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1,136 results on '"Vrije Universiteit Amsterdam [Amsterdam] (VU)"'

1. Sub-diffraction computational imaging via a flexible multicore-multimode fiber

Author

Zhouping Lyu, Ksenia Abrashitova, Johannes F. de Boer, Esben R. Andresen, Hervé Rigneault, Lyubov V. Amitonova, LaserLaB - Biophotonics and Microscopy, Biophotonics and Medical Imaging, Physics and Astronomy, Amsterdam Neuroscience - Brain Imaging, Ophthalmology, Amsterdam Neuroscience - Systems & Network Neuroscience, Vrije Universiteit Amsterdam [Amsterdam] [VU], Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 [PhLAM], Institut FRESNEL [FRESNEL], MOSAIC [MOSAIC], Vrije Universiteit Amsterdam [Amsterdam] (VU), Advanced Research Center for Nanolithography (ARCNL), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut FRESNEL (FRESNEL), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), MOSAIC (MOSAIC), and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], SDG 7 - Affordable and Clean Energy, Atomic and Molecular Physics, and Optics
Abstract

An ultra-thin multimode fiber is an ideal platform for minimally invasive microscopy with the advantages of a high density of modes, high spatial resolution, and a compact size. In practical applications, the probe needs to be long and flexible, which unfortunately destroys the imaging capabilities of a multimode fiber. In this work, we propose and experimentally demonstrate sub-diffraction imaging through a flexible probe based on a unique multicore-multimode fiber. A multicore part consists of 120 Fermat’s spiral distributed single-mode cores. Each of the cores offers stable light delivery to the multimode part, which provides optimal structured light illumination for sub-diffraction imaging. As a result, perturbation-resilient fast sub-diffraction fiber imaging by computational compressive sensing is demonstrated.

Published
2023

2. Deglacial climate changes as forced by different ice sheet reconstructions

Author

Nathaelle Bouttes, Fanny Lhardy, Aurélien Quiquet, Didier Paillard, Hugues Goosse, Didier M. Roche, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Earth and Life Institute - Environmental Sciences (ELIE), Université Catholique de Louvain = Catholic University of Louvain (UCL), Cluster Earth and Climate [Amsterdam], Department of Earth Sciences [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), and UCL - SST/ELI/ELIC - Earth & Climate

Subjects
Global and Planetary Change, [SDU]Sciences of the Universe [physics], Stratigraphy, Paleontology
Abstract

During the last deglaciation, the climate evolves from a cold state at the Last Glacial Maximum (LGM) at 21 ka (thousand years ago) with large ice sheets to the warm Holocene at ∼9 ka with reduced ice sheets. The deglacial ice sheet melt can impact the climate through multiple ways: changes of topography and albedo, bathymetry and coastlines, and freshwater fluxes (FWFs). In the PMIP4 (Paleoclimate Modelling Intercomparison Project – Phase 4) protocol for deglacial simulations, these changes can be accounted for or not depending on the modelling group choices. In addition, two ice sheet reconstructions are available (ICE-6G_C and GLAC-1D). In this study, we evaluate all these effects related to ice sheet changes on the climate using the iLOVECLIM model of intermediate complexity. We show that the two reconstructions yield the same warming to a first order but with a different amplitude (global mean temperature of 3.9 ∘C with ICE-6G_C and 3.8 ∘C with GLAC-1D) and evolution. We obtain a stalling of temperature rise during the Antarctic Cold Reversal (ACR, from ∼14 to ∼12 ka) similar to proxy data only with the GLAC-1D ice sheet reconstruction. Accounting for changes in bathymetry in the simulations results in a cooling due to a larger sea ice extent and higher surface albedo. Finally, freshwater fluxes result in Atlantic meridional overturning circulation (AMOC) drawdown, but the timing in the simulations disagrees with proxy data of ocean circulation changes. This questions the causal link between reconstructed freshwater fluxes from ice sheet melt and recorded AMOC weakening.

