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201. C−C Cross-Couplings from a Cyclometalated Au(III) C∧ N Complex: Mechanistic Insights and Synthetic Developments

Author

Mathilde Rigoulet, Angela Casini, Giampaolo Barone, Sophie R. Thomas, Didier Bourissou, Riccardo Bonsignore, Alexander Pöthig, Christian Jandl, Bonsignore R., Thomas S.R., Rigoulet M., Jandl C., Pothig A., Bourissou D., Barone G., Casini A., Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Palermo - University of Palermo, ANR-19-CE07-0037,Gold-III,Chimie de l'or(III)(2019), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), and Technical University of Munich (TUM)

Subjects
Coordination sphere, Heteroatom, 010402 general chemistry, 01 natural sciences, Catalysis, Reductive elimination, NMR spectroscopy, Nucleophile, cross-coupling, Reactivity (chemistry), Full Paper, 010405 organic chemistry, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, reductive elimination, General Chemistry, Nuclear magnetic resonance spectroscopy, [CHIM.CATA]Chemical Sciences/Catalysis, Full Papers, Transition state, 0104 chemical sciences, gold cyclometalated complexes, Crystallography, Zinc, Settore CHIM/03 - Chimica Generale E Inorganica, Gold, Two-dimensional nuclear magnetic resonance spectroscopy, organometallics
Abstract

In recent years, the reactivity of gold complexes was shown to extend well beyond π‐activation and to hold promises to achieve selective cross‐couplings in several C−C and C−E (E=heteroatom) bond forming reactions. Here, with the aim of exploiting new organometallic species for cross‐coupling reactions, we report on the Au(III)‐mediated C(sp2)−C(sp) occurring upon reaction of the cyclometalated complex [Au(CCH2N)Cl2] (1, CCH2N=2‐benzylpyridine) with AgPhCC. The reaction progress has been monitored by NMR spectroscopy, demonstrating the involvement of a number of key intermediates, whose structures have been unambiguously ascertained through 1D and 2D NMR analyses (1H, 13C, 1H‐1H COSY, 1H‐13C HSQC and 1H‐13C HMBC) as well as by HR‐ESI‐MS and X‐ray diffraction studies. Furthermore, crystallographic studies have serendipitously resulted in the authentication of zwitterionic Au(I) complexes as side‐products arising from cyclization of the coupling product in the coordination sphere of gold. The experimental work has been paralleled and complemented by DFT calculations of the reaction profiles, providing valuable insight into the structure and energetics of the key intermediates and transition states, as well as on the coordination sphere of gold along the whole process. Of note, the broader scope of the cross‐coupling at the Au(III) CCH2N centre has also been demonstrated studying the reaction of 1 with C(sp2)‐based nucleophiles, namely vinyl and heteroaryl tin and zinc reagents. These reactions stand as rare examples of C(sp2)−C(sp2) cross‐couplings at Au(III)., The mechanism of C(sp2)−C(sp) coupling templated by the Au(III) cyclometalated complex [Au(CCH2N)Cl2] has been investigated. By tuning the reaction conditions and monitoring its progress by NMR, a number of intermediate species involved in the reductive elimination process could be isolated and characterised by different spectroscopic and analytical methods, including XRD, as well as by DFT studies.

Published
2021
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202. A genetic risk score and diabetes predict development of alcohol-related cirrhosis in drinkers

Author

Munir Pirmohamed, Guruprasad P. Aithal, Felix Stickel, Mark Thursz, David Goldman, Paul S. Haber, John Whitfield, Romain Moirand, Bertrand Nalpas, Devanshi Seth, Christophe Moreno, Andrew Thompson, Eric Trepo, Stephen R. Atkinson, Rebecca Darlay, Beat Müllhaupt, Timothy R. Morgan, Dermot Gleeson, Sylvie Naveau, Ann K. Daly, Helmut K. Seitz, Michael Soyka, Christopher P. Day, Tatiana Foroud, Jean-Marc Jacquet, Laura E. Nagy, Naga Chalasani, Pascal Perney, Philippe Mathurin, Marsha Y. Morgan, Pierre Nahon, Sebastian Mueller, Tiebing Liang, Florian Eyer, Suthat Liangpunsakul, Heather J. Cordell, Steven Masson, Tae-Hwi Schwantes-An, Ramon Bataller, Greg Botwin, Andrew McQuillin, QIMR Berghofer Medical Research Institute, Indiana University School of Medicine, Indiana University System, Newcastle University [Newcastle], University of Nottingham, UK (UON), Imperial College London, University of Pittsburgh Medical Center [Pittsburgh, PA, États-Unis] (UPMC), California State University [Long Beach] (CSULB ), Indiana University - Purdue University Indianapolis (IUPUI), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), National Institute on Alcohol Abuse and Alcoholism (NIAAA), National Institutes of Health [Bethesda] (NIH), The University of Sydney, Hôpital Universitaire Carémeau [Nîmes] (CHU Nîmes), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Hôpital Claude Huriez [Lille], CHU Lille, Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University College of London [London] (UCL), Université libre de Bruxelles (ULB), University of Heidelberg, Medical Faculty, University hospital of Zurich [Zurich], Lerner Research Institute, Cleveland Clinic, Génomique Fonctionnelle des Tumeurs Solides (U1162), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), 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, University of Liverpool, University-Hospital Munich-Großhadern [München], University of California, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Lerner Research Institute [Cleveland, OH, USA], University of California (UC), Technical University of Munich (TUM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
Liver Cirrhosis, Male, Cirrhosis, Hepatocellular carcinoma, [SDV]Life Sciences [q-bio], Alcohol, Disease, risk stratification, Gastroenterology, Oral and gastrointestinal, Cohort Studies, Liver disease, Alcohol Use and Health, Substance Misuse, chemistry.chemical_compound, 0302 clinical medicine, Liver Cirrhosis, Alcoholic, single nucleotide polymorphism, Cancer, 2. Zero hunger, 0303 health sciences, Framingham Risk Score, genome wide association, Liver Disease, Single Nucleotide, Middle Aged, Alcoholic, 3. Good health, Alcoholism, Public Health and Health Services, 030211 gastroenterology & hepatology, Female, Risk assessment, Liver Cancer, Adult, medicine.medical_specialty, Alcohol Drinking, Chronic Liver Disease and Cirrhosis, Clinical Sciences, coffee, Polymorphism, Single Nucleotide, Risk Assessment, Article, 03 medical and health sciences, GenomALC Consortium, Rare Diseases, Clinical Research, Diabetes mellitus, Internal medicine, Genetics, Diabetes Mellitus, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Polymorphism, Metabolic and endocrine, 030304 developmental biology, Gastroenterology & Hepatology, Hepatology, business.industry, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Odds ratio, medicine.disease, chronic alcohol use, Good Health and Well Being, chemistry, Case-Control Studies, genome-wide association, Digestive Diseases, business, Body mass index, Genome-Wide Association Study
Abstract

International audience; BACKGROUND and AIMS: Only a minority of excess alcohol drinkers develop cirrhosis. We developed and evaluated risk stratification scores to identify those at highest risk. METHODS: Three cohorts (GenomALC-1: n=1690, GenomALC-2: n=3037, UK Biobank: relevant n=6898) with a history of heavy alcohol consumption (≥80 g/day (men), ≥50 g/day (women), for ≥10 years) were included. Cases were participants with alcohol-related cirrhosis. Controls had a history of similar alcohol consumption but no evidence of liver disease. Risk scores were computed from up to eight genetic loci identified previously as associated with alcohol-related cirrhosis and three clinical risk factors. Score performance for the stratification of alcohol-related cirrhosis risk was assessed and compared across the alcohol-related liver disease spectrum, including hepatocellular carcinoma (HCC). RESULTS: A combination of three single nucleotide polymorphisms (SNPs) (PNPLA3:rs738409, SUGP1-TM6SF2:rs10401969, HSD17B13:rs6834314) and diabetes status best discriminated for cirrhosis risk. The odds ratio (OR) and 95% confidence intervals (CI) for the extreme score quintiles (Q1-Q5) of the 3-SNP score, based on independent allelic effect size estimates, were 5.99 (4.18;8.60) (GenomALC-1); 2.81 (2.03;3.89) (GenomALC-2); and 3.10 (2.32;4.14) (UK Biobank). Patients with diabetes and high-risk score, compared to those without diabetes and a low-risk score, had ORs increased to 14.7 (7.69;28.1) (GenomALC-1) and 17.1 (11.3;25.7) (UK Biobank). Patients with cirrhosis and HCC had significantly higher mean risk scores than patients with cirrhosis alone (0.76±0.06 versus 0.61±0.02, p=0.007). Score performance was not significantly enhanced by information on additional genetic risk variants, body mass index or coffee consumption. CONCLUSIONS: A risk score based on three genetic risk variants and diabetes status can provide meaningful risk stratification for cirrhosis in excess drinkers, allowing earlier prevention planning including intensive intervention. LAY SUMMARY: Excessive chronic drinking leads to liver cirrhosis in some people, but so far there is no way to identify those at high risk of developing this debilitating disease. Our study has developed a genetic risk score (GRS) test that can identify patients at high risk and shows that the risk of cirrhosis is increased >10-fold with just two risk factors - diabetes and high GRS. Risk assessment using this test has potential for early and personalised management of this disease in high-risk patients.

Published
2021
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203. Secure Email -- A Usability Study

Author

Ahmed Abdelmaksoud, Adrian Reuter, Wadie Lemrazzeq, Karima Boudaoud, Marco Winckler, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Scalable and Pervasive softwARe and Knowledge Systems (Laboratoire I3S - SPARKS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Web-Instrumented Man-Machine Interactions, Communities and Semantics (WIMMICS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Scalable and Pervasive softwARe and Knowledge Systems (Laboratoire I3S - SPARKS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Interactive Critical Systems (IRIT-ICS), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Matthew Bernhard, Andrea Bracciali, L. Jean Camp, Shin'ichiro Matsuo, Alana Maurushat, Peter B. Rønne, Massimiliano Sala, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, and Technische Universität München [München] (TUM)

Subjects
FOS: Computer and information sciences, 050101 languages & linguistics, User study, Computer Science - Cryptography and Security, computer.internet_protocol, Computer science, Internet privacy, Usability, Computer Science - Human-Computer Interaction, Face (sociological concept), 02 engineering and technology, S/MIME, Encryption, Human-Computer Interaction (cs.HC), MIME, Public-key cryptography, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], Software, Email encryption, Identity theft, Mail encryption, 0202 electrical engineering, electronic engineering, information engineering, 0501 psychology and cognitive sciences, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], business.industry, 05 social sciences, PGP, pEp, 020201 artificial intelligence & image processing, business, computer, Cryptography and Security (cs.CR)
Abstract

International audience; Several end-to-end encryption technologies for emails such as PGP and S/MIME exist since decades. However, end-to-end encryption is barely applied. To understand why users hesitate to secure their email communication and which usability issues they face with PGP, S/MIME as well as with pEp (Pretty Easy Privacy), a fairly new technology, we conducted an online survey and user testing. We found that more than 60% of e-mail users are unaware of the existence of such encryption technologies and never tried to use one. We observed that above all, users are overwhelmed with the management of public keys and struggle with the setup of encryption technology in their mail software. Even though users struggle to put email encryption into practice, we experienced roughly the same number of users being aware of the importance of email encryption. Particularly, we found that users are very concerned about identity theft, as 78% want to make sure that no other person is able to write email in their name.

Published
2021
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204. The politics of scaling

Author

and Jack Stilgoe, Sebastian M. Pfotenhauer, Brice Laurent, Kyriaki Papageorgiou, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Centre de Sociologie de l'Innovation i3 (CSI i3), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), ESADE Barcelona - Sant Cugat, and Technical University of Munich (TUM)

Subjects
platform technologies, History, Technology, Big data, Public Policy, 050905 science studies, scale, Politics, History and Philosophy of Science, Political science, 0502 economics and business, Social Change, Scaling, [SHS.SOCIO]Humanities and Social Sciences/Sociology, business.industry, 05 social sciences, General Social Sciences, living labs, Articles, innovation, ddc, Political economy, Scale (social sciences), randomized controlled trials, 0509 other social sciences, business, 050203 business & management
Abstract

International audience; A fixation on ‘scaling up’ has captured current innovation discourses and, with it, political and economic life at large. Perhaps most visible in the rise of platform technologies, big data and concerns about a new era of monopolies, scalability thinking has also permeated public policy in the search for solutions to ‘grand societal challenges’, ‘mission-oriented innovation’ or transformations through experimental ‘living labs’. In this paper, we explore this scalability zeitgeist as a key ordering logic of current initiatives in innovation and public policy. We are interested in how the explicit preoccupation with scalability reconfigures political and economic power by invading problem diagnoses and normative understandings of how society and social change function. The paper explores three empirical sites – platform technologies, living labs and experimental development economics – to analyze how scalability thinking is rationalized and operationalized. We suggest that social analysis of science and technology needs to come to terms with the ‘politics of scaling’ as a powerful corollary of the ‘politics of technology’, lest we accept the permanent absence from key sites where decisions about the future are made. We focus in on three constitutive elements of the politics of scaling: solutionism, experimentalism and future-oriented valuation. Our analysis seeks to expand our vocabulary for understanding and questioning current modes of innovation that increasingly value scaling as an end in itself, and to open up new spaces for alternative trajectories of social transformation.

Published
2021
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205. Topology identifies emerging adaptive mutations in SARS-CoV-2

Author

Bleher, Michael, Hahn, Lukas, Patiño-Galindo, Juanángel, Carriere, Mathieu, Bauer, Ulrich, Rabadán, Raúl, Ott, Andreas, Heidelberg University, Department of biology [Columbia University], Columbia University [New York], Understanding the Shape of Data (DATASHAPE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria), Technical University of Munich (TUM), Karlsruhe Institute of Technology (KIT), The authors acknowledge scientists and laboratories for sharing SARS-CoV-2 genome sequencing datawith the research community via the GISAID database. A list of all contributions used in this workdetailing authors from the originating laboratories responsible for obtaining the specimens and the submitting laboratories where genetic sequence data were generated is available in Table S1. This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A,031A537B, 031A537C, 031A537D, 031A538A). The authors acknowledge the use of de.NBI cloud and the support by the High Performance and Cloud Computing Group at the Zentrum für Datenverar-beitung of the University of Tübingen and the Federal Ministry of Education and Research (BMBF)through grant no 031 A535A. They thank M. Hanussek for IT support and early access to VALET. The authors further acknowledge support from the Interdisciplinary Center for Scientific Computing at Heidelberg University and the development work of the Scientific Software Center of Heidelberg University carried out by D. Kempf and L. Keegan. This research was supported by the DFG Collaborative Research Center SFB/TRR 109 'Discretization in Geometry and Dynamics'. M.B.was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC 2181/1 - 390900948 (the Heidelberg STRUCTURES ExcellenceCluster). L.H. thanks the Evangelisches Studienwerk Villigst for their support. A.O. acknowledgesfunding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 281869850(RTG 2229)., and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
[MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG]
Abstract

The COVID-19 pandemic has lead to a worldwide effort to characterize its evolution through the mapping of mutations in the genome of the coronavirus SARS-CoV-2. As the virus spreads and evolves it acquires new mutations that could have important public health consequences, including higher transmissibility, morbidity, mortality, and immune evasion, among others. Ideally, we would like to quickly identify new mutations that could confer adaptive advantages to the evolving virus by leveraging the large number of SARS-CoV-2 genomes. One way of identifying adaptive mutations is by looking at convergent mutations, mutations in the same genomic position that occur independently. The large number of currently available genomes, more than a million at this moment, however precludes the efficient use of phylogeny-based techniques. Here, we establish a fast and scalable Topological Data Analysis approach for the early warning and surveillance of emerging adaptive mutations of the coronavirus SARS-CoV-2 in the ongoing COVID-19 pandemic. Our method relies on a novel topological tool for the analysis of viral genome datasets based on persistent homology. It systematically identifies convergent events in viral evolution merely by their topological footprint and thus overcomes limitations of current phylogenetic inference techniques. This allows for an unbiased and rapid analysis of large viral datasets. We introduce a new topological measure for convergent evolution and apply it to the complete GISAID dataset as of February 2021, comprising 303,651 high-quality SARS-CoV-2 isolates taken from patients all over the world since the beginning of the pandemic. A complete list of mutations showing topological signals of convergence is compiled. We find that topologically salient mutations on the receptor-binding domain appear in several variants of concern and are linked with an increase in infectivity and immune escape. Moreover, for many adaptive mutations the topological signal precedes an increase in prevalence. We demonstrate the capability of our method to effectively identify emerging adaptive mutations at an early stage. By localizing topological signals in the dataset, we are able to extract geo-temporal information about the early occurrence of emerging adaptive mutations. The identification of these mutations can help to develop an alert system to monitor mutations of concern and guide experimentalists to focus the study of specific circulating variants.

