation, Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Instituto de Salud Carlos III, Fundación La Caixa, European Research Area Network on Cardiovascular Diseases, FWF Austrian Science Fund, Fundación ProCNIC, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación. Centro de Excelencia Severo Ochoa (España), Acciona, Comunidad de Madrid, Austrian Science Fund, and Subprograma de Apoyo a Centros de Excelencia Severo Ochoa (MINECO), España
Subjects: Sarcomeres, Heart Diseases, Myocardium, Organic Chemistry, Clinical Biochemistry, Biochemistry, Elasticity, Mice, Animals, Humans, Connectin, Cysteine, Oxidation-Reduction, Protein Kinases
Abstract: Titin, as the main protein responsible for the passive stiffness of the sarcomere, plays a key role in diastolic function and is a determinant factor in the etiology of heart disease. Titin stiffness depends on unfolding and folding transitions of immunoglobulin-like (Ig) domains of the I-band, and recent studies have shown that oxidative modifications of cryptic cysteines belonging to these Ig domains modulate their mechanical properties in vitro. However, the relevance of this mode of titin mechanical modulation in vivo remains largely unknown. Here, we describe the high evolutionary conservation of titin mechanical cysteines and show that they are remarkably oxidized in murine cardiac tissue. Mass spectrometry analyses indicate a similar landscape of basal oxidation in murine and human myocardium. Monte Carlo simulations illustrate how disulfides and S-thiolations on these cysteines increase the dynamics of the protein at physiological forces, while enabling load- and isoform-dependent regulation of titin stiffness. Our results demonstrate the role of conserved cysteines in the modulation of titin mechanical properties in vivo and point to potential redox-based pathomechanisms in heart disease. This work was supported by the Ministerio de Ciencia e Innovación (MCIN/AEI/10.13039/501100011033) grants BIO2014-54768-P, BIO2017-83640-P (AEI/FEDER, UE), PID2020-120426GB-I00, RYC2014-16604 to JAC and PGC2018-097019-B-I00 to JV, the Regional Government of Madrid grants S2018/NMT-4443 (Tec4Bio, 50% cofinanced by the European Social Fund and the European Regional Development Fund for the programming period 2014-2020) and PEJ16/MED/TL-1593 to JAC and the Instituto de Salud Carlos III (Fondo de Investigacion ´ Sanitaria grant PRB3, PT17/0019/0003- ISCIII-SGEFI /ERDF, ProteoRed), and “la Caixa” Banking Foundation (project code HR17-00247) to JV. We acknowledge funding from the European Research Area Network on Cardiovascular Diseases through grant MINOTAUR to SS (The Austrian Science Fund – FWF, I3301) and JAC (ISCIII-AC16/00045). The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovacion ´ (MCIN) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MCIN/AEI/10.13039/501100011033). IMM was the recipient of a CNIC-ACCIONA Masters Fellowship and holds a fellowship from “La Caixa” Foundation (ID 100010434, fellowship code LCF/BQ/DR20/11790009). CSC is the recipient of an FPI-SO predoctoral fellowship BES-2016-076638. We thank Wolfgang A. Linke and Pablo García-Pavía for critical feedback. We are also thankful for the insights of four anonymous reviewers. Sí
Published: 2022
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196. ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity

Author: Anne Fougerat, Gabriele Schoiswohl, Arnaud Polizzi, Marion Régnier, Carina Wagner, Sarra Smati, Tiffany Fougeray, Yannick Lippi, Frederic Lasserre, Ilyès Raho, Valentine Melin, Blandine Tramunt, Raphaël Métivier, Caroline Sommer, Fadila Benhamed, Chantal Alkhoury, Franziska Greulich, Céline Jouffe, Anthony Emile, Michael Schupp, Pierre Gourdy, Patricia Dubot, Thierry Levade, Delphine Meynard, Sandrine Ellero-Simatos, Laurence Gamet-Payrastre, Ganna Panasyuk, Henriette Uhlenhaut, Ez-Zoubir Amri, Céline Cruciani-Guglielmacci, Catherine Postic, Walter Wahli, Nicolas Loiseau, Alexandra Montagner, Dominique Langin, Achim Lass, Hervé Guillou, Graz University of Technology [Graz] (TU Graz), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre hospitalier universitaire de Nantes (CHU Nantes), Transcriptomic impact of Xenobiotics (E23 TRiX), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Unité de Biologie Fonctionnelle et Adaptative (BFA (UMR_8251 / U1133)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Institut des Maladies Métaboliques et Casdiovasculaires (UPS/Inserm U1297 - I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Toulouse [Toulouse], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Helmholtz-Zentrum München (HZM), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Santé Digestive (IRSD ), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), German Research Center for Environmental Health - Helmholtz Center München (GmbH), Institut de Biologie Valrose (IBV), 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 de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Nanyang Technological University [Singapour], University of Lausanne (UNIL), BioTechMed-Graz, Graz University of Technology [Graz] (TU Graz)-Karl-Franzens-Universität [Graz, Autriche]-Medical University Graz, Région Occitanie, FRM (FDM201906008682), Boulos Foundation, ERC-2018-COG-MetaboSENS-819543, German Research Foundation (DFG) (SCH 2546/5-1), the Leuchtturmprojekt/Flagship Project 'Lipases and Lipid Signaling' funded by BioTechMed-Graz, ANR-16-CE14-0029,NUTRISENSPIK,Déterminants moléculaires de l'homéostasie hépatique nutritive(2016), ANR-17-CE14-0015,HepAdialogue,Impact du métabolisme des acides gras des tissus adipeux et du foie sur l'insulinorésistance(2017), ANR-21-CE14-0079,Hepatologic,Réseau de controle des réponses transcriptionnelles hépatiques aux challenges nutritionnels par des récepteurs nucléaires(2021), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Medical University of Graz, Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service Diabétologie [CHU Toulouse], Pôle Cardiovasculaire et Métabolique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lee Kong Chian School of Medicine, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Technische Universität Graz (TU Graz), Région Occitanie B.T. was supported by FRM (FDM201906008682)., Boulos Foundation and FRM., German Research Foundation (DFG) (SCH 2546/5-1 to M.S.), I3535, andP34899 (A.L.) by Austrian Science Fund (FWF, ERC-2018-COG-MetaboSENS- 819543 (G.P.), the Leuchtturmprojekt/Flagship Project ‘‘Lipases and Lipid Signaling’’ (A.L.), funded by BioTechMed-Graz, and by P28882-B21 (G.S.), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, LESUR, Hélène, Impact du métabolisme des acides gras des tissus adipeux et du foie sur l'insulinorésistance - - HepAdialogue2017 - ANR-17-CE14-0015 - AAPG2017 - VALID, Réseau de controle des réponses transcriptionnelles hépatiques aux challenges nutritionnels par des récepteurs nucléaires - - Hepatologic2021 - ANR-21-CE14-0079 - AAPG2021 - VALID, Déterminants moléculaires de l'homéostasie hépatique nutritive - - NUTRISENSPIK2016 - ANR-16-CE14-0029 - AAPG2016 - VALID, and AgreenSkills+ - AGREENSKILLSPLUS - - EC:FP7:PEOPLE2014-05-05 - 2019-05-04 - 609398 - VALID
Subjects: fasting, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Adipose Tissue, White, Metabolism, Fgf21, Pparα, Fasting, Ketogenesis, Lipolysis [Atgl, Cp], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Ketone Bodies, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, PPARα, General Biochemistry, Genetics and Molecular Biology, ATGL, FGF21, Adipose Tissue, Brown, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], PPAR alpha, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, CP: Metabolism, ketogenesis, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Adipose Tissue, Hepatocytes, lipolysis, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; In hepatocytes, peroxisome proliferator-activated receptor α (PPARα) orchestrates a genomic and metabolic response required for homeostasis during fasting. This includes the biosynthesis of ketone bodies and of fibroblast growth factor 21 (FGF21). Here we show that in the absence of adipose triglyceride lipase (ATGL) in adipocytes, ketone body and FGF21 production is impaired upon fasting. Liver gene expression analysis highlights a set of fasting-induced genes sensitive to both ATGL deletion in adipocytes and PPARα deletion in hepatocytes. Adipose tissue lipolysis induced by activation of the β3-adrenergic receptor also triggers such PPARα-dependent responses not only in the liver but also in brown adipose tissue (BAT). Intact PPARα activity in hepatocytes is required for the cross-talk between adipose tissues and the liver during fat mobilization.