Published
2021

206. Testing and Reliability Enhancement of Security Primitives

Author

Jean-Luc Danger, Toufiq Hasan Anik, Mohammad Ebrahimabadi, Omar Diankha, Naghmeh Karimi, Sylvain Guilley, Sofiane Takarabt, Michael Pehl, Christoph Frisch, Département Communications & Electronique (COMELEC), Télécom ParisTech, Secure and Safe Hardware (SSH), Laboratoire Traitement et Communication de l'Information (LTCI), Institut Mines-Télécom [Paris] (IMT)-Télécom Paris-Institut Mines-Télécom [Paris] (IMT)-Télécom Paris, Institut Polytechnique de Paris (IP Paris), University of Maryland [Baltimore], Université Paris 8 Vincennes-Saint-Denis (UP8), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Secure-IC S.A.S, Institut Mines-Télécom [Paris] (IMT), and Technical University of Munich (TUM)

Subjects
Cryptographic primitive, business.industry, Random number generation, Computer science, Reliability (computer networking), Physical unclonable function, Cryptography, [SPI.TRON]Engineering Sciences [physics]/Electronics, Symmetric-key algorithm, Embedded system, Netlist, business, Dimensioning, ComputingMilieux_MISCELLANEOUS
Abstract

The test of security primitives is particularly strategic as any bias coming from the implementation or environment can wreck havoc on the security it is intended to provide. This paper presents how some security properties are tested on leading primitives: True Random Number Generation (TRNG), Physically Unclonable Function (PUF), cryptographic primitives and Digital Sensor (DS). The test of TRNG and PUF to ensure a high level of security is mainly about the entropy assessment, which requires specific statistical tests. The security against side-channel analysis (SCA) of cryptographic primitives, like the substitution box in symmetric cryptography, is generally ensured by masking. But the hardware implementation of masking can be damaged by glitches, which create leakages on sensitive variables. A test method is to search for nets of the cryptographic netlist, which are vulnerable to glitches. The DS is an efficient primitive to detect disturbances and rise alarms in case of fault injection attack (FIA). The dimensioning of this primitive requires a precise test to take into account the environment variations including the aging.

Published
2021
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207. Microwave optomechanical measurement of non-metallized SiN strings at mK temperatures

Author

Kumar, Sumit, Klaß, Yannick, Alperin, Baptiste, Venkatachalam, Srisaran, Zhou, Xin, Weig, Eva, Collin, Eddy, Fefferman, Andrew, Ultra-basses températures (UBT), 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), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Ultra-basses températures (NEEL - UBT), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Nano and Microsystems - IEMN (NAM6 - IEMN), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), and Technical University of Munich (TUM)

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), FOS: Physical sciences, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat]
Abstract

The mechanical properties of amorphous materials (glasses) at low temperatures are dominated by effects of low energy excitations that are thought to be atomic-scale tunneling two level systems (TTLS). In nanometer-scale glass samples, the temperature dependence of the sound speed and dissipation is modified relative to that of bulk glass samples. In addition to this size effect, the usual presence of a polycrystalline metal in nanomechanical resonators leads to a further departure from the well-studied behavior of insulating bulk glass. We report a dual chip optomechanical measurement technique used to characterize non-metallized amorphous SiN strings at low temperatures. A harp consisting of SiN strings of width 350 nm and lengths 40 to 80 $\mu$m is coupled to an Al superconducting microwave cavity on a separate chip. The strings are driven dielectrically and their motion is detected via its modulation of the microwave resonance frequency.

Published
2021

208. Repositioning TH cell polarization from single cytokines to complex help

Author

Thomas Korn, Francisco J. Quintana, Matteo Iannacone, Florent Ginhoux, Anne Dejean, Burkhard Becher, Selma Tuzlak, Ari Waisman, Universität Zürich [Zürich] = University of Zurich (UZH), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), 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), IRCCS San Raffaele Scientific Institute [Milan, Italie], Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), University Medical Center of the Johannes Gutenberg-University Mainz, Singapore Immunology Network (SIgN), Biomedical Sciences Institute (BMSI), Duke-NUS Medical School [Singapore], Shangaï Jiao Tong University [Shangaï], Technische Universität München = Technical University of Munich (TUM), Munich Cluster for systems neurology [Munich] (SyNergy), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Ludwig-Maximilians-Universität München (LMU), ARSEP foundation (ARSEP R19191BB, FRM (R20097BB), Italian Ministry of Health grants RF-2018-12365801 and COVID-2020-12371617, Lombardy Foundation for Biomedical Research grant 2015-0010, ANR-16-CE15-0007,FOxOTiC,Rôle du facteur de transcription Foxo3 dans les lymphocytes T CD4(2016), European Project: 957502,ERC, Tuzlak, S., Dejean, A. S., Iannacone, M., Quintana, F. J., Waisman, A., Ginhoux, F., Korn, T., Becher, B., 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), Pistre, Karine, Rôle du facteur de transcription Foxo3 dans les lymphocytes T CD4 - - FOxOTiC2016 - ANR-16-CE15-0007 - AAPG2016 - VALID, and Proof of Concept grant - ERC - 957502 - INCOMING

Subjects
[SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV]Life Sciences [q-bio], Immunology, Cell, Cell Plasticity, MESH: Cell Plasticity / immunology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Epithelium, 03 medical and health sciences, 0302 clinical medicine, Immune system, MESH: Eosinophils / immunology, MESH: Phagocytes / immunology, Cell polarity, medicine, Immunology and Allergy, Animals, Humans, MESH: Animals, MESH: Cytokines / immunology, Lymphocytes, Transcription factor, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, MESH: Immunity, Innate / immunology, 030304 developmental biology, 0303 health sciences, B-Lymphocytes, Phagocytes, MESH: Epithelium / immunology, MESH: Humans, Innate lymphoid cell, T-Lymphocytes, Helper-Inducer, Phenotype, Immunity, Innate, Cell biology, MESH: B-Lymphocytes / immunology, [SDV] Life Sciences [q-bio], Eosinophils, MESH: Lymphocytes / immunology, medicine.anatomical_structure, Cytokines, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: T-Lymphocytes, Helper-Inducer / immunology, 030215 immunology
Abstract

International audience; When helper T (TH) cell polarization was initially described three decades ago, the TH cell universe grew dramatically. New subsets were described based on their expression of few specific cytokines. Beyond TH1 and TH2 cells, this led to the coining of various TH17 and regulatory (Treg) cell subsets as well as TH22, TH25, follicular helper (TFH), TH3, TH5 and TH9 cells. High-dimensional single-cell analysis revealed that a categorization of TH cells into a single-cytokine-based nomenclature fails to capture the complexity and diversity of TH cells. Similar to the simple nomenclature used to describe innate lymphoid cells (ILCs), we propose that TH cell polarization should be categorized in terms of the help they provide to phagocytes (type 1), to B cells, eosinophils and mast cells (type 2) and to non-immune tissue cells, including the stroma and epithelium (type 3). Studying TH cells based on their helper function and the cells they help, rather than phenotypic features such as individual analyzed cytokines or transcription factors, better captures TH cell plasticity and conversion as well as the breadth of immune responses in vivo.

Published
2021
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209. A Multi-Scale and Multi-Technique Approach for the Characterization of the Effects of Spatially Fractionated X-ray Radiation Therapies in a Preclinical Model

Author

Cinzia Giannini, Oliver Bunk, Marianna Alunni-Fabbroni, Giacomo E. Barbone, Stefan Bartzsch, Alberto Mittone, Lucie Sancey, Heidrun Hirner-Eppeneder, Armin Giese, Dmitry Karpov, Alberto Bravin, Audrey Bouchet, Mariele Romano, Alicia Eckhardt, Jens Ricke, Viktoria Ruf, Julien Dinkel, Paola Coan, Ludwig-Maximilians-Universität München (LMU), European Synchrotron Radiation Facility (ESRF), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), ALBA-CELLS, 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), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Helmholtz-Zentrum München (HZM), Paul Scherrer Institute (PSI), Romano, M, Bravin, A, Mittone, A, Eckhardt, A, Barbone, G, Sancey, L, Dinkel, J, Bartzsch, S, Ricke, J, Alunni-Fabbroni, M, Hirner-Eppeneder, H, Karpov, D, Giannini, C, Bunk, O, Bouchet, A, Ruf, V, Giese, A, Coan, P, and Technical University of Munich (TUM)

Subjects
Cancer Research, Materials science, MRT, medicine.medical_treatment, [SDV]Life Sciences [q-bio], FIS/07 - FISICA APPLICATA (A BENI CULTURALI, AMBIENTALI, BIOLOGIA E MEDICINA), Animal Model, Flash, Glioblastoma, Hydroxyapatite, Mrt, Spatially Fractionated Radiotherapy, Virtual Histology, X-ray Phase-contrast Imaging, FLASH, Article, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Nuclear magnetic resonance, medicine, Radiosensitivity, Irradiation, ddc:610, RC254-282, [PHYS]Physics [physics], medicine.diagnostic_test, animal model, X-ray, glioblastoma, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, hydroxyapatite, Magnetic resonance imaging, Microbeam, 3. Good health, X-ray phase-contrast imaging, Radiation therapy, virtual histology, spatially fractionated radiotherapy, Oncology, 030220 oncology & carcinogenesis, X-Ray Phase-Contrast Imaging, Tomography
Abstract

Simple Summary This study aims at using a multi-technique approach to detect and analyze the effects of high dose rate spatially fractionated radiation therapies and to compare them to seamless broad beam irradiation targeting healthy and glioblastoma-bearing rat brains and delivering three different doses per each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray phase contrast imaging–computed tomography, histology, immunohistochemistry, X-ray fluorescence, and small- and wide-angle X-ray scattering to achieve detailed visualization, characterization and classification in 3D of the radio-induced effects on brain tissues. The original results bring new insights to the understanding of the response of cerebral tissue and tumors treated with high dose rate spatially fractioned radiotherapies and put the basis for channeling studies of in-vivo applications for monitoring RT effects. Abstract The purpose of this study is to use a multi-technique approach to detect the effects of spatially fractionated X-ray Microbeam (MRT) and Minibeam Radiation Therapy (MB) and to compare them to seamless Broad Beam (BB) irradiation. Healthy- and Glioblastoma (GBM)-bearing male Fischer rats were irradiated in-vivo on the right brain hemisphere with MRT, MB and BB delivering three different doses for each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray Phase Contrast Imaging–Computed Tomography (XPCI-CT), histology, immunohistochemistry, X-ray Fluorescence (XRF), Small- and Wide-Angle X-ray Scattering (SAXS/WAXS). XPCI-CT discriminates with high sensitivity the effects of MRT, MB and BB irradiations on both healthy and GBM-bearing brains producing a first-time 3D visualization and morphological analysis of the radio-induced lesions, MRT and MB induced tissue ablations, the presence of hyperdense deposits within specific areas of the brain and tumor evolution or regression with respect to the evaluation made few days post-irradiation with an in-vivo magnetic resonance imaging session. Histology, immunohistochemistry, SAXS/WAXS and XRF allowed identification and classification of these deposits as hydroxyapatite crystals with the coexistence of Ca, P and Fe mineralization, and the multi-technique approach enabled the realization, for the first time, of the map of the differential radiosensitivity of the different brain areas treated with MRT and MB. 3D XPCI-CT datasets enabled also the quantification of tumor volumes and Ca/Fe deposits and their full-organ visualization. The multi-scale and multi-technique approach enabled a detailed visualization and classification in 3D of the radio-induced effects on brain tissues bringing new essential information towards the clinical implementation of the MRT and MB radiation therapy techniques.

Published
2021
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210. Proceedings of the 2021 International Conference on the Network of the Future

Author

Machuca, Carmen Mas, MARTINS, Lucia, Sargento, Susana, Wauters, Tim, Jorge, Maria Luísa, Salhab, Nazih, CHEMOUIL, Prosper, Technical University of Munich (TUM), Institute for Systems Engineering and Computers at Coimbra [INESC Coimbra], Department of Electronics, Telecommunications and Informatics [Aveiro] (DETI), Universidade de Aveiro, Universiteit Gent = Ghent University [Belgium] (UGENT), Auteur indépendant, CEDRIC. Réseaux et Objets Connectés (CEDRIC - ROC), Centre d'études et de recherche en informatique et communications (CEDRIC), Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
[INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021
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211. Extreme lows of wheat production in Brazil

Author

Marijn van der Velde, Tamara Ben-Ari, Pierre Martre, Rogério de Souza Nóia Júnior, Frank Ewert, Heidi Webber, Alex C. Ruane, Robert Finger, Senthold Asseng, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Management, Technology, and Economics [ETH Zürich] (D-MTEC), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), European Commission - Joint Research Centre [Ispra] (JRC), Centre International de Recherche sur l'Environnement et le Développement (CIRED), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École des hautes études en sciences sociales (EHESS)-AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), and Technical University of Munich (TUM)

Subjects
2. Zero hunger, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, 010504 meteorology & atmospheric sciences, Renewable Energy, Sustainability and the Environment, Public Health, Environmental and Occupational Health, Climate change, 15. Life on land, 01 natural sciences, ddc, 03 medical and health sciences, Extreme weather, Geography, climate change, 13. Climate action, extreme weather, Climatology, food price and food security, Food price and food security, Production (economics), 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science
Abstract

Wheat production in Brazil is insufficient to meet domestic demand and falls drastically in response to adverse climate events. Multiple, agro-climate-specific regression models, quantifying regional production variability, were combined to estimate national production based on past climate, cropping area, trend-corrected yield, and national commodity prices. Projections with five CMIP6 climate change models suggest extremes of low wheat production historically occurring once every 20 years would become up to 90% frequent by the end of this century, depending on representative concentration pathway, magnified by wheat and in some cases by maize price fluctuations. Similar impacts can be expected for other crops and in other countries. This drastic increase in frequency in extreme low crop production with climate change will threaten Brazil's and many other countries progress toward food security and abolishing hunger. ISSN:1748-9326 ISSN:1748-9318

Published
2021
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212. Modeling Interactions of Autonomous Vehicles and Pedestrians with Deep Multi-Agent Reinforcement Learning for Collision Avoidance

Author

Trumpp, Raphael, Bayerlein, Harald, Gesbert, David, Technical University of Munich (TUM), Eurecom [Sophia Antipolis], ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
FOS: Computer and information sciences, Computer Science - Robotics, Computer Science - Machine Learning, Artificial Intelligence (cs.AI), Computer Science - Artificial Intelligence, Computer Science - Multiagent Systems, [INFO.INFO-IA]Computer Science [cs]/Computer Aided Engineering, Robotics (cs.RO), Machine Learning (cs.LG), Multiagent Systems (cs.MA)
Abstract

Reliable pedestrian crash avoidance mitigation (PCAM) systems are crucial components of safe autonomous vehicles (AVs). The nature of the vehicle-pedestrian interaction where decisions of one agent directly affect the other agent's optimal behavior, and vice versa, is a challenging yet often neglected aspect of such systems. We address this issue by modeling a Markov decision process (MDP) for a simulated AV-pedestrian interaction at an unmarked crosswalk. The AV's PCAM decision policy is learned through deep reinforcement learning (DRL). Since modeling pedestrians realistically is challenging, we compare two levels of intelligent pedestrian behavior. While the baseline model follows a predefined strategy, our advanced pedestrian model is defined as a second DRL agent. This model captures continuous learning and the uncertainty inherent in human behavior, making the AV-pedestrian interaction a deep multi-agent reinforcement learning (DMARL) problem. We benchmark the developed PCAM systems according to the collision rate and the resulting traffic flow efficiency with a focus on the influence of observation uncertainty on the decision-making of the agents. The results show that the AV is able to completely mitigate collisions under the majority of the investigated conditions and that the DRL pedestrian model learns an intelligent crossing behavior., IEEE Intelligent Vehicles Symposium 2022

Published
2021

213. Resiliency in numerical algorithm design for extreme scale simulations

Author

Emmanuel Agullo, Mirco Altenbernd, Hartwig Anzt, Leonardo Bautista-Gomez, Tommaso Benacchio, Luca Bonaventura, Hans-Joachim Bungartz, Sanjay Chatterjee, Florina M Ciorba, Nathan DeBardeleben, Daniel Drzisga, Sebastian Eibl, Christian Engelmann, Wilfried N Gansterer, Luc Giraud, Dominik Göddeke, Marco Heisig, Fabienne Jézéquel, Nils Kohl, Xiaoye Sherry Li, Romain Lion, Miriam Mehl, Paul Mycek, Michael Obersteiner, Enrique S Quintana-Ortí, Francesco Rizzi, Ulrich Rüde, Martin Schulz, Fred Fung, Robert Speck, Linda Stals, Keita Teranishi, Samuel Thibault, Dominik Thönnes, Andreas Wagner, Barbara Wohlmuth, High-End Parallel Algorithms for Challenging Numerical Simulations (HiePACS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universität Stuttgart [Stuttgart], Karlsruher Institut für Technologie (KIT), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Politecnico di Milano [Milan] (POLIMI), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), NVIDIA Corporation [Bangalore], NVIDIA Research [Austin], University Hospital Basel [Basel], Los Alamos National Laboratory (LANL), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, University of Vienna [Vienna], Performance et Qualité des Algorithmes Numériques (PEQUAN), LIP6, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Assas (UP2), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Université de Bordeaux (UB), CERFACS, Universitat Politècnica de València (UPV), NexGen Analytics (NGA), Australian National University (ANU), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Sandia National Laboratories - Corporation, Technische Universität München [München] (TUM), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, STatic Optimizations, Runtime Methods (STORM), Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique (CERFACS), and Barcelona Supercomputing Center

Subjects
G.4, FOS: Computer and information sciences, Numerical algorithms, Large scale systems, G.1, 010103 numerical & computational mathematics, 02 engineering and technology, 01 natural sciences, Theoretical Computer Science, Simulació per ordinador, 0202 electrical engineering, electronic engineering, information engineering, parallel computer architecture, 0101 mathematics, Informàtica::Arquitectura de computadors::Arquitectures paral·leles [Àrees temàtiques de la UPC], resilience, D.4.5, D.4.4, 020203 distributed computing, Parallel computer architecture, Resilience, Fault tolerance, Computer Science - Distributed, Parallel, and Cluster Computing, Hardware and Architecture, Fault tolerance (Engineering), Distributed, Parallel, and Cluster Computing (cs.DC), fault tolerance, ddc:004, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Software, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract

This work is based on the seminar titled ``Resiliency in Numerical Algorithm Design for Extreme Scale Simulations'' held March 1-6, 2020 at Schloss Dagstuhl, that was attended by all the authors. Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge., Comment: 45 pages, 3 figures, submitted to The International Journal of High Performance Computing Applications

Published
2021
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214. SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species

Author

V. Bernardes-Genisson, P. Rulliere, M. V. de Brito, P. R. A. Zanon, Julien Marcoux, C. Barthes, M. Marcellin, Odile Burlet-Schiltz, Pascal Demange, Etienne Joly, Patrick Calsou, Sébastien Britton, R. Hee, K. Pradines, Maria da Conceição F. de Oliveira, S. M. Hacker, Olivier Bouchez, Dymytrii Listunov, Céline Noirot, J.-B. Izquierdo, Remi Chauvin, Valérie Maraval, Stéphanie Ballereau, Remy-Felix Serre, Yves Genisson, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (SPCMIB), Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie de coordination (LCC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade Federal do Ceará = Federal University of Ceará (UFC), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Britton, Sébastien, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Technical University of Munich (TUM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Toulouse (UT)

Subjects
[SDV]Life Sciences [q-bio], Dehydrogenase, [SDV.GEN] Life Sciences [q-bio]/Genetics, 01 natural sciences, 03 medical and health sciences, [CHIM] Chemical Sciences, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cytotoxic T cell, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cytotoxicity, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, 010405 organic chemistry, Endoplasmic reticulum, 3. Good health, 0104 chemical sciences, [SDV] Life Sciences [q-bio], Enzyme, chemistry, Biochemistry, Mechanism of action, Unfolded protein response, medicine.symptom, Proto-oncogene tyrosine-protein kinase Src
Abstract

Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxic dialkynylcarbinols, involves a bioactivation by HSD17B11, a short-chain dehydrogenase/reductase (SDR) known to oxidize the C-17 carbinol center of androstan-3-alpha,17-beta-diol to the corresponding ketone. A similar oxidation of dialkynylcarbinols generates dialkynylketones, that we characterize as highly protein-reactive electrophiles. We established that, once bioactivated in cells, the dialkynylcarbinols covalently modify several proteins involved in protein-quality control mechanisms, resulting in their lipoxidation on cysteines and lysines through Michael addition. For some proteins, this triggers their association to cellular membranes and results in endoplasmic reticulum stress, unfolded protein response activation, ubiquitin-proteasome system inhibition and cell death by apoptosis. Finally, as a proof-of-concept, we show that generic lipidic alkynylcarbinols can be devised to be bioactivated by other SDRs, including human RDH11 and HPGD/15-PGDH. Given that the SDR superfamily is one of the largest and most ubiquitous, this unique cytotoxic mechanism-of-action could be widely exploited to treat diseases, in particular cancer, through the design of tailored prodrugs. Graphical abstract

Published
2021

215. Intronic elements associated with insomnia and restless legs syndrome exhibit cell type-specific epigenetic features contributing to MEIS1 regulation

Author

Nazanin Mirza-Schreiber, Wojciech Krezel, Juliane Winkelmann, Ana Antic Nikolic, Konrad Oexle, Daniel D. Lam, Chen Zhao, Helmholtz Zentrum München = German Research Center for Environmental Health, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technische Universität München = Technical University of Munich (TUM), and univOAK, Archive ouverte

Subjects
Cell type, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Biology, Epigenesis, Genetic, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Restless Legs Syndrome, Sleep Initiation and Maintenance Disorders, Genetics, Humans, Epigenetics, Myeloid Ecotropic Viral Integration Site 1 Protein, Enhancer, Molecular Biology, Genetics (clinical), regulatory element, Regulation of gene expression, enhancer-promoter interaction, CRISPR interference, Developmental maturation, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, ATAC-seq, General Medicine, DNA methylation: eQTLs, Introns, Cell biology, Chromatin, 4C-seq, chromatin accessibility, in vitro differentiation, DNA methylation, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], enhancer
Abstract

A highly evolutionarily conserved MEIS1 intronic region is strongly associated with restless legs syndrome (RLS) and insomnia. To understand its regulatory function, we dissected the region by analyzing chromatin accessibility, enhancer-promoter contacts, DNA methylation, and eQTLs in different human neural cell types and tissues. We observed specific activity with respect to cell type and developmental maturation, indicating a prominent role for distinct highly conserved intronic elements in forebrain inhibitory neuron differentiation. Two elements were hypomethylated in neural cells with higher MEIS1 expression, suggesting a role of enhancer demethylation in gene regulation. MEIS1 eQTLs showed a striking modular chromosomal distribution, with forebrain eQTLs clustering in intron 8/9. CRISPR interference targeting of individual elements in this region attenuated MEIS1 expression, revealing a complex regulatory interplay of distinct elements. In summary, we found that MEIS1 regulation is organized in a modular pattern. Disease-associated intronic regulatory elements control MEIS1 expression with cell type and maturation stage specificity, particularly in the inhibitory neuron lineage. The precise spatiotemporal activity of these elements likely contributes to the pathogenesis of insomnia and RLS.

Published
2021
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216. The contribution of insects to global forest deadwood decomposition

Author

David B. Lindenmayer, Michael D. Ulyshen, Wolfgang W. Weisser, Hassan Barimani Varandi, Jacques S. Rakotondranary, Jacques Beauchêne, Romina Daiana Fernandez, Gergely Boros, Jean-Baptiste Ramanamanjato, Stephen M. Pawson, Joakim Hjältén, Petr Baldrian, Grizelle González, Erika Berenguer, Jari Kouki, Naili Zhang, Hervé Brustel, Torsten Hothorn, Sung-Soo Yoon, John O'Halloran, Yu Liu, Sharif A. Mukul, Byambagerel Suran, Philip J. Burton, Pablo E. Martina, Liana Chesini Rossi, Sebastian Seibold, Jürgen Schmidl, Stefan Hotes, Tyler P. Cobb, Janina Lorz, Kurtis Nisbet, Jorge Castro, Stephen Seaton, Anne Oxbrough, Roxana Aragón, Jennifer Firn, Werner Rammer, Roland Brandl, Thibault Lachat, Tone Birkemoe, Jos Barlow, Nina Farwig, Mark Schulze, Martin M. Gossner, Jeev Nath Pandey, Soyeon Bae, Ya-Huang Luo, Simon Thorn, Baatarbileg Nachin, Tim Wardlaw, Kee Seng Gan, Yvonne Tété Cakpo-Tossou, Jie Liu, Claus Bässler, Ganesh Thyagarajan, Yagya Prasad Adhikari, Damasa M. Macandog, Claudia Hemp, Tomáš Pavlíček, Osmo Heikkala, Jan Christian Habel, Marisa J. Stone, Christian Hébert, Christoph Heibl, Nigel E. Stork, Rupert Seidl, Rodrigo Scarton Bergamin, Eugénie Cateau, Jörg Müller, Andreas Hemp, Anne Sverdrup-Thygeson, Marc W. Cadotte, Technical University of Munich (TUM), Institute of Silviculture, Department of Forest and Soil Sciences, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Natural Resources and Life Sciences (BOKU), USDA Forest Service Rocky Mountain Forest and Range Experiment Station, United States Department of Agriculture (USDA), Field Station Fabrikschleichach, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), University of Toronto [Scarborough, Canada], Climate Change Institute at the Australian National University, Australian National University (ANU), University of Bayreuth, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales [Mendoza] (CONICET-IANIGLA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de Cuyo [Mendoza] (UNCUYO), University of Würzburg, Institute of Microbiology of the Czech Academy of Sciences (MBU / CAS), Czech Academy of Sciences [Prague] (CAS), University of Mazandaran, Lancaster Environment Centre, Lancaster University, Goethe-University Frankfurt am Main, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Federal University of Rio Grande do Sul, Norwegian University of Life Sciences (NMBU), CENTRE FOR ECOLOGICAL RESEARCH VACRATOT HUN, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Philipps University of Marburg, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Northern British Columbia [Prince George] (UNBC), University of Abomey Calavi (UAC), University of Granada [Granada], Réserves Naturelles de France, Royal Alberta Museum, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Queensland University of Technology [Brisbane] (QUT), Forest Research Institute Malaysia (FRIM), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, University of Salzburg, Canadian Forest Service - CFS (CANADA), Bavarian Forest National Park, Eurofins Ahma Oy, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Technical University of Munich, Berchtesgaden National Park, University of Zurich, USDA Forest Service, University of Toronto Scarborough, The Australian National University, CONICET-Universidad Nacional de Tucumán, The Czech Academy of Sciences, Agricultural and Natural Resources Research Centre of Mazandaran, Universidade Federal de Lavras (UFLA), Goethe-University Frankfurt, Universite de Guyane, University of Oxford, Norwegian University of Life Sciences, Centre for Ecological Research, Hungarian University of Agriculture and Life Sciences, University of Marburg, UMR 1201 Dynafor, University of Northern British Columbia, University of Abomey-Calavi, University of Granada, Queensland University of Technology, Institute for Future Environments, Forest Research Institute Malaysia, Swiss Federal Research Institute WSL, Canadian Forest Service, Swedish University of Agricultural Sciences, Chuo University, University of Eastern Finland, Bern University of Applied Sciences, Chinese Academy of Sciences, East China Normal University, University of the Philippines Los Banos, Universidad Nacional del Nordeste, University of the Sunshine Coast, National University of Mongolia, Griffith University, University College Cork, Edge Hill University, Tribhuvan University, University of Haifa, Scion (New Zealand Forest Research Institute), University of Canterbury, University of Hamburg, Université d’Antananarivo, Tropical Biodiversity and Social Enterprise, Universidade Estadual Paulista (UNESP), University Erlangen-Nuremberg, H. J. Andrews Experimental Forest, Murdoch University, Ashoka Trust for Research in Ecology and the Environment, University of Tasmania, National Institute of Ecology, and Beijing Forestry University

Subjects
0106 biological sciences, Carbon Sequestration, Insecta, 010504 meteorology & atmospheric sciences, Climate, International Cooperation, chemistry.chemical_element, Geographic Mapping, Forests, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, Decomposer, Carbon cycle, Carbon Cycle, Trees, Forest ecology, Temperate climate, Animals, Ecosystem, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Multidisciplinary, Taiga, 15. Life on land, Decomposition, Deadwood, Insects, chemistry, 13. Climate action, Environmental science, Ecosystem ecology, Carbon
Abstract

Made available in DSpace on 2022-04-28T19:44:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-09-02 The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2–5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle. Ecosystem Dynamics and Forest Management Group School of Life Sciences Technical University of Munich Berchtesgaden National Park Epidemiology Biostatistics and Prevention Institute University of Zurich Southern Research Station USDA Forest Service Field Station Fabrikschleichach University of Würzburg Biological Sciences University of Toronto Scarborough Fenner School of Environment and Society The Australian National University Department of Biogeography University of Bayreuth Department of Disturbance Ecology University of Bayreuth Instituto de Ecología Regional CONICET-Universidad Nacional de Tucumán Department of Animal Ecology and Tropical Biology University of Würzburg Laboratory of Environmental Microbiology Institute of Microbiology The Czech Academy of Sciences Agricultural and Natural Resources Research Centre of Mazandaran Lancaster Environment Centre Lancaster University Universidade Federal de Lavras Department of Biodiversity Conservation Goethe-University Frankfurt Bavarian Forest National Park CIRAD UMR Ecologie des Forêts de Guyane (EcoFoG) AgroParisTech CNRS INRA Universite des Antilles Universite de Guyane Environmental Change Institute University of Oxford Grassland Vegetation Lab Federal University of Rio Grande do Sul Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Institute of Ecology and Botany Centre for Ecological Research Institute for Wildlife Management and Nature Conservation Hungarian University of Agriculture and Life Sciences Animal Ecology University of Marburg École d’Ingénieurs de Purpan Université de Toulouse UMR 1201 Dynafor Ecosystem Science and Management Program University of Northern British Columbia Laboratory of Applied Ecology University of Abomey-Calavi Department of Ecology University of Granada Réserves Naturelles de France Royal Alberta Museum Conservation Ecology University of Marburg Science and Engineering Faculty Queensland University of Technology Centre for the Environment Institute for Future Environments Forest Research Institute Malaysia International Institute of Tropical Forestry USDA Forest Service Forest Entomology Swiss Federal Research Institute WSL Evolutionary Zoology University of Salzburg Natural Resources Canada Canadian Forest Service Eurofins Ahma Oy Department of Plant Systematics University of Bayreuth Department of Wildlife Fish and Environmental Studies Swedish University of Agricultural Sciences Applied Landscape Ecology Chuo University School of Forest Sciences University of Eastern Finland School of Agricultural Forest and Food Sciences Bern University of Applied Sciences CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences ECNU-Alberta Joint Lab for Biodiversity Study Tiantong National Station for Forest Ecosystem Research East China Normal University Institute of Biological Sciences University of the Philippines Los Banos Department of Thermodynamics Universidad Nacional del Nordeste Tropical Forests and People Research Centre University of the Sunshine Coast Forest Ecosystem Monitoring Laboratory National University of Mongolia School of Environment and Science Griffith University School of Biological Earth and Environmental Sciences University College Cork Edge Hill University Institute of Forestry Tribhuvan University Institute of Evolution University of Haifa Scion (New Zealand Forest Research Institute) School of Forestry University of Canterbury Institute of Zoology University of Hamburg Faculté des Sciences Université d’Antananarivo Tropical Biodiversity and Social Enterprise Departamento de Ecologia Universidade Estadual Paulista Ecology Group University Erlangen-Nuremberg H. J. Andrews Experimental Forest Environmental and Conservation Sciences Murdoch University Environmental Futures Research Institute Griffith University Ashoka Trust for Research in Ecology and the Environment ARC Centre for Forest Value University of Tasmania Terrestrial Ecology Research Group School of Life Sciences Technical University of Munich EcoBank Team National Institute of Ecology College of Forestry Beijing Forestry University Departamento de Ecologia Universidade Estadual Paulista

Published
2021
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217. An increase in food production in Europe could dramatically affect farmland biodiversity

Author

Philippe Pointereau, Zoltán Elek, Tiziano Gomiero, Sebastian Wolfrum, Wendy Jane Fjellstad, Gergely Jerkovich, Jean-Pierre Sarthou, Mario Díaz, Pippa Gillingham, Manuel K. Schneider, Michaela Arndorfer, Jean-Philippe Choisis, Juri Nascimbene, Katalin Balázs, Peter Dennis, Sebastian Eiter, Philippe Jeanneret, Daniele Sommaggio, Rob H. G. Jongman, Thomas Frank, Anikó Kovács-Hostyánszki, Gerardo Moreno, Norman Siebrecht, Marie-Louise Oschatz, Jürgen K. Friedel, Max Kainz, Felix Herzog, Maurizio G. Paoletti, András Báldi, Debra Bailey, Gisela Lüscher, Ilse R. Geijzendorffer, European Commission, Federal Ministry of Science, Research and Economy (Austria), Hungarian Academy of Sciences, Agroscope, University of Applied Science Schmalkalden, SOLAGRO, Arche Noah, University Natural Resources and Life, Department of Radiation Medicine, MTA Centre for Ecological Research, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, CSIC, Museo Nacl Ciencias Nat, Norwegian Forest and Landscape Institute, University of Natural Resources and Life Sciences, Vienna, Wageningen Environmental Research (Alterra), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Universita degli Studi di Padova, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University of Extremadura, University of Bologna, AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Commission 227161, Austrian Ministry for Science and Research, Lendulet program of the Hungarian Academy of Sciences, Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Technical University of Munich (TUM), Association Solagro (Solagro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Università degli Studi di Padova = University of Padua (Unipd), Universidad de Extremadura - University of Extremadura (UEX), University of Bologna/Università di Bologna, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Jeanneret, Philippe, Lüscher, Gisela, Schneider, Manuel K., Pointereau, Philippe, Arndorfer, Michaela, Bailey, Debra, Balázs, Katalin, Báldi, Andrá, Choisis, Jean-Philippe, Dennis, Peter, Diaz, Mario, Eiter, Sebastian, Elek, Zoltán, Fjellstad, Wendy, Frank, Thoma, Friedel, Jürgen K., Geijzendorffer, Ilse R., Gillingham, Pippa, Gomiero, Tiziano, Jerkovich, Gergely, Jongman, Rob H. G., Kainz, Max, Kovács-Hostyánszki, Anikó, Moreno, Gerardo, Nascimbene, Juri, Oschatz, Marie-Louise, Paoletti, Maurizio G., Sarthou, Jean-Pierre, Siebrecht, Norman, Sommaggio, Daniele, Wolfrum, Sebastian, and Herzog, Felix

Subjects
0106 biological sciences, RAREFACTION, 010504 meteorology & atmospheric sciences, DEMAND, CONSERVATION, Biodiversity, DIVERSITY, 010603 evolutionary biology, 01 natural sciences, Biodiversity and Policy, Permanent crop, SUSTAINABILITY, Agricultural land, Biodiversiteit en Beleid, MANAGEMENT, Life Science, GE1-350, Agricultural productivity, 0105 earth and related environmental sciences, General Environmental Science, biodiversity, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, QE1-996.5, Land use, LANDSCAPE, Agroforestry, business.industry, INTENSITY, INTENSIFICATION, EXTRAPOLATION, Geology, 15. Life on land, Environmental sciences, Habitat destruction, Geography, 13. Climate action, Agriculture, General Earth and Planetary Sciences, Arable land, business
Abstract

Conversion of semi-natural habitats, such as field margins, fallows, hedgerows, grassland, woodlots and forests, to agricultural land could increase agricultural production and help meet rising global food demand. Yet, the extent to which such habitat loss would impact biodiversity and wild species is unknown. Here we survey species richness for four taxa (vascular plants, earthworms, spiders, wild bees) and agricultural yield across a range of arable, grassland, mixed, horticulture, permanent crop, for organic and non-organic agricultural land on 169 farms across 10 European regions. We find that semi-natural habitats currently constitute 23% of land area with 49% of species unique to these habitats. We estimate that conversion of semi-natural land that achieves a 10% increase in agricultural production will have the greatest impact on biodiversity in arable systems and the least impact in grassland systems, with organic practices having better species retention than nonorganic practices., This work was funded by the European Union through FP7 project BioBio (Indicators for biodiversity in organic and low-input farming systems; www.biobio-indicator.org; Agreement Nr. 227161), by the Austrian Ministry for Science and Research, and by the Lendület program of the Hungarian Academy of Sciences.