Published: 2022
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197. Resistance–recovery trade‐off of soil microbial communities under altered rain regimes: An experimental test across European agroecosystems

Author: Arnaud Foulquier, Lijbert Brussaard, Jean-Christophe Clément, Filipa Reis, Cindy Arnoldi, José Paulo Sousa, Pedro Martins da Silva, Gerlinde B. De Deyn, Katarina Hedlund, Laura B. Martínez-García, Gabin Piton, Nicolas Legay, Eduardo Nascimento, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Wageningen University and Research [Wageningen] (WUR), Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Lund University [Lund], Universidade de Coimbra [Coimbra], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Portuguese Foundation for Science and TechnologyEuropean CommissionBiodivERsA/001/2014National Council for Scientific and Technological Development (CNPq) Spanish Government Austrian Science Fund (FWF) Swedish Research Council Formas Netherlands Organization for Scientific Research (NWO)European CommissionSwiss Federal Office of Agriculture, ANR-16-CE02-0009,GlobNets,Biogéographie globale des réseaux écologiques des forêts du monde(2016), and Centre National de la Recherche Scientifique (CNRS)-Université de Tours
Subjects: 0106 biological sciences, Nutrient cycle, drought, 010603 evolutionary biology, 01 natural sciences, Soil management, Nutrient, oligotrophs, Ecosystem, bacteria, Water content, resilience, Bodembiologie, 2. Zero hunger, copiotrophs, Biomass (ecology), Ecology, Resistance (ecology), 010604 marine biology & hydrobiology, extracellular enzyme, Soil Biology, 15. Life on land, PE&RC, Agronomy, Microbial population biology, 13. Climate action, PLFA, Environmental science, fungi, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; With the increased occurrence of climate extremes, there is an urgent need to better understand how management strategies affect the capacity of the soil microbial community to maintain its ecosystem functions (e.g. nutrient cycling).To address this issue, intact monoliths were extracted from conventional and ecological managed grasslands in three countries across Europe and exposed under common air condition (temperature and moisture) to one of three altered rain regimes (dry, wet and intermittent wet/dry) as compared to a normal regime. Subsequently, we compared the resistance and recovery of the soil microbial biomass, potential enzyme activities and community composition.The microbial community composition differed with soil management and rain regimes. Soil microbial biomass increased from the wetter to the dryer rain regime, paralleling an increase of available carbon and nutrients, suggesting low sensitivity to soil moisture reduction but nutritional limitations of soil microbes. Conversely, enzyme activities decreased with all altered rain regimes.Resistance and recovery (considering absolute distance between normal and altered rain regime) of the microbial communities depended on soil management. Conventional-intensive management showed higher resistance of two fundamental properties for nutrient cycling (i.e. bacterial biomass and extracellular enzyme activities) yet associated with more important changes in microbial community composition. This suggests an internal community reorganization promoting biomass and activity resistance. Conversely, under ecological management bacterial biomass and enzyme activities showed better recovery capacity, whereas no or very low recovery of these properties was observed under conventional management. These management effects were consistent across the three altered rain regimes investigated, indicating common factors controlling microbial communities' response to different climate-related stresses.Synthesis and applications. Our study provides experimental evidence for an important trade-off for agroecosystem management between (a) stabilizing nutrient cycling potential during an altered rain regime period at the expense of very low recovery capacity and potential long-term effect (conventional sites) and (b) promoting the capacity of the microbial community to recover its functional potential after the end of the stress (ecological sites). Thus, management based on ecologically sound principles may be the best option to sustain long-term soil functioning under climate change.