Published
2021
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218. M‐CSF‐mediated macrophage development is dominantly inhibited by NOD2 signaling for replenishment of immunogenic dendritic cells

Author

Chauvin, Camille, Alvarez-Simon, Daniel, Régnier, Paul, Radulovic, Katarina, Boulard, Olivier, Delacre, Myriam, Waldschmitt, Nadine, Peyrin-Biroulet, Laurent, Kluza, Jérôme, Darrasse-Jèze, Guillaume, Chamaillard, Mathias, Poulin, Lionel Franz, Institut Pasteur [Paris] (IP), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Immunologie - Immunopathologie - Immunothérapie [CHU Pitié Salpêtrière] (I3), CHU Charles Foix [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre hospitalier [Valenciennes, Nord], Laboratoire de Physiologie Cellulaire : Canaux ioniques, inflammation et cancer - U 1003 (PHYCELL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Chair of Nutrition and Immunology, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Service d'Hépato-gastro-entérologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 (CANTHER), Immunologie - Immunopathologie - Immunothérapeutique (I3), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract

International audience; Despite recent advances, it remains unclear whether monocyte‐derived dendritic cells (moDCs) represent alternative context‐dependent fate in the gut. We found here that Nod2‐ dependent sensing of bacteria lowers the ability of circulating monocytes to respond to M‐CSF for generating moDCs. Such inhibitory effect on monocyte‐to‐macrophage transition was prevented upon blockade of TNF‐α. Recognition of the gut microbiota by Nod2 was sufficient to promote the expansion of moDCs within the colonic mucosa. A competitive bone marrow transplant model further demonstrated that Nod2 promotes the conversion of monocytes into dendritic cells. Equally of importance, tumours with the highest transcript levels of NOD2 were associated with a favorable prognosis and characterized by an enrichment of a gene signature related to moDCs. This study implicates that Nod2‐dependent sensing of the gut microbiota influences monocytic lineage commitment into dendritic cells, which sets the stage for future investigations to achieve accurate outcome prediction in colorectal cancer.

Published
2021
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219. EAACI guideline: Anaphylaxis (2021 update)

Author

Lynne Regent, Elizabeth Angier, Lene H. Garvey, Margitta Worm, Diola Bijlhout, Debra de Silva, Victoria Cardona, Cherry Alviani, Audrey DunnGalvin, Susanne Halken, Angel Sánchez, Britt Jensen, Antonella Muraro, Louise J Michaelis, Maria Beatrice Bilò, Montserrat Fernandez-Rivas, Berber Vlieg-Boerstra, Graham Roberts, Hanneke Oude Elberink, Knut Brockow, Ekaterina Khaleva, Kirsten Beyer, Abdelouahab Bellou, Carsten Bindslev-Jensen, Stefania Arasi, Carmen Riggioni, University Hospital of Padua, University of Southampton, Vall d'Hebron University Hospital [Barcelona], University College Cork (UCC), Yong Loo Lin School of Medicine [Singapore], Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Wayne State University School of Medicine, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos [Madrid, Spain] (IdISSC), University Medical Center Groningen [Groningen] (UMCG), OLVG Hospital, Technical University of Munich (TUM), Groningen Research Institute for Asthma and COPD (GRIAC), Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP), and Université de Rennes (UR)

Subjects
Allergy, Epinephrine, First line, [SDV]Life Sciences [q-bio], Immunology, Guidelines, 03 medical and health sciences, 0302 clinical medicine, children, Autoinjector, adults, anaphylaxis, Humans, Immunology and Allergy, Medicine, Adults, guidelines, Anaphylaxis, Children, 030304 developmental biology, 0303 health sciences, Health professionals, business.industry, Guideline, medicine.disease, 3. Good health, Clinical trial, 030228 respiratory system, Tryptases, Medical emergency, business, Blood sampling
Abstract

Anaphylaxis is a clinical emergency which all healthcare professionals need to be able to recognise and manage. The European Academy of Allergy and Clinical Immunology Anaphylaxis multidisciplinary Task Force has updated the 2014 guideline. The guideline was developed using the AGREE II framework and the GRADE approach. The evidence was systematically reviewed and recommendations were created by weighing up benefits and harms. The guideline was peer-reviewed by external experts and reviewed in a public consultation. The use of clinical criteria to identify anaphylaxis is suggested with blood sampling for the later measurement of tryptase. The prompt use of intramuscular adrenaline as first line management is recommended with the availability of adrenaline autoinjectors to patients in the community. Pharmacokinetic data should be provided for adrenaline autoinjector devices. Structured, comprehensive training for people at risk of anaphylaxis is recommended. Simulation training and visual prompts for healthcare professionals are suggested to improve the management of anaphylaxis. It is suggested that school policies reflect anaphylaxis guidelines. The evidence for the management of anaphylaxis remains mostly at a very low level. There is an urgent need to prioritise clinical trials with the potential to improve the management of patients at risk of anaphylaxis. Anaphylaxis is a clinical emergency which all healthcare professionals need to be able to recognize and manage. The European Academy of Allergy and Clinical Immunology Anaphylaxis multidisciplinary Task Force has updated the 2014 guideline. The guideline was developed using the AGREE II framework and the GRADE approach. The evidence was systematically reviewed and recommendations were created by weighing up benefits and harms. The guideline was peer-reviewed by external experts and reviewed in a public consultation. The use of clinical criteria to identify anaphylaxis is suggested with blood sampling for the later measurement of tryptase. The prompt use of intramuscular adrenaline as first-line management is recommended with the availability of adrenaline autoinjectors to patients in the community. Pharmacokinetic data should be provided for adrenaline autoinjector devices. Structured, comprehensive training for people at risk of anaphylaxis is recommended. Simulation training and visual prompts for healthcare professionals are suggested to improve the management of anaphylaxis. It is suggested that school policies reflect anaphylaxis guidelines. The evidence for the management of anaphylaxis remains mostly at a very low level. There is an urgent need to prioritize clinical trials with the potential to improve the management of patients at risk of anaphylaxis.

Published
2021
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220. Tailoring the Oxygen Reduction Activity of Pt Nanoparticles through Surface Defects: A Simple Top-Down Approach

Author

Regina M. Kluge, Weijin Li, Jan Michalička, Hany A. El-Sayed, Raphaël Chattot, Thomas Gigl, Aliaksandr S. Bandarenka, Felix Haimerl, Batyr Garlyyev, Di Wang, Christoph Hugenschmidt, Wu Wang, Jan M. Macak, Johannes Fichtner, Sebastian Watzele, Laetitia Dubau, Frédéric Maillard, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Electrochimie Interfaciale et Procédés (EIP), Laboratoire d'Electrochimie et de Physico-chimie des Matériaux et des Interfaces (LEPMI), Institut de Chimie du CNRS (INC)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-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 de Chimie du CNRS (INC)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-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), European Synchrotron Radiation Facility (ESRF), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institute of Nanotechnology [Karlsruhe] (INT), Karlsruhe Institute of Technology (KIT), and Forschungszentrum Julich, Heinz Maier Leibnitz Zentrum MLZ, JCNS, Lichtenbergstr 1, D-85747 Garching, Germany

Subjects
Surface (mathematics), Technology, Materials science, 010405 organic chemistry, Kinetics, food and beverages, [CHIM.CATA]Chemical Sciences/Catalysis, [CHIM.MATE]Chemical Sciences/Material chemistry, General Chemistry, 2019-022-025989, 010402 general chemistry, Platinum nanoparticles, Electrocatalyst, 01 natural sciences, Catalysis, Oxygen reduction, 0104 chemical sciences, Chemical engineering, TEM, Oxygen reduction reaction, Pt nanoparticles, ddc:600, ComputingMilieux_MISCELLANEOUS
Abstract

Results from Pt model catalyst surfaces have demonstrated that surface defects, in particular surface concavities, can improve the oxygen reduction reaction (ORR) kinetics. It is, however, a challe...

Published
2020
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221. Energy-aware scheduling in reconfigurable multiple path shop floors

Author

Michael F. Zaeh, Julia Schulz, Damien Lamy, École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT), Institut Henri Fayol (FAYOL-ENSMSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Département Génie mathématique et industriel (FAYOL-ENSMSE), Ecole Nationale Supérieure des Mines de St Etienne-Institut Henri Fayol, and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
0209 industrial biotechnology, 021103 operations research, Energy Efficiency, Scheduling, business.industry, Computer science, Reconfigurable Manufacturing Systems, 0211 other engineering and technologies, Scheduling (production processes), Geodetic datum, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], 02 engineering and technology, Industrial engineering, Personalization, Energy aware scheduling, 020901 industrial engineering & automation, Assembly systems, Energy Flexibility, General Earth and Planetary Sciences, Architecture, business, General Environmental Science, Agile software development, Efficient energy use
Abstract

International audience; In today's business environment, the trend towards more product variety and customization is unbroken. Due to this development, the need of agile and reconfigurable production systems emerged to cope with various products and product families. To design and optimize production systems as well as to choose the optimal product matches, product analysis methods are needed. Indeed, most of the known methods aim to analyze a product or one product family on the physical level. Different product families, however, may differ largely in terms of the number and nature of components. This fact impedes an efficient comparison and choice of appropriate product family combinations for the production system. A new methodology is proposed to analyze existing products in view of their functional and physical architecture. The aim is to cluster these products in new assembly oriented product families for the optimization of existing assembly lines and the creation of future reconfigurable assembly systems. Based on Datum Flow Chain, the physical structure of the products is analyzed. Functional subassemblies are identified, and a functional analysis is performed. Moreover, a hybrid functional and physical architecture graph (HyFPAG) is the output which depicts the similarity between product families by providing design support to both, production system planners and product designers. An illustrative example of a nail-clipper is used to explain the proposed methodology. An industrial case study on two product families of steering columns of thyssenkrupp Presta France is then carried out to give a first industrial evaluation of the proposed approach.

Published
2020
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222. OBEDIS Core Variables Project: European Expert Guidelines on a Minimal Core Set of Variables to Include in Randomized, Controlled Clinical Trials of Obesity Interventions

Author

António L. Palmeira, Thorkild I. A. Sørensen, Martin Neovius, Martine Laville, Mikael Rydén, Andrea Natali, Maud Alligier, Romain Barrès, Kristina Campbell, David Jacobi, I. Sadaf Farooqi, Jean-Michel Oppert, Helen M. Roche, André Scheen, Karine Clément, Ellen E. Blaak, Yves Boirie, Gijs H. Goossens, Jason C.G. Halford, Luc Tappy, Nathalie Farpour-Lambert, Hannele Yki-Järvinen, Uberto Pagotto, Chantal Simon, Jörg Hager, Jildau Bouwman, Paul Brunault, Gema Frühbeck, Dominique Langin, Olivier Ziegler, Chantal Julia, Hans Hauner, Centre de Recherche en Nutrition Humaine Rhône-Alpes (CRNH-RA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-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 Grenoble Alpes (UGA), University of Copenhagen = Københavns Universitet (KU), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], CHU Clermont-Ferrand, Netherlands Organization for Applied Scientific Research (TNO), TNO Science and Industry, Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Tours (UT), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Imagerie et cerveau (iBrain - Inserm U1253 - UNIV Tours ), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), KC Microbiome Communications Group, Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), NIHR Biomedical Research Centre [London], Guy's and St Thomas' NHS Foundation Trust-King‘s College London, University of Cambridge [UK] (CAM), Université de Genève (UNIGE), Geneva University Hospitals and Geneva University, Clínica Universidad de Navarra [Pamplona], Nestlé Institute of Health Sciences SA [Lausanne, Switzerland], University of Liverpool, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Klinikums rechts der Isar, Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-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 des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Pisa - Università di Pisa, Karolinska Institutet [Stockholm], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Alma Mater Studiorum University of Bologna (UNIBO), Université de Lisbonne, University College Dublin [Dublin] (UCD), Centre Hospitalier Universitaire de Liège (CHU-Liège), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Université de Lausanne (UNIL), Minerva Foundation Institute for Medical Research, University of Helsinki, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Joint Programming Initiative Heathy Diet for Healthy Life, Alligier M., Barres R., Blaak E.E., Boirie Y., Bouwman J., Brunault P., Campbell K., Clement K., Farooqi I.S., Farpour-Lambert N.J., Fruhbeck G., Goossens G.H., Hager J., Halford J.C.G., Hauner H., Jacobi D., Julia C., Langin D., Natali A., Neovius M., Oppert J.M., Pagotto U., Palmeira A.L., Roche H., Ryden M., Scheen A.J., Simon C., Sorensen T.I.A., Tappy L., Yki-Jarvinen H., Ziegler O., Laville M., FCRIN/FORCE Network, Centre de Recherche en Nutrition Humaine Rhône-Alpes, Novo Nordisk, Department of Human Biology, Maastricht University Medical Center (MUMC), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Nutrition clinique, Centre Hospitalier Universitaire Gabriel Montpied, TNO,Netherlands Organisation for Applied Scientific Research, UMR U 1253, Université de Tours, Nutrition et obésité : approches systémiques, Sorbonne Université, Wellcome-MRC Institute of Metabolic Science and NIHR Biomedical Research Centre, University of Cambridge, Service of Therapeutic Education for Chronic Diseases, Department of Community Health, Primary Care and Emergency, Geneva University Hospitals, Department of Endocrinology and Nutrition, Navarra Public Health Institute, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición - Biomedical Research Center in Red-Physiopathology of Obesity and Nutrition (CIBEROBN), University of Navarra, University of Cape Town, Metabolic Phenotyping, Nestlé Institute of Health Sciences, Psychological Sciences, University of Liverpool (University of Liverpool), Institut für Ernährungsmedizin des Klinikums Rechts der Isar, Technical University of Munich (TUM), Institut du Thorax, Centre Hospitalier Universitaire de Nantes, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC), Université Toulouse III - Paul Sabatier, Centre Hospitalier Universitaire de Toulouse, Department of Clinical and Experimental Medicine, Università degli studi di Napoli Federico II, Department of Medicine (Solna), Nutrition, Institut de Cardiométabolisme et Nutrition (ICAN), CHU Pitié-Salpêtrière [APHP], Department of Medical and Surgical Sciences, Universita degli Studi di Padova, CIPER, PANO-SR, Faculty of Human Kinetics, University of Lisbon, UCD Institute of Food and Health, University College Dublin (UCD), Department of Medicine, The University of Sydney, Diabètes, Nutrition et maladies métaboliques, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Physiologie, Université de Picardie Jules Verne (UPJV), Helsinki University Central Hospital, Endocrinologie, Diabetes et Nutrition, Hôpital Brabois, Maastricht University [Maastricht]-Maastricht University [Maastricht], Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ProdInra, Archive Ouverte, Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet - Saint-Étienne (UJM)-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 Grenoble Alpes (UGA), University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Université de Genève = University of Geneva (UNIGE), Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Lausanne = University of Lausanne (UNIL), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, HUS Internal Medicine and Rehabilitation, Humane Biologie, and RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health

Subjects
0301 basic medicine, Research design, Gerontology, Health (social science), Psychological intervention, Choice Behavior, 0302 clinical medicine, QUALITY-OF-LIFE, OBSTRUCTIVE SLEEP-APNEA, Medicine, Medical History Taking, lcsh:RC620-627, Interventions, METABOLIC SYNDROME, Randomized Controlled Trials as Topic, ddc:616, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Precision medicine, Prognosis, C-REACTIVE PROTEIN, 3. Good health, Europe, lcsh:Nutritional diseases. Deficiency diseases, CARDIOVASCULAR-DISEASE, Research Design, Variable, lcsh:Nutrition. Foods and food supply, Human, Prognosi, education, WEIGHT-LOSS, lcsh:TX341-641, Intervention, 030209 endocrinology & metabolism, GASTRIC BYPASS-SURGERY, Guidelines, Patient care, 03 medical and health sciences, Variables, Physiology (medical), Humans, CORONARY-HEART-DISEASE, Obesity, Expert Testimony, Core set, 030109 nutrition & dietetics, business.industry, Stratification, medicine.disease, Diet, BODY-MASS INDEX, Clinical trial, PHYSICAL-ACTIVITY, Biological Variation, Population, 3121 General medicine, internal medicine and other clinical medicine, Metabolic syndrome, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Heterogeneity of interindividual and intraindividual responses to interventions is often observed in randomized, controlled trials for obesity. To address the global epidemic of obesity and move toward more personalized treatment regimens, the global research community must come together to identify factors that may drive these heterogeneous responses to interventions. This project, called OBEDIS (OBEsity Diverse Interventions Sharing - focusing on dietary and other interventions), provides a set of European guidelines for a minimal set of variables to include in future clinical trials on obesity, regardless of the specific endpoints. Broad adoption of these guidelines will enable researchers to harmonize and merge data from multiple intervention studies, allowing stratification of patients according to precise phenotyping criteria which are measured using standardized methods. In this way, studies across Europe may be pooled for better prediction of individuals' responses to an intervention for obesity - ultimately leading to better patient care and improved obesity outcomes. © 2020 The Author(s) Published by S. Karger AG, Basel.

Published
2020
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223. Cross-European initial survey on the use of mathematical models in food industry

Author

Photis Papademas, Kamal Kansou, Alberto Tonda, Aleksandra Nikolić, Nickolas G. Kavallieratos, Ilija Djekic, Rallou Thomopoulos, Igor Tomasevic, Alen Mujčinović, Alexandrina Sirbu, Aberham Hailu Feyissa, Heiko Briesen, Alexandru Mihnea Moisescu, Anet Režek Jambrak, Urška Vrabič Brodnjak, Cristina L. M. Silva, Christos G. Athanassiou, Maria N. Charalambides, Department of Food Safety and Quality Management [Belgrade], Faculty of Agriculture [Belgrade], University of Belgrade [Belgrade]-University of Belgrade [Belgrade], Faculty of Agriculture and Food Sciences [Sarajevo], UNIVERZITET U SARAJEVU, Faculty of Food Technology & Biotechnology [Zagreb], University of Zagreb, Department of Agricultural Sciences, Biotechnology and Food Science [Limassol], Cyprus University of Technology, National Food Institute [Lyngby] (Forside), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Graphs for Inferences on Knowledge (GRAPHIK), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Chair Process Systems Engineering [Freising], Technische Universität München [München] (TUM), Faculty of Crop Science [Athens], Agricultural University of Athens, Department of Agriculture Crop Production and Rural Environment [Volos], University of Thessaly [Volos] (UTH), Escola Superior de Biotecnologia [Porto], Universidade Católica Portuguesa [Porto], Constantin Brancoveanu University [Râmnicu Vâlcea], University Politehnica of Bucharest [Romania] (UPB), Department of Animal Origin Products Technology [Belgrade], Faculty of Natural Sciences and Engineering [Ljubljana], University of Ljubljana, Department of Chemical Engineering [London], Imperial College London, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The authors would like to acknowledge the networking support by COST Action CA15118 (Mathematical and Computer Science Methods for Food Science and Industry - FoodMC) as well the help in conducting the survey provided by Prof. Dr Serafim Bakalis (Nottingham University), Dr. Efstathios Kaliviotis (Cyprus University of Technology), Mirza Uzunović (University of Sarajevo) and Erifili P. Nika (Agricultural University of Athens)., UNIVERSITY OF SARAJEVO - UNIVERZITET U SARAJEVU, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), European Project: 605414,EC:FP7:TPT,FP7-AAT-2013-RTD-1,CAPPADOCIA(2013), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), and Veritati - Repositório Institucional da Universidade Católica Portuguesa

Subjects
Micro level, Relation (database), Food industry, Knowledge in modellling, Context (language use), 03 medical and health sciences, 0404 agricultural biotechnology, 0302 clinical medicine, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Lack of knowledge, Industrial organization, 2. Zero hunger, Mathematical models, Usage of models, Mathematical model, business.industry, 04 agricultural and veterinary sciences, Limiting, 040401 food science, ddc, [STAT]Statistics [stat], Food sector, 030221 ophthalmology & optometry, Business, Knowledge in modelling, 0908 Food Sciences, Food Science
Abstract

International audience; Mathematical modelling plays an important role in food engineering having various mathematical models tailored for different food topics. However, mathematical models are followed by limited information on their application in food companies. This paper aims to discuss the extent and the conditions surrounding the usage of mathematical models in the context of European food and drinks industry. It investigates the knowledge, nature and current use of modelling approaches in relation to the industry main characteristics. A total of 203 food companies from 12 European countries were included in this research.Results reveal that the country where the company operates, and size of the company, are more important predictors on the usage of mathematical models followed by the type of food sector. The more developed countries are positioned at the higher level of knowledge and use of available models. Similar pattern was observed at the micro level showing that small or medium sized companies exhibit lack of knowledge, resources and limiting usage of models.

Published
2019
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224. Shakey Ever After? Questioning Tacit Assumptions in Robotics and Artificial Intelligence

Author

Alexandra Kirsch, Human-Computer Interaction and Artificial Intelligence, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Intelligent Autonomous Systems, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institute for Advanced Studies, and Independent Scientist

Subjects
business.industry, Computer science, Shakey the robot, 05 social sciences, Design elements and principles, Robotics, Space (commercial competition), 050105 experimental psychology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], law.invention, 03 medical and health sciences, 0302 clinical medicine, Artificial Intelligence, law, Milestone (project management), Robot, 0501 psychology and cognitive sciences, Point (geometry), Artificial intelligence, business, 030217 neurology & neurosurgery
Abstract

International audience; Shakey the robot was a milestone of autonomous robots and artificial intelligence. Its design principles have dominated research until now. Tacit philosophical and architectural assumptions have impoverished the space of research topics and methods. I point out ways to overcome this impasse with sideglances to other scientific fields.

Published
2019
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225. Petrophysical properties of the Muschelkalk from the Soultz-sous-Forêts geothermal site (France), an important lithostratigraphic unit for geothermal exploitation in the Upper Rhine Graben

Author

Heap, Michael J., Kushnir, Alexandra R. L., Gilg, H. Albert, Violay, Marie, Harlé, Pauline, Baud, Patrick, Géophysique expérimentale (IPGS) (IPGS-GE), Institut de physique du globe de Strasbourg (IPGS), Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), and Technical University of Munich (TUM)

Subjects
lcsh:Geology, Thermal properties, P-wave velocity, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], lcsh:TJ807-830, lcsh:QE1-996.5, lcsh:Renewable energy sources, Uniaxial compressive strength, Muschelkalk, Porosity, Microstructure, ComputingMilieux_MISCELLANEOUS
Abstract

The Muschelkalk, composed of Triassic limestones, marls, dolomites, and evaporites, forms part of the Permo-Triassic cover of sedimentary rocks that directly overlies the fractured granitic reservoir used for geothermal energy exploitation in the Upper Rhine Graben. Petrophysical data for this lithostratigraphic unit are sparse, but are of value for reservoir prospection, stimulation, and optimisation strategies at existing and prospective geothermal sites throughout the Upper Rhine Graben. To this end, we present here a systematic microstructural, mineralogical, and petrophysical characterisation of the Muschelkalk core (from the Middle to Lower Muschelkalk; from a depth of ~ 930 to ~ 1001 m) from exploration borehole EPS-1 at Soultz-sous-Forêts (France). First, we assessed the microstructure and mineral content of samples from six depths that we consider represent the variability of the available core. The majority of the core is composed of fine-grained, interbedded dolomites and marls; however, anhydrite and a dolomitic sandstone bank were found in the Upper and Lower Muschelkalk core, respectively. A larger suite of samples (from fifteen depths, including the six depths chosen for microstructural and mineral content analysis) were then characterised in terms of their petrophysical properties. The matrix porosity of the measured Muschelkalk samples is low, from ~ 0.01 to ~ 0.1, and their matrix permeability is below the resolution of our permeameter (≪ 10−18 m2). P-wave velocity, thermal conductivity, thermal diffusivity, specific heat capacity per unit volume, Young’s modulus, and uniaxial compressive strength range from 2.60 to 5.37 km/s, 2.42 to 5.72 W/mK, 1.19 to 2.46 mm2/s, 1.63 to 2.46 MJ/m3 K, 9.4 to 39.5 GPa, and 55.1 to 257.6 MPa, respectively. Therefore, and despite the narrow range of porosity, the petrophysical properties of the Muschelkalk are highly variable. We compare these new data with those recently acquired for the Buntsandstein unit (the Permo-Triassic unit immediately below the Muschelkalk) and thus provide an overview of the petrophysical properties of the two sedimentary units that directly overly the fractured granitic reservoir.

Published
2019
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226. Localization and modeling of reaction and diffusion to explain folate behavior during soaking of cowpea

Author

Philippe Bohuon, Christian Mestres, Aurélien Briffaz, Lisa Striegel, Christine Sanier, Michael Rychlik, Fanny Coffigniez, Démarche intégrée pour l'obtention d'aliments de qualité (UMR Qualisud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme d'histocytologie et d'imagerie cellulaire végétale (PHIV), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Agropolis Fondation, Daniel et Nina Carasso Fondation1507-031, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Technical University of Munich (TUM)

Subjects
[SDV]Life Sciences [q-bio], Diffusion, Interconversion, Reaction rate, 03 medical and health sciences, 0404 agricultural biotechnology, 0302 clinical medicine, Q02 - Traitement et conservation des produits alimentaires, Folates, Food science, Reaction kinetics, Niébé, Chemistry, Modèle de simulation, 04 agricultural and veterinary sciences, 040401 food science, Legume, Bioavailability, Vitesse, Folic acid, Trempage, 030221 ophthalmology & optometry, Soaking, Acide folique, Vigna unguiculata, Food Science
Abstract

International audience; A first modeling approach was used to understand the behavior of folate in cowpea seeds during soaking at different temperatures (30 degrees C, 60 degrees C and 95 degrees C). Folic acid, 10-formylfolic acid, 5-methyltetrahydrofolate, and 5-formyltetrahydrofolate were quantified in both the seeds and the soaking water during the process. A 2D-axisymmetric seed soaking simulator was then built considering these 4 folate vitamers to simultaneously describe diffusion, oxidation and interconversion of the single vitamers. The model adjustments revealed the predominance of folate diffusion at 60 degrees C and 95 degrees C (apparent diffusivity 2-3 x 10(-11) m(2) s-(1))whereas at 30 degrees C enzymatic interconversions of all vitamers into 5-methyltetrahydrofolate were observed (reaction rate of 8.0 x 10(-5) s(-1) for 5-formyltetrahydrofolate). The results of this study allow us to recommend a preliminary soaking step to retain folate in seeds and to improve the bioavailability of folates for human nutrition.

Published
2019
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227. Transferring bulk chemistry to interfacial synthesis of TFC-membranes to create chemically robust poly(epoxyether) films

Author

Elke Dom, Anthony Szymczyk, Marcel Dickmann, Werner Egger, Wouter Arts, Guy Koeckelberghs, Rhea Verbeke, Ivo F.J. Vankelecom, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Universität der Bundeswehr München [Neubiberg], Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), KU Leuven [OT/11/061], Belgian Federal Government [IAP 6/27], Flemish Government [Nanomexico AIO/150474/SBO], Research Foundation Flanders (FWO) [1S00917N], Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Technology, Engineering, Chemical, Polymer Science, Filtration and Separation, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Biochemistry, REVERSE-OSMOSIS, MECHANISMS, Membrane technology, chemistry.chemical_compound, Engineering, Methyl orange, TFC-membranes, General Materials Science, Interfacial initiation of polymerization, Physical and Theoretical Chemistry, Extreme conditions, Science & Technology, PERFORMANCE, DEGRADATION, SYSTEM PLEPS, 021001 nanoscience & nanotechnology, Interfacial polymerization, Nanofiltration, 0104 chemical sciences, INSIGHTS, [CHIM.POLY]Chemical Sciences/Polymers, Membrane, Monomer, POLYAMIDE MEMBRANES, chemistry, Chemical engineering, Polymerization, Physical Sciences, Poly(epoxyether), Chlorine-resistance, Chemical stability, SOLVENT RESISTANT NANOFILTRATION, 0210 nano-technology
Abstract

© 2019 Elsevier B.V. Membrane technology is currently still excluded from separations in more aggressive feeds due to limited chemical robustness. To extent its applicability, a novel thin-film composite (TFC)membrane was synthesized via the homopolymerization of epoxide monomers, resulting in robust poly(epoxyether)top-layers with >90% rose bengal (MW = 1017 Da)and 70% methyl orange (MW = 327 Da)retention with reasonable water fluxes (>2 L m -2 h −1 bar −1 ). The superior chemical stability of this novel nanofiltration membrane type was proven via treatments in pH 1 and 500 ppm NaOCl (pH 4)for, respectively, 48 h and 2.5 h, after which an unchanged or even improved membrane performance was observed. Additionally, the synthesis of the thin top-layer occurred via an interfacial initiation of the polymerization (IIP), rather than via state-of-the-art interfacial polymerization (IP). This IIP approach allowed to convert well-known monophasic bulk epoxide polymerization (commonly used in e.g. the automotive and coating industry), into the synthesis of thin, yet cross-linked top-layers. ispartof: JOURNAL OF MEMBRANE SCIENCE vol:582 pages:442-453 status: published

Published
2019
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228. Electrochemical triggering of the Chardonnay wine metabolome

Author

Régis D. Gougeon, Chloé Roullier-Gall, Basem Kanawati, Daniel Hemmler, Philippe Schmitt-Kopplin, Gregory K. Druschel, Research Unit Analytical BioGeoChemistry (BGC), Helmholtz-Zentrum München (HZM), Chair of Analytical Food Chemistry, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut Universitaire de la Vigne et du Vin 'Jules Guyot' (IUVV Jules Guyot), Université de Bourgogne (UB), Université Bourgogne Franche-Comté [COMUE] (UBFC), and AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
business.product_category, oxidation, Sulfur Oxides, SO2, Wine, Electrochemistry, 01 natural sciences, Mass Spectrometry, Analytical Chemistry, Dc voltage, 0404 agricultural biotechnology, Metabolomics, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Metabolome, Bottle, Cluster Analysis, Food science, Pressing, Chemistry, 010401 analytical chemistry, Chardonnay wine, food and beverages, electrochemistry (EC), Electrochemical Techniques, 04 agricultural and veterinary sciences, General Medicine, 040401 food science, 0104 chemical sciences, Ft icr ms, business, FT-ICR-MS, Oxidation-Reduction, Chardonnay Wine, Oxidation, So2, Ft-icr-ms, Electrochemistry (ec), Food Science
Abstract

International audience; Oxidation of wine upon bottle ageing is a crucial matter of concern for the qualitative long-term storage of white wines. However, understanding the various molecular mechanisms potentially involved, which can impact the wine composition, requires that top-down analytical strategies are implemented. Here, we report the analysis of bottle aged Chardonnay wines made from the same must, but differing by the amount of SO2 initially added to the must at pressing (0 and 8 g.hL-1). Metabolomics fingerprints obtained from electrochemical simulation of oxidative reactions were obtained by the coupling of either on-line or off-line electrochemical oxidation to FT-ICR-MS detection. We reveal that, whatever the electrochemical DC voltage, wines with initial SO2 addition displayed molecular fingerprints, which remained more similar to the non-oxidized wine without initial SO2 addition. We further show that a diversity of sulfur-containing compounds appeared to be the most sensitive to oxidation, whereas nitrogen-containing compounds were mostly formed.