Published: 2021
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198. 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
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199. Destruction of the cosmic γ-ray emitter 26 Al in massive stars: Study of the key 26 Al ( n , p ) reaction

Author: Lederer Woods, Claudia, Woods, P. J., Davinson, T., Kahl, D., Lonsdale, S. J., Aberle, O., Chiaveri, Enrico, Cortés Giraldo, Miguel Antonio, Ferrer Fernández, Francisco Javier, Guerrero Sánchez, Carlos, Lerendegui Marco, Jorge, Quesada Molina, José Manuel, Sabaté Gilarte, Marta, Žugec, P., Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear, Austrian Science Fund (FWF). Austria, Consejo de Instalaciones Científicas y Tecnológicas (STFC). Reino Unido, and Consejo Europeo de Investigación. Unión Europea
Abstract: The 26 Al (n ,p) 26 Mg reaction is the key reaction impacting on the abundances of the cosmic y-ray emitter 26 Al produced in massive stars and impacts on the potential pollution of the early solar system with 26 Al by asymptotic giant branch stars. We performed a measurement of the 26 Al ( n , p ) 26 Mg cross section at the high-flux beam line EAR-2 at the n_TOF facility (CERN). We report resonance strengths for eleven resonances, nine being measured for the first time, while there is only one previous measurement for the other two. Our resonance strengths are significantly lower than the only previous values available. Our cross-section data range to 150 keV neutron energy, which is sufficient for a reliable determination of astrophysical reactivities up to 0.5 GK stellar temperature. Austrian Science Fund (FWF) J3503 Consejo de Instalaciones Científicas y Tecnológicas del Reino Unido (STFC) ST/L005824/1 y ST/M006085/1, Consejo Europeo de Investigación ERC-2015-STG Nr. 677497
Published: 2021

200. Long-lived charged states of single porphyrin-tape junctions under ambient conditions

Author: Leary E., Kastlunger G., Limburg B., Rincón-García L., Hurtado-Gallego J., González M.T., Bollinger G.R., Agrait N., Higgins S.J., Anderson H.L., Stadler R., Nichols R.J. and R. J. N., S. H., E. L., and A. H. acknowledge the UK Engineering and Physical Sciences Research Council (EPSRC) for the funding of this research under grant numbers EP/M014169/1, P/M029522/1, and EP/M005046/1. E. L. thanks the Comunidad de Madrid grant Atracción de Talento 2019-T1/IND-16384. H. L. A. thanks the EPSRC (grants EP/N017188/1, EP/D076552/1 and EP/M016110/1), UK National Mass Spectrometry Facility at Swansea University, for recording mass spectra. N. A. and G. R. B. acknowledge the Spanish Ministry of Science and Innovation through grant MAT2017-88693-R and through the ‘María de Maeztu’ Programme for Units of Excellence in R&D (CEX2018-000805-M). N. A. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 767187. IMDEA Nano-ciencia acknowledges support from the ‘Severo Ochoa’ Programme for Centres of Excellence in R&D (MINECO, Grant SEV-2016-0686). N. A. and L. R.-G. acknowledge funding from the Education and Research Council of the Comunidad de Madrid and the European Social Fund (Ref. PEJD-2019-POST/IND-16353). We also acknowledge the Comunidad de Madrid (NanoMagCOST-CM, S2018/NMT-4321). G. K. acknowledges the Center of Computation and Visualization (CCV) at Brown University, where the DFT calculations were performed. R. S. is funded by the Austrian Science Fund FWF through project P 31631.
Published: 2021

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