Published
2019
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229. Human–Robot Team Interaction Through Wearable Haptics for Cooperative Manipulation

Author

Francesco Chinello, Pablo Budde gen. Dohmann, Sandra Hirche, Gionata Salvietti, Domenico Prattichizzo, Selma Music, Istituto Italiano di Tecnologia (IIT), Italian Institute of Technology (IIT), SIRSlab, and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
Male, 0209 industrial biotechnology, Computer science, Wearable computer, Aerospace electronics, 02 engineering and technology, Human–robot interaction, User-Computer Interface, 020901 industrial engineering & automation, Feedback, Sensory, Human–computer interaction, Cooperative Behavior, Haptic technology, Robot kinematics, FINGERTIP, Robotics, Equipment Design, Haptic interfaces, Mobile robots, Multi-robot systems, Task analysis, ddc, Computer Science Applications, TELEOPERATION, Teleoperation, Female, wearable haptics, Wireless Technology, cooperative manipulation, 0206 medical engineering, telerobotics, IMPEDANCE CONTROL, TELEMANIPULATION, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Fingers, Wearable Electronic Devices, Physical Stimulation, Humans, FEEDBACK, business.industry, COVEMAS, DFG, SPP1914, Cyber-Physical Networking, H2020 European project ”SoftPro"/ GA no. 688857, Mobile robot, 020601 biomedical engineering, Human-Computer Interaction, Robot, Artificial intelligence, Human-robot interaction, business
Abstract

International audience; The interaction of robot teams and single human in teleoperation scenarios is beneficial in cooperative tasks, for example the manipulation of heavy and large objects in remote or dangerous environments. The main control challenge of the interaction is its asymmetry, arising because robot teams have a relatively high number of controllable degrees of freedom compared to the human operator. Therefore, we propose a control scheme that establishes the interaction on spaces of reduced dimensionality taking into account the low number of human command and feedback signals imposed by haptic devices. We evaluate the suitability of wearable haptic fingertip devices for multi-contact teleoperation in a user study. The results show that the proposed control approach is appropriate for human-robot team interaction and that the wearable haptic fingertip devices provide suitable assistance in cooperative manipulation tasks.

Published
2019
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230. Stability of 5-methyltetrahydrofolate in fortified apple and carrot purées

Author

Nicolas Delchier, Catherine M.G.C. Renard, Lisa Striegel, Anna-Lena Herbig, Michael Rychlik, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chair of Analytical Food Chemistry, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Département Caractérisation et Elaboration des Produits Issus de l'Agriculture (CEPIA), Institut National de la Recherche Agronomique (INRA), European Project: 318563,EC:FP7:ICT,FP7-ICT-2011-8,CRS-I(2012), and Technische Universität München [München] (TUM)

Subjects
0106 biological sciences, Folate, TEMPERATURE DECREASE, Vitamin C, [SDV]Life Sciences [q-bio], Fortification, 5-Methyltetrahydrofolate, 04 agricultural and veterinary sciences, Ascorbic acid, 040401 food science, 01 natural sciences, Degradation, chemistry.chemical_compound, 0404 agricultural biotechnology, chemistry, Folic acid, Impacts, 010608 biotechnology, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Food matrix, Vitamer, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Formate, Food science, Food Science
Abstract

International audience; 5-Methyltetrahydrofolate, the naturally abundant folate vitamer, has been proposed as an alternative to folic acid for fortification. However, it is less stable than folic acid. In a formate buffer (pH 3.5), folic acid was entirely preserved after heating the solution for 3 h at 80 °C. In contrast, 5-methyltetrahydrofolate was completely degraded in less than 15 min. As in the buffer, 5-methyltetrahydrofolate in apple or carrot purées degraded rapidly without the addition of ascorbic acid. By adding ascorbic acid, the stability could be increased, but the chosen amount was crucial. An excess of vitamin C compared to 5-methyltetrahydrofolate was not always sufficient for the complete protection of 5-methyltetrahydrofolate during 3 h at 80 °C. Only by adding 2840 μmol/kg of ascorbic acid (equivalent to 500 mg/kg), 5-methyltetrahydrofolate seemed to remain stable. Degradation started after approximately 60 min when 570 μmol/kg of ascorbic acid (equivalent to 100 mg/kg) were added; after 120 min with 1420 μmol/kg (equivalent to 250 mg/kg). In addition, a temperature decrease to 70 °C or 60 °C did not increase the stability of 5-methyltetrahydrofolate.

Published
2019
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231. Block Low Rank Single Precision Coarse Grid Solvers for Extreme Scale Multigrid Methods

Author

Buttari, Alfredo, Huber, Markus, Leleux, Philippe, Mary, Théo, Ruede, Ulrich, Wohlmuth, Barbara, Algorithmes Parallèles et Optimisation (IRIT-APO), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique (CERFACS), CERFACS, Performance et Qualité des Algorithmes Numériques (PEQUAN), LIP6, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Friedrich-Alexander Universität Erlangen-Nürnberg (FAU)

Subjects
sparse direct solver, high-performance computing, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], hierarchical hybrid grids, block low-rank, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], MUMPS, geometric multigrid, multifrontal, efficient coarse level solver
Abstract

International audience; Extreme scale simulation requires fast and scalable algorithms, such as multigrid methods. To achieve asymptotically optimal complexity it is essential to employ a hierarchy of grids. The cost to solve the coarsest grid system can often be neglected in sequential computings, but cannot be ignored in massively parallel executions. In this case, the coarsest grid can be large and its efficient solution becomes a challenging task. We propose solving the coarse grid system using modern, approximate sparse direct methods and investigate the expected gains compared with traditional iterative methods. Since the coarse grid system only requires an approximate solution, we show that we can leverage block low-rank techniques, combined with the use of single precision arithmetic, to significantly reduce the computational requirements of the direct solver. In the case of extreme scale computing, the coarse grid system is too large for a sequential solution, but too small to permit massively parallel efficiency. We show that the agglomeration of the coarse grid system to a subset of processors is necessary for the sparse direct solver to achieve performance. We demonstrate the efficiency of the proposed method on a Stokes-type saddle point system. We employ a monolithic Uzawa multigrid method. In particular, we show that the use of an approximate sparse direct solver for the coarse grid system can outperform that of a preconditioned minimal residual iterative method. This is demonstrated for the multigrid solution of systems of order up to 1+e11 degrees of freedom on a petascale supercomputer using 43 200 processes.

Published
2021

232. Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

Author

Ana Djukovic, María José Garzón, Cécile Canlet, Vitor Cabral, Rym Lalaoui, Marc García-Garcerá, Julia Rechenberger, Marie Tremblay-Franco, Iván Peñaranda, Leonor Puchades-Carrasco, Antonio Pineda-Lucena, Eva María González-Barberá, Miguel Salavert, José Luis López-Hontangas, Miguel Á. Sanz, Jaime Sanz, Bernhard Kuster, Jean-Marc Rolain, Laurent Debrauwer, Karina B. Xavier, Joao B. Xavier, Carles Ubeda, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana [Espagne] (FISABIO), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Metatoul AXIOM (E20 ), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Université de Lausanne = University of Lausanne (UNIL), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Instituto de Investigación Sanitaria de Aragón [Zaragoza] (IIS Aragón), Universidad de Navarra [Pamplona] (UNAV), Hospital Universitari i Politècnic La Fe = University and Polytechnic Hospital La Fe, Instituto de Salud Carlos III [Madrid] (ISC), Memorial Sloan-Kettering Cancer Institute, Memorial Sloane Kettering Cancer Center [New York], C.U. was supported by the InfectERA-ERANET-Acciones complementarias grant [PCIN-2015-094] from the Spanish Ministerio de Economia y Competitividad and the 7th Research framework program from EU, grants from Conselleria d'Innovacio, Universitats, Ciencia i Societat Digital [AICO/2019/266, CIPROM/2021/053] and a grant from the Spanish MICINN [PID2020-120292RB-I00]. A.D. was supported by a Boehringer Ingelheim Fonds travel grant, and with J.B.X. by grant R01 AI137269/AI/NIAID from the US National Institutes of Health. B.K. was supported by the BMBF FloraStopMRE grant [031L0089]. V.C. was supported by an European Commission grant [MSCA-IF-2018-843183]. J.S. was supported by an InfectERA-ERANET-Acciones complementarias de programacion conjunta internacional grant (AC15/00070) and Proyectos de Investigacion en Salud del Instituto Carlos III (PI18/00280). K.B.X. was supported by FundacAo para a Ciencia e a Tecnologia grant (InfectERA/0004/2015). J.M.R. was supported by ANR FloraStopInfectMRE project., 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)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-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), 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), and LESUR, Hélène

Subjects
Clostridiales, Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology, Anti-Bacterial Agents, [SDV] Life Sciences [q-bio], Butyrates, Lactobacillus, Mice, Enterobacteriaceae, Animals, Prospective Studies
Abstract

Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients.

Published
2021
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233. Myocardial Infarction Quantification from Late Gadolinium Enhancement MRI Using Top-Hat Transforms and Neural Networks

Author

de La Rosa, Ezequiel, Sidibé, Désiré, Decourselle, Thomas, Leclercq, Thibault, Cochet, Alexandre, Lalande, Alain, Laboratoire d'Electronique, d'Informatique et d'Image [EA 7508] (Le2i), Université de Technologie de Belfort-Montbeliard (UTBM)-Université de Bourgogne (UB)-École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Icometrix [Leuven], Service de Cardiologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), and université de Bourgogne, IMVIA

Subjects
FOS: Computer and information sciences, scar segmentation, late gadolinium enhancement, Industrial engineering. Management engineering, Computer Vision and Pattern Recognition (cs.CV), Electronic computers. Computer science, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, Computer Science - Computer Vision and Pattern Recognition, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, deep learning, QA75.5-76.95, T55.4-60.8, cardiac magnetic resonance
Abstract

Significance: Late gadolinium enhanced magnetic resonance imaging (LGE-MRI) is the gold standard technique for myocardial viability assessment. Although the technique accurately reflects the damaged tissue, there is no clinical standard for quantifying myocardial infarction (MI), demanding most algorithms to be expert dependent. Objectives and Methods: In this work a new automatic method for MI quantification from LGE-MRI is proposed. Our novel segmentation approach is devised for accurately detecting not only hyper-enhanced lesions, but also microvascular-obstructed areas. Moreover, it includes a myocardial disease detection step which extends the algorithm for working under healthy scans. The method is based on a cascade approach where firstly, diseased slices are identified by a convolutional neural network (CNN). Secondly, by means of morphological operations a fast coarse scar segmentation is obtained. Thirdly, the segmentation is refined by a boundary-voxel reclassification strategy using an ensemble of CNNs. For its validation, reproducibility and further comparison against other methods, we tested the method on a big multi-field expert annotated LGE-MRI database including healthy and diseased cases. Results and Conclusion: In an exhaustive comparison against nine reference algorithms, the proposal achieved state-of-the-art segmentation performances and showed to be the only method agreeing in volumetric scar quantification with the expert delineations. Moreover, the method was able to reproduce the intra- and inter-observer variability ranges. It is concluded that the method could suitably be transferred to clinical scenarios., Comment: Submitted to IEEE

Published
2021

234. Ant colony optimization for mining gradual patterns

Author

Dickson Odhiambo Owuor, Edmond Odhiambo Menya, Joseph Onderi Orero, Anne Laurent, Thomas A. Runkler, Faculty of Information Technology [Strathmore University], Strathmore University [Nairobi], Technische Universität München [München] (TUM), Corporate technology Siemens, Siemens AG [Munich], WEB-CUBE, Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
FOS: Computer and information sciences, Computer science, Population, Computational intelligence, 02 engineering and technology, Field (computer science), 03 medical and health sciences, 0302 clinical medicine, Knowledge extraction, Computer Science - Databases, Artificial Intelligence, Genetic algorithm, 0202 electrical engineering, electronic engineering, information engineering, Neural and Evolutionary Computing (cs.NE), education, ComputingMilieux_MISCELLANEOUS, education.field_of_study, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Ant colony optimization algorithms, Particle swarm optimization, Computer Science - Neural and Evolutionary Computing, Databases (cs.DB), 030220 oncology & carcinogenesis, Pattern recognition (psychology), 020201 artificial intelligence & image processing, Computer Vision and Pattern Recognition, Algorithm, Software
Abstract

Gradual pattern extraction is a field in (KDD) Knowledge Discovery in Databases that maps correlations between attributes of a data set as gradual dependencies. A gradual dependency may take a form of "the more Attribute K , the less Attribute L". In this paper, we propose an ant colony optimization technique that uses a probabilistic approach to learn and extract frequent gradual patterns. Through computational experiments on real-world data sets, we compared the performance of our ant-based algorithm to an existing gradual item set extraction algorithm and we found out that our algorithm outperforms the later especially when dealing with large data sets., Comment: 35 pages, journal article

Published
2021
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235. A Measure Theoretical Approach to the Mean-field Maximum Principle for Training NeurODEs

Author

Benoît Bonnet, Cristina Cipriani, Massimo Fornasier, Hui Huang, Control And GEometry (CaGE ), 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), Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University of Calgary, C.C., H.H., and M.F. acknowledge the support of the DFG Project 'Identification of Energies from Observation of Evolutions' and the DFG SPP 1962 'Non-smooth and Complementarity-based Distributed Parameter Systems: Simulation and Hierarchical Optimization'. C.C. and M.F. acknowledge also the partial support of the project 'Online Firestorms And Resentment Propagation On Social Media: Dynamics, Predictability and Mitigation' of the TUM Institutefor Ethics in Artificial Intelligence., Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Technical University of Munich (TUM)

Subjects
Mean-Field Optimal Control, Optimization and Control (math.OC), NeurODEs, Mean-Field Maximum Principle, Applied Mathematics, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, FOS: Mathematics, Lagrange Multiplier Theorem, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics - Optimization and Control, Analysis
Abstract

In this paper we consider a measure-theoretical formulation of the training of NeurODEs in the form of a mean-field optimal control with $L^2$-regularization of the control. We derive first order optimality conditions for the NeurODE training problem in the form of a mean-field maximum principle, and show that it admits a unique control solution, which is Lipschitz continuous in time. As a consequence of this uniqueness property, the mean-field maximum principle also provides a strong quantitative generalization error for finite sample approximations. Our derivation of the mean-field maximum principle is much simpler than the ones currently available in the literature for mean-field optimal control problems, and is based on a generalized Lagrange multiplier theorem on convex sets of spaces of measures. The latter is also new, and can be considered as a result of independent interest.

Published
2021

236. Spatial network metrics for characterizing brain-computer interface mental states

Author

Gonzalez-Astudillo, Juliana, Ceballos-Dominguez, Eric Gabriel, Cattai, Tiziana, Corsi, Marie-Constance, De Vico Fallani, Fabrizio, Algorithms, models and methods for images and signals of the human brain (ARAMIS), Sorbonne Université (SU)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Technical University of Munich (TUM), Institut du Cancer de Montpellier (ICM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), GONZALEZ-ASTUDILLO, Juliana, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

237. Internalization of Foldamer-Based DNA Mimics through a Site-Specific Antibody Conjugate to Target HER2-Positive Cancer Cells

Author

Ivan Huc, Maguy Del Rio, Céline Gongora, Philippe Pourquier, Caroline Denevault-Sabourin, Véronique Garambois, Valentina Corvaglia, Nicolas Joubert, Aurélie Garcin, Stéphanie Letast, Imène Ait Mohamed Amar, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Groupe innovation et ciblage cellulaire (GICC), EA 7501 [2018-...] (GICC EA 7501), Université de Tours (UT), Center for Integrated Protein Science (CIPSM), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Ludwig-Maximilians-Universität München (LMU)-Helmholtz Zentrum München = German Research Center for Environmental Health, GICC EA 7501, IMT (Innovation moléculaire et thérapeutique) (IMT), Université de Tours (UT)-Université de Tours (UT), Gongora, Céline, and Université de Tours

Subjects
Antibody-drug conjugate, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Pharmaceutical Science, [SDV.CAN]Life Sciences [q-bio]/Cancer, Article, antibody-drug conjugate, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Pharmacy and materia medica, [SDV.CAN] Life Sciences [q-bio]/Cancer, foldamer, HER2, Drug Discovery, Cytotoxic T cell, Internalization, 030304 developmental biology, media_common, 0303 health sciences, Chemistry, Foldamer, Transfection, In vitro, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], RS1-441, trastuzumab, 030220 oncology & carcinogenesis, Cancer cell, Molecular Medicine, Medicine, DNA mimics, DNA
Abstract

International audience; Inhibition of protein–DNA interactions represents an attractive strategy to modulate essential cellular functions. We reported the synthesis of unique oligoamide-based foldamers that adopt single helical conformations and mimic the negatively charged phosphate moieties of B-DNA. These mimics alter the activity of DNA interacting enzymes used as targets for cancer treatment, such as DNA topoisomerase I, and they are cytotoxic only in the presence of a transfection agent. The aim of our study was to improve internalization and selective delivery of these highly charged molecules to cancer cells. For this purpose, we synthesized an antibody-drug conjugate (ADC) using a DNA mimic as a payload to specifically target cancer cells overexpressing HER2. We report the bioconjugation of a 16-mer DNA mimic with trastuzumab and its functional validation in breast and ovarian cancer cells expressing various levels of HER2. Binding of the ADC to HER2 increased with the expression of the receptor. The ADC was internalized into cells and was more efficient than trastuzumab at inhibiting their growth in vitro. These results provide proof of concept that it is possible to site-specifically graft high molecular weight payloads such as DNA mimics onto monoclonal antibodies to improve their selective internalization and delivery in cancer cells.

Published
2021
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238. Molecular biogeography of the fungus-dwelling saproxylic beetle Bolitophagus reticulatus indicates rapid expansion from glacial refugia

Author

Jacob Heilmann-Clausen, Jonas Eberle, Werner Ulrich, Jan Christian Habel, Inken Doerfler, Christophe Bouget, Kris Vandekerkhove, Jürgen Schmidl, Martin Husemann, Thibault Lachat, Antoine Brin, Gunnar Isacsson, Anton Krištín, Jörg Müller, Martin M. Gossner, Laurent Larrieu, Andreas Rigling, Sebastian Seibold, University of Salzburg, University of Hamburg, Carl Von Ossietzky Universität Oldenburg, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Nicolaus Copernicus University [Toruń], Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Bavarian Forest National Park, Ecosystèmes forestiers (UR EFNO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, University of Copenhagen = Københavns Universitet (KU), Swedish Forest Agency, Institute of Forest Ecology - SAS, Bern University of Applied Sciences (BFH), CNPF-CRPF Occitanie, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), National Park of Berchtesgaden, Partenaires INRAE, Research Institute for Nature and Forest (INBO), Bayerisches Staatsministerium fur Ernahrung, Landwirtschaft und Forst, Munich, Germany, Technical University Munich, Germany, internal Excellence Initiative -Research University (IDUB) grant of the Nicolaus Copernicus University, Torun, Poland, and Technical University of Munich (TUM)

Subjects
0106 biological sciences, 0301 basic medicine, Fomes fomentarius, Biogeography, genetic analysis, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, expansion, refugia, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Fagus sylvatica, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Fagus orientalis, Temperate climate, Glacial period, Beech, Ecology, Evolution, Behavior and Systematics, biogeography, biology, Ecology, 15. Life on land, biology.organism_classification, mobility, phalanx-wise, 030104 developmental biology, Interglacial, broadleaf forest
Abstract

The geographical distributions of species associated with European temperate broadleaf forests have been significantly influenced by glacial–interglacial cycles. During glacial periods, these species persisted in Mediterranean and extra-Mediterranean refugia and later, during interglacial periods, expanded northwards. The widespread saproxylic beetle Bolitophagus reticulatus depends closely on European temperate broadleaf forests. It usually develops in the tinder fungus Fomes fomentarius, a major decomposer of broadleaf-wood. We sampled B. reticulatus in sporocarps from European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis) across Europe and the Caucasus region. We analysed mitochondrial gene sequences (cox1, cox2, cob) and 17 microsatellites to reconstruct the geographical distribution of glacial refugia and postglacial recolonization pathways. We found only marginal genetic differentiation of B. reticulatus, except for a significant split between populations of the Caucasus region and Europe. This indicates the existence of past refugia south of the Great Caucasus, and a contact zone with European populations in the Crimean region. Further potential refugia might have been located at the foothills of the Pyrenees and in the Balkan region. Our genetic data suggest a phalanx-wise recolonization of Europe, a reflection of the high mobility of B. reticulatus.

Published
2021
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239. Tocilizumab in COVID-19 therapy: who benefits, and how?

Author

Avidan U. Neumann, Guy Gorochov, Mehmet Goekkaya, Karim Dorgham, Claudia Traidl-Hoffmann, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Technical University of Munich (TUM), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Dorgham, Karim

Subjects
2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], General Medicine, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, Virology, [SDV] Life Sciences [q-bio], 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Tocilizumab, chemistry, Correspondence, Medicine, ddc:610, [SDV.IMM.IMM] Life Sciences [q-bio]/Immunology/Immunotherapy, 030223 otorhinolaryngology, business, ComputingMilieux_MISCELLANEOUS, 030215 immunology
Abstract

International audience; No abstract available

Published
2021
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240. Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria

Author

Klaus Neuhaus, Eva Miriam Buhl, Esther Wortmann, Birte Abt, Thomas Riedel, Thomas Clavel, Thomas C. A. Hitch, Bernd Kaspers, Christian Zenner, Philippe Velge, Jörg Overmann, Stefan Tiede, Department for Veterinary Sciences, Ludwig Maximilians University of Munich, Institute of Medical Microbiology, Functional Microbiome Research Group, University Hospital RWTH Aachen, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Electron microscopy facility, Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (UKA), RWTH Aachen University-RWTH Aachen University, Else Kroener Fresenius Centre - Zentralinstitut für Ernährungs und Lebensmittelfors (ZIEL), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Technical University of Munich (TUM), and Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Physiology, medicine.drug_class, chicken, Antibiotics, gut microbiome, Colonisation resistance, Gut flora, Biochemistry, Microbiology, 03 medical and health sciences, Immune system, mucosal immunology, Genetics, medicine, Colonization, Microbiome, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Feces, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, [SDV.BA]Life Sciences [q-bio]/Animal biology, anaerobes, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR1-502, Computer Science Applications, synthetic bacterial community, Mucosal immunology, Modeling and Simulation, Research Article
Abstract

MSystems 6(3), e01300-20 (2021). doi:10.1128/mSystems.01300-20, Published by American Society for Microbiology, Washington, DC

Published
2021
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241. INFRAFRONTIER quality principles in systemic phenotyping

Author

Hilke Ehlich, Reetta Vuolteenaho, Michael Raess, Vasileios Ntafis, Ana Zarubica, Bernard Malissen, Dimitris L. Kontoyiannis, Mohammed Selloum, Tania Sorg, Ann M Flenniken, Martin Hrabě de Angelis, Claudia Stoeger, Yann Herault, Isabelle Goncalves Da Cruz, George Kollias, Sarka Suchanova, Heather Cater, Reetta Hinttala, Radislav Sedlacek, Sara Wells, Colin McKerlie, Anne-Marie Mura, Steve D.M. Brown, Jan Rozman, MRC Harwell Institute [UK], Lunenfeld-Tanenbaum Research Institute [Toronto, Canada], Institut Clinique de la Souris (ICS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunophénomique (CIPHE), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Alexander Fleming Biomedical Sciences Research Center, Partenaires INRAE, Helmholtz-Zentrum München (HZM), Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), University of Oulu, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), German Center for Diabetes Research - Deutsches Zentrum für Diabetesforschung [Neuherberg] (DZD), Technische Universität München [München] (TUM), The Hospital for sick children [Toronto] (SickKids), University of Toronto, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), INFRAFRONTIER GmbH [Neuherberg], Biomedical Sciences Research Centre Alexander Fleming [Vari, Greece] (BSRC), and Helmholtz Zentrum München = German Research Center for Environmental Health

Subjects
Service (systems architecture), media_common.quotation_subject, [SDV]Life Sciences [q-bio], Interoperability, Context (language use), Biology, 03 medical and health sciences, Preclinical research, Mice, 0302 clinical medicine, Genetics, Animals, Quality (business), 030304 developmental biology, media_common, Mammals, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genome, European research, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproducibility of Results, Internal quality, Disease Models, Animal, Risk analysis (engineering), Key (cryptography), 030217 neurology & neurosurgery
Abstract

Improving reproducibility and replicability in preclinical research is a widely discussed and pertinent topic, especially regarding ethical responsibility in animal research. INFRAFRONTIER, the European Research Infrastructure for the generation, phenotyping, archiving, and distribution of model mammalian genomes, is addressing this issue by developing internal quality principles for its different service areas, that provides a quality framework for its operational activities. This article introduces the INFRAFRONTIER Quality Principles in Systemic Phenotyping of genetically altered mouse models. A total of 11 key principles are included, ranging from general requirements for compliance with guidelines on animal testing, to the need for well-trained personnel and more specific standards such as the exchange of reference lines. Recently established requirements such as the provision of FAIR (Findable, Accessible, Interoperable, Reusable) data are also addressed. For each quality principle, we have outlined the specific context, requirements, further recommendations, and key references.

Published
2021
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242. MasakhaNER: Named entity recognition for African languages

Author

Julia Kreutzer, Ayodele Awokoya, Ignatius Ezeani, Rubungo Andre Niyongabo, Happy Buzaaba, Adewale Akinfaderin, Samuel Oyerinde, Stephen Mayhew, Emmanuel Anebi, Mofetoluwa Adeyemi, Kelechi Ogueji, Abdoulaye Diallo, Seid Muhie Yimam, Jade Abbott, Joyce Nakatumba-Nabende, Victor Akinode, Blessing Sibanda, Catherine Gitau, Chester Palen-Michel, Shamsuddeen Hassan Muhammad, Degaga Wolde, Graham Neubig, Tendai Marengereke, Paul Rayson, Derguene Mbaye, Eric Peter Wairagala, Daniel D'souza, Tosin P. Adewumi, Jonathan Mukiibi, Chris Chinenye Emezue, David Ifeoluwa Adelani, Shruti Rijhwani, Iroro Orife, Verrah Otiende, Maurice Katusiime, Yvonne Wambui, Dibora Gebreyohannes, Kelechi Nwaike, Salomey Osei, Chiamaka Chukwuneke, Henok Tilaye, Deborah Nabagereka, Thierno Ibrahima Diop, Orevaoghene Ahia, Jesujoba O. Alabi, Sebastian Ruder, Davis David, Mouhamadane Mboup, Samba Ngom, Tajuddeen R. Gwadabe, Bonaventure F. P. Dossou, Temilola Oloyede, Perez Ogayo, Clemencia Siro, Gerald Muriuki, Aremu Anuoluwapo, Nkiruka Odu, Tobius Saul Bateesa, Abdoulaye Faye, Israel Abebe Azime, Constantine Lignos, Saarland University [Saarbrücken], Masakhane NLP, Retro Rabbit, Carnegie Mellon University [Pittsburgh] (CMU), ProQuest, Google Research, Brandeis University, Université de Tsukuba = University of Tsukuba, DeepMind, DeepMind Technologies, Duolingo, African Institute for Mathematical Sciences (AIMS), University of Porto, Bayero University Kano (BUK), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Makerere University [Kampala, Ouganda] (MAK), African Leadership University, University of Lagos, Max Planck Institute for Informatics [Saarbrücken], Universität Hamburg (UHH), University of Chinese Academy of Sciences [Beijing] (UCAS), Lancaster University, University of Electronic Science and Technology of China (UESTC), United States International University - Africa, Niger-Volta Language Technologies Institute, Luleå University of Technology (LUT), African University of Science and Technology (AUST), University of Ibadan, Namibia University of Science and Technology (NUST), InstaDeep, Jacobs University [Bremen], University of Waterloo [Waterloo], European Project: 825081,H2020,COMPRISE(2018), Technical University of Munich (TUM), DeepMind [London], Universidade do Porto = University of Porto, and University of Electronic Science and Technology of China [Chengdu] (UESTC)

Subjects
FOS: Computer and information sciences, Linguistics and Language, Computer Science - Computation and Language, Computer science, business.industry, Computer Science - Artificial Intelligence, Communication, Languages of Africa, computer.software_genre, Code (semiotics), [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL], Computer Science Applications, Human-Computer Interaction, Artificial Intelligence (cs.AI), Named-entity recognition, Artificial Intelligence, Artificial intelligence, Transfer of learning, business, computer, Computation and Language (cs.CL), Natural language processing
Abstract

We take a step towards addressing the under-representation of the African continent in NLP research by creating the first large publicly available high-quality dataset for named entity recognition (NER) in ten African languages, bringing together a variety of stakeholders. We detail characteristics of the languages to help researchers understand the challenges that these languages pose for NER. We analyze our datasets and conduct an extensive empirical evaluation of state-of-the-art methods across both supervised and transfer learning settings. We release the data, code, and models in order to inspire future research on African NLP., Comment: Accepted to TACL 2021, pre-MIT Press publication version

Published
2021
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243. Interpretable Hyperspectral Artificial Intelligence: When nonconvex modeling meets hyperspectral remote sensing

Author

Liangpei Zhang, Xiao Xiang Zhu, Wei He, Jing Yao, Naoto Yokoya, Danfeng Hong, Lianru Gao, Jocelyn Chanussot, Technical University of Munich (TUM), Wuhan University [China], The University of Tokyo (UTokyo), Chinese Academy of Sciences [Beijing] (CAS), Wuhan Polytechnic University, GIPSA - Signal Images Physique (GIPSA-SIGMAPHY), GIPSA Pôle Sciences des Données (GIPSA-PSD), Grenoble Images Parole Signal Automatique (GIPSA-lab), 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)-Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Grenoble Alpes (UGA), German Aerospace Center (DLR), ANR-19-P3IA-0003,MIAI,MIAI @ Grenoble Alpes(2019), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
Artificial intelligence, General Computer Science, Computer science, Process (engineering), 0211 other engineering and technologies, 02 engineering and technology, Data modeling, Imaging, 0202 electrical engineering, electronic engineering, information engineering, Redundancy (engineering), Analytical models, Electrical and Electronic Engineering, Instrumentation, 021101 geological & geomatics engineering, Remote sensing, Interpretability, Data processing, Landmark, business.industry, Spectrometry, Data models, Hyperspectral imaging, Two dimensional displays, Convex optimization, Task analysis, General Earth and Planetary Sciences, 020201 artificial intelligence & image processing, business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing
Abstract

International audience; Hyperspectral (HS) imaging, also known as image spectrometry, is a landmark technique in geoscience and remote sensing (RS). In the past decade, enormous efforts have been made to process and analyze these HS products, mainly by seasoned experts. However, with an ever-growing volume of data, the bulk of costs in manpower and material resources poses new challenges for reducing the burden of manual labor and improving efficiency. For this reason, it is urgent that more intelligent and automatic approaches for various HS RS applications be developed. Machine learning (ML) tools with convex optimization have successfully undertaken the tasks of numerous artificial intelligence (AI)-related applications; however, their ability to handle complex practical problems remains limited, particularly for HS data, due to the effects of various spectral variabilities in the process of HS imaging and the complexity and redundancy of higher-dimensional HS signals. Compared to convex models, nonconvex modeling, which is capable of characterizing more complex real scenes and providing model interpretability technically and theoretically, has proven to be a feasible solution that reduces the gap between challenging HS vision tasks and currently advanced intelligent data processing models.

Published
2021
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244. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23

Author

Aida Telegrafi, Susanne Liptay, Korbinian M. Riedhammer, Katherine G. Langley, Florencia del Viso, Ilaria Parenti, Divya Ramachandra, Jolanta Wierzba, Lynne M. Bird, Joseph Porrmann, Sophie Gößwein, Isabelle Thiffault, Richard Steet, Michael J. Lyons, Neda Zadeh, William Boyce Burns, Boris Keren, Kendra Engleman, Heather M. McLaughlin, Delphine Héron, Shivarajan Manickavasagam Amudhavalli, Raymond J. Louie, Andrea Fischer, Frank J. Kaiser, Red Hat Inc., The Greenwood Genetic Center, University of California, CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Advocate Hope Children's Hospital, Children's Mercy Hospital [Kansas City], Universität Duisburg-Essen [Essen], Medical University of Gdańsk, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Genetics Center, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Invitae Corporation, GeneDx [Gaithersburg, MD, USA], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Technical University of Munich (TUM), University of California (UC), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Gestionnaire, HAL Sorbonne Université 5

Subjects
Male, 0301 basic medicine, RNA helicase, DEAD box, Autism Spectrum Disorder, RNA Splicing, Medizin, Mutation, Missense, [SDV.GEN] Life Sciences [q-bio]/Genetics, 030105 genetics & heredity, Genomic Instability, DEAD-box RNA Helicases, 03 medical and health sciences, Neurodevelopmental disorder, Seizures, Intellectual Disability, Genetics, medicine, Humans, Genetic Predisposition to Disease, Global developmental delay, Child, Gene, Genetics (clinical), RNA, Double-Stranded, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, neurodevelopment, Infant, Newborn, Infant, Helicase, RNA, medicine.disease, RNA Helicase A, 030104 developmental biology, Neurodevelopmental Disorders, Child, Preschool, RNA splicing, biology.protein, Female, DDX23
Abstract

The DEAD/DEAH box RNA helicases are a superfamily of proteins involved in the processing and transportation of RNA within the cell. A growing literature supports this family of proteins as contributing to various types of human disorders from neurodevelopmental disorders to syndromes with multiple congenital anomalies. This article presents a cohort of nine unrelated individuals with de novo missense alterations in DDX23 (Dead-Box Helicase 23). The gene is ubiquitously expressed and functions in RNA splicing, maintenance of genome stability, and the sensing of double-stranded RNA. Our cohort of patients, gathered through GeneMatcher, exhibited features including tone abnormalities, global developmental delay, facial dysmorphism, autism spectrum disorder, and seizures. Additionally, there were a variety of other findings in the skeletal, renal, ocular, and cardiac systems. The missense alterations all occurred within a highly conserved RecA-like domain of the protein, and are located within or proximal to the DEAD box sequence. The individuals presented in this article provide evidence of a syndrome related to alterations in DDX23 characterized predominantly by atypical neurodevelopment.

Published
2021
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245. Shifts in perspective: Operational aspects in (non-) autonomous ride-pooling simulations

Author

Felix Zwick, Nico Kühnel, Sebastian Hörl, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), MOIA GmbH, IRT SystemX (IRT SystemX), and Technical University of Munich (TUM)

Subjects
ride-sharing, Ride-sharing, Ride-splitting, Pooled on-demand mobility, MATSim, Electric vehicles, Operations research, Aerospace Engineering, Transportation, Management Science and Operations Research, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SPI.GCIV.IT]Engineering Sciences [physics]/Civil Engineering/Infrastructures de transport, Business, Management and Accounting (miscellaneous), pooled on-demand mobility, [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Civil and Structural Engineering, electric vehicles, operations research
Abstract

On-demand ride-pooling systems have gained increasing attention in science and practice in recent years. Simulation studies have shown an enormous potential to reduce fleet sizes and vehicle kilometers traveled if private car trips are replaced with ride-pooling services. However, existing simulation studies assume operation with autonomous vehicles, with no restrictions on operational tasks required when the vehicles are operated by manual drivers. In this article, we simulate and evaluate the operational challenges of non-autonomous ride-pooling systems through driver shifts and breaks and compare their capacity and efficiency to autonomous on-demand services. Based on the existing ride-pooling service MOIA in Hamburg, Germany, we introduce shift and break schedules and implement a new hub return logic to perform the respective tasks at different types of vehicle hubs. This way, currently operating on-demand services are modeled more realistically and the efficiency gains of such services through autonomous vehicles are quantified. The results suggest that operational challenges substantially limit the ride-pooling capacity in terms of served rides with a given number of vehicles. While results largely depend on the chosen shift plan, the presented operational factors should be considered for the assessment of current operational real-world services. The contribution of this study is threefold: From a technical perspective, it is shown that the explicit simulation of operational constraints of current services is crucial to assess ride-pooling services. From a policy perspective, the study shows the operational challenges of a ride-pooling service with non-autonomous vehicles and the potential of future autonomous services. Lastly, the paper adds to the literature a practical ride-pooling simulation use case based on observed real-world demand and shift data., Transportation Research Part A: Policy and Practice, 165, ISSN:0965-8564, ISSN:1879-2375

Published
2021

246. Multi-UAV Path Planning for Wireless Data Harvesting with Deep Reinforcement Learning

Author

Harald Bayerlein, Mirco Theile, Marco Caccamo, David Gesbert, Eurecom [Sophia Antipolis], Technical University of Munich (TUM), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Information Theory (cs.IT), Computer Science - Information Theory, multi-agent reinforcement learning (MARL), Systems and Control (eess.SY), TK5101-6720, Electrical Engineering and Systems Science - Systems and Control, Machine Learning (cs.LG), Internet of Things (IoT), Computer Science - Robotics, map-based planning, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], unmanned aerial vehicle (UAV), [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], FOS: Electrical engineering, electronic engineering, information engineering, Telecommunication, Computer Science - Multiagent Systems, trajectory planning, Robotics (cs.RO), Transportation and communications, Multiagent Systems (cs.MA), HE1-9990
Abstract

Harvesting data from distributed Internet of Things (IoT) devices with multiple autonomous unmanned aerial vehicles (UAVs) is a challenging problem requiring flexible path planning methods. We propose a multi-agent reinforcement learning (MARL) approach that, in contrast to previous work, can adapt to profound changes in the scenario parameters defining the data harvesting mission, such as the number of deployed UAVs, number, position and data amount of IoT devices, or the maximum flying time, without the need to perform expensive recomputations or relearn control policies. We formulate the path planning problem for a cooperative, non-communicating, and homogeneous team of UAVs tasked with maximizing collected data from distributed IoT sensor nodes subject to flying time and collision avoidance constraints. The path planning problem is translated into a decentralized partially observable Markov decision process (Dec-POMDP), which we solve through a deep reinforcement learning (DRL) approach, approximating the optimal UAV control policy without prior knowledge of the challenging wireless channel characteristics in dense urban environments. By exploiting a combination of centered global and local map representations of the environment that are fed into convolutional layers of the agents, we show that our proposed network architecture enables the agents to cooperate effectively by carefully dividing the data collection task among themselves, adapt to large complex environments and state spaces, and make movement decisions that balance data collection goals, flight-time efficiency, and navigation constraints. Finally, learning a control policy that generalizes over the scenario parameter space enables us to analyze the influence of individual parameters on collection performance and provide some intuition about system-level benefits., Modifications: final formatting; Code available under https://github.com/hbayerlein/uav_data_harvesting, article extends on arXiv:2007.00544

Published
2021
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247. Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23

Author

Magdalena Harakalova, Benjamin Meder, Philippe Charron, Manuel Gómez-Bueno, Jorg J. A. Calis, François Cambien, David-Alexandre Trégouët, Maurizia Grasso, Steven McGinn, Uwe Völker, Thomas Meitinger, Stefan Weiss, L. Duboscq-Bidot, Richard Dorent, Vera Regitz-Zagrosek, Folkert W. Asselbergs, Hélène Blanché, Olivier Dubourg, Patrick Lacolley, Pierre Boutouyrie, Delphine Bacq-Daian, Vincent Fontaine, Volker Ruppert, Marine Germain, K Lehnert, Jean-Noël Trochu, Stuart A. Cook, Angélique Curjol, Brendan J. Keating, Ibticem Raji, Anne Boland, J. Erdmann, Michael Morley, Jean-François Aupetit, Paloma Remior, Luigi Tavazzi, Gérard Roizès, Michal Mokry, Konstantin Strauch, Richard Isnard, Jean-Philippe Empana, Robert Olaso, Kenneth B. Marguiles, Zofia T. Bilińska, Stephan B. Felix, Marcus Dörr, Thomas P. Cappola, Stefan Blankenberg, Jan Haas, Céline Besse, Jean-François Deleuze, Christine E. Seidman, Christian Hengstenberg, Jessica van Setten, Hakon Hakonarson, Sanjay K Prasad, Daiane Hemerich, Pascal de Groote, Thomas Wichter, Alain van Mil, Michel Komajda, Renee Maas, Carole Proust, Declan P. O'Regan, Xavier Jouven, Ganapathi Varma Saripella, Georgios Kararigas, Eloisa Arbustini, Jin Li, Klaus Stark, Laurent Fauchier, Flavie Ader, Melanie Waldenberger, Martina Müller-Nurasyid, Eric Villard, Sophie Garnier, Cardiology, Imperial College Healthcare NHS Trust- BRC Funding, British Heart Foundation, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de Cardiologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Tenon [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité Fonctionnelle de Cardiogénétique et Myogénétique Moléculaire et Cellulaire, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Centre hospitalier Saint-Joseph [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique-Hôpitaux de Paris, Fondation Leducq, Société Française de Cardiologie, Deutsche Forschungsgemeinschaft, Helmholtz Zentrum München, Université de Bordeaux, Medical Research Council, ANR-10-LABX-0013,GENMED,Medical Genomics(2010), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University Medical Center [Utrecht], Universität Greifswald - University of Greifswald, German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], University of Pennsylvania, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), National Heart Centre Singapore (NHCS), Children’s Hospital of Philadelphia (CHOP ), University of Regensburg, Royal Brompton Hospital, Imperial College London, Istituti Clinici Scientifici Maugeri [Pavia] (IRCCS Pavia - ICS Maugeri), Helmholtz Zentrum München = German Research Center for Environmental Health, Ludwig-Maximilians-Universität München (LMU), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University Medical Center of the Johannes Gutenberg-University Mainz, Perelman School of Medicine, Harvard Medical School [Boston] (HMS), University of Iceland [Reykjavik], Heidelberg University, Stanford University Medical School, 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), Défaillance Cardiovasculaire Aiguë et Chronique (DCAC), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Universität zu Lübeck = University of Lübeck [Lübeck], Universitätklinikum Gießen und Marburg GmbH, Maria Cecilia Hospital [Cotignola], Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Hôpital cardiologique, Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Centre hospitalier Saint Joseph - Saint Luc [Lyon], National Institute of Cardiology [Varsovie, Pologne], University of Medicine Greifswald, Centre de Référence Maladies Cardiaques Héréditaires, Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratory of Excellence GENMED [Paris] (Medical Genomics), Hospital Universitario Puerta de Hierro-Majadahonda [Madrid, Spain], Swedish University of Agricultural Sciences (SLU), Centre d'Etude du Polymorphisme Humain (CEPH), Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Fondation Jean Dausset-Université Paris Cité (UPCité), Faculté de Pharmacie de Paris - Université Paris Descartes (UPD5 Pharmacie), Université Paris Descartes - Paris 5 (UPD5), Groupe Hospitalier Paris Saint Joseph, Fondation Jean Dausset - Centre d’Etudes du Polymorphisme Humain [Paris] (CEPH), and University College of London [London] (UCL)

Subjects
Cardiac & Cardiovascular Systems, Cardiomyopathy, Dilated/genetics, [SDV]Life Sciences [q-bio], Signal Transducing/genetics, Dilated cardiomyopathy, Genome-wide association study, Adaptor Proteins, Signal Transducing/genetics, 030204 cardiovascular system & hematology, TAURINE, 0302 clinical medicine, GWAS, Medicine, POSITION STATEMENT, 1102 Cardiorespiratory Medicine and Haematology, Genetics, 0303 health sciences, education.field_of_study, Genetic Predisposition to Disease/genetics, Adaptor Proteins, 4C-sequencing, Polymorphism, Single Nucleotide/genetics, Genetic risk score, Cardiology and Cardiovascular Medicine, Life Sciences & Biomedicine, Single Nucleotide/genetics, Cardiomyopathy, Dilated, Cardiomyopathy, Population, Locus (genetics), Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, Chromosomes, 03 medical and health sciences, Systolic/genetics, Heart Failure, Systolic/genetics, SNP, Animals, Humans, Genetic Predisposition to Disease, Allele, Polymorphism, education, Imputation, Adaptor Proteins, Signal Transducing, 030304 developmental biology, Heart Failure, Science & Technology, business.industry, WORKING GROUP, 1103 Clinical Sciences, medicine.disease, Genetic architecture, Cardiovascular System & Hematology, Dilated/genetics, Cardiovascular System & Cardiology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Apoptosis Regulatory Proteins, Heart Failure, Systolic, Genome-Wide Association Study
Abstract

Aims Our objective was to better understand the genetic bases of dilated cardiomyopathy (DCM), a leading cause of systolic heart failure. Methods and results We conducted the largest genome-wide association study performed so far in DCM, with 2719 cases and 4440 controls in the discovery population. We identified and replicated two new DCM-associated loci on chromosome 3p25.1 [lead single-nucleotide polymorphism (SNP) rs62232870, P = 8.7 × 10−11 and 7.7 × 10−4 in the discovery and replication steps, respectively] and chromosome 22q11.23 (lead SNP rs7284877, P = 3.3 × 10−8 and 1.4 × 10−3 in the discovery and replication steps, respectively), while confirming two previously identified DCM loci on chromosomes 10 and 1, BAG3 and HSPB7. A genetic risk score constructed from the number of risk alleles at these four DCM loci revealed a 3-fold increased risk of DCM for individuals with 8 risk alleles compared to individuals with 5 risk alleles (median of the referral population). In silico annotation and functional 4C-sequencing analyses on iPSC-derived cardiomyocytes identify SLC6A6 as the most likely DCM gene at the 3p25.1 locus. This gene encodes a taurine transporter whose involvement in myocardial dysfunction and DCM is supported by numerous observations in humans and animals. At the 22q11.23 locus, in silico and data mining annotations, and to a lesser extent functional analysis, strongly suggest SMARCB1 as the candidate culprit gene. Conclusion This study provides a better understanding of the genetic architecture of DCM and sheds light on novel biological pathways underlying heart failure.

Published
2021
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248. Application of Optimal Control Theory to Fourier Transform Ion Cyclotron Resonance

Author

Steffen J. Glaser, Dominique Sugny, V. Martikyan, Camille Beluffi, Marc-André Delsuc, Laboratoire Interdisciplinaire Carnot de Bourgogne [Dijon] (LICB), Université de Bourgogne (UB)-Université de Technologie de Belfort-Montbeliard (UTBM)-Centre National de la Recherche Scientifique (CNRS), CASC4DE S.A.S (CASC4DE), Technische Universität München [München] (TUM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire Carnot de Bourgogne (LICB), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Laboratoire Interdisciplinaire Carnot de Bourgogne (ICB), Université de Technologie de Belfort-Montbeliard (UTBM)-Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and DELSUC, Marc-André

Subjects
Cyclotron, Pharmaceutical Science, Organic chemistry, 02 engineering and technology, [INFO] Computer Science [cs], 01 natural sciences, Fourier transform ion cyclotron resonance, Article, Analytical Chemistry, law.invention, Ion, Medicinal and Biomolecular Chemistry, optimal control, QD241-441, Ion Cyclotron Resonance, law, Theoretical and Computational Chemistry, Physics::Plasma Physics, 0103 physical sciences, Drug Discovery, [INFO]Computer Science [cs], Physical and Theoretical Chemistry, 010306 general physics, Adiabatic process, Physics, Organic Chemistry, 021001 nanoscience & nanotechnology, Optimal control, atomic_molecular_physics, Computational physics, Chemistry (miscellaneous), Excited state, Molecular Medicine, robust protocol, 0210 nano-technology, Excitation, Ion cyclotron resonance
Abstract

International audience; We study the application of Optimal Control Theory to Ion Cyclotron Resonance. We test the validity and the efficiency of this approach for the robust excitation of an ensemble of ions with a wide range of cyclotron frequencies. Optimal analytical solutions are derived in the case without any pulse constraint. A gradient-based numerical optimization algorithm is proposed to take into account limitation in the control intensity. The efficiency of optimal pulses is investigated as a function of control time, maximum amplitude and range of excited frequencies. A comparison with adiabatic and SWIFT pulses is done. On the basis of recent results in Nuclear Magnetic Resonance, this study highlights the potential usefulness of optimal control in Ion Cyclotron Resonance.

Published
2021
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249. Inertial Parameter Identification in Robotics: A Survey

Author

Quentin Leboutet, Julien Roux, Alexandre Janot, Julio Rogelio Guadarrama-Olvera, Gordon Cheng, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Interactive Digital Humans (IDH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), DTIS, ONERA, Université Paris Saclay [Palaiseau], ONERA-Université Paris-Saclay, and Technical University of Munich (TUM)

Subjects
Technology, Chemistry, QH301-705.5, Physics, QC1-999, performance evaluation and benchmarking, TA1-2040, Biology (General), Engineering (General). Civil engineering (General), QD1-999, dynamic parameters identification, [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract

International audience; This work aims at reviewing, analyzing and comparing a range of state-of-the-art approaches to inertial parameter identification in the context of robotics. We introduce “BIRDy (Benchmark for Identification of Robot Dynamics)”, an open-source Matlab toolbox, allowing a systematic and formal performance assessment of the considered identification algorithms on either simulated or real serial robot manipulators. Seventeen of the most widely used approaches found in the scientific literature are implemented and compared to each other, namely: the Inverse Dynamic Identification Model with Ordinary, Weighted, Iteratively Reweighted and Total Least-Squares (IDIM-OLS, -WLS, -IRLS, -TLS); the Instrumental Variables method (IDIM-IV), the Maximum Likelihood (ML) method; the Direct and Inverse Dynamic Identification Model approach (DIDIM); the Closed-Loop Output Error (CLOE) method; the Closed-Loop Input Error (CLIE) method; the Direct Dynamic Identification Model with Nonlinear Kalman Filtering (DDIM-NKF), the Adaline Neural Network (AdaNN), the Hopfield-Tank Recurrent Neural Network (HTRNN) and eventually a set of Physically Consistent (PC-) methods allowing the enforcement of parameter physicality using Semi-Definite Programming, namely the PC-IDIM-OLS, -WLS, -IRLS, PC-IDIM-IV, and PC-DIDIM. BIRDy is robot-agnostic and features a complete inertial parameter identification pipeline, from the generation of symbolic kinematic and dynamic models to the identification process itself. This includes functionalities for excitation trajectory computation as well as the collection and pre-processing of experiment data. In this work, the proposed methods are first evaluated in simulation, following a Monte Carlo scheme on models of the 6-DoF TX40 and RV2SQ industrial manipulators, before being tested on the real robot platforms. The robustness, precision, computational efficiency and context of application the different methods are investigated and discussed.

Published
2021
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250. Novel genomic approaches to study antagonistic coevolution between hosts and parasites

Author

Peter D. Fields, Hanna Märkle, Aurélien Tellier, Sona John, Amandine Cornille, Technische Universität München [München] (TUM), University of Chicago, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Basel (Unibas), and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)

Subjects
0106 biological sciences, 0301 basic medicine, balancing selection, Antagonistic Coevolution, Genomics, Biology, Host Parasite Interactions, Balancing selection, Natural Selection and Contemporary Evolution, 010603 evolutionary biology, 01 natural sciences, Genome, Host-Parasite Interactions, Population genomics, 03 medical and health sciences, Host–parasite coevolution, Genetic drift, positive selection, Genetics, Animals, Parasites, Molecular Ecology Coevolution, Experimental Evolution, Ecology, Evolution, Behavior and Systematics, Coevolution, inference, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Evolution, ddc, 030104 developmental biology, Evolutionary biology, host-parasite coevolution, Ecological Genetics, genetic drift, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, Genome-Wide Association Study
Abstract

International audience; Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.

Published
2021
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