Published
2023

3. A proxy modelling approach to assess the potential of extracting ENSO signal from tropical Pacific planktonic foraminifera

Author

Didier M. Roche, Brett Metcalfe, Bryan C Lougheed, Claire Waelbroeck, Earth and Climate, Earth Sciences, Cluster Earth and Climate [Amsterdam], Department of Earth Sciences [Amsterdam], VU University Amsterdam-VU University Amsterdam, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Department of Earth Sciences [Uppsala], Uppsala University, Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ANR-10-LABX-0018,L-IPSL,LabEx Institut Pierre Simon Laplace (IPSL): Understand climate and anticipate future changes(2010), European Project: 339108,EC:FP7:ERC,ERC-2013-ADG,ACCLIMATE(2014), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)-Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)

Subjects
010506 paleontology, Climate Research, 010504 meteorology & atmospheric sciences, lcsh:Environmental protection, Stratigraphy, Population, 01 natural sciences, Proxy (climate), Klimatforskning, Foraminifera, lcsh:Environmental pollution, lcsh:TD169-171.8, 14. Life underwater, SDG 14 - Life Below Water, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, education, lcsh:Environmental sciences, Globigerinoides, Seabed, 0105 earth and related environmental sciences, lcsh:GE1-350, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, education.field_of_study, biology, Paleontology, Plankton, biology.organism_classification, El Niño Southern Oscillation, Oceanography, 13. Climate action, lcsh:TD172-193.5, Environmental science, Climate model
Abstract

A complete understanding of past El Niño–Southern Oscillation (ENSO) fluctuations is important for the future predictions of regional climate using climate models. One approach to reconstructing past ENSO dynamics uses planktonic foraminifera as recorders of past climate to assess past spatio-temporal changes in upper ocean conditions. In this paper, we utilise a model of planktonic foraminifera populations, Foraminifera as Modelled Entities (FAME), to forward model the potential monthly average δ18Oc and temperature signal proxy values for Globigerinoides ruber, Globigerinoides sacculifer, and Neogloboquadrina dutertrei from input variables covering the period of the instrumental record. We test whether the modelled foraminifera population δ18Oc and Tc associated with El Niño events statistically differ from the values associated with other climate states. Provided the assumptions of the model are correct, our results indicate that the values of El Niño events can be differentiated from other climate states using these species. Our model computes the proxy values of foraminifera in the water, suggesting that, in theory, water locations for a large portion of the tropical Pacific should be suitable for differentiating El Niño events from other climate states. However, in practice it may not be possible to differentiate climate states in the sediment record. Specifically, comparison of our model results with the sedimentological features of the Pacific Ocean shows that a large portion of the hydrographically/ecologically suitable water regions coincide with low sediment accumulation rate at the sea floor and/or of sea floor that lie below threshold water depths for calcite preservation.

Published
2020

4. Can DEB models infer metabolic differences between intertidal and subtidal morphotypes of the Antarctic limpet Nacella concinna (Strebel, 1908)?

Author

Simon A. Morley, Thomas Saucède, Starrlight Augustine, Sebastiaan A.L.M. Kooijman, Bruno Danis, Charlène Guillaumot, Laboratoire de Biologie Marine, Université libre de Bruxelles (ULB), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Akvaplan-Niva [Tromsø], Norwegian Institute for Water Research (NIVA), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Work supported by a 'Fonds pour la formation à la Recherche dans l'Industrie et l'Agriculture' (FRIA) and 'Bourse fondation de la mer' grants and by Natural Environment Research Council core funding to the British Antarctic Survey., and Molecular Cell Biology

Subjects
0106 biological sciences, Nacella, Dynamic energy budget, Field experiment, Species distribution, Intertidal zone, 010603 evolutionary biology, 01 natural sciences, model relevance, 14. Life underwater, SDG 14 - Life Below Water, Southern Ocean, Invertebrate, biology, Ecology, 010604 marine biology & hydrobiology, Ecological Modeling, Limpet, biology.organism_classification, model accuracy, Benthic zone, marine benthic species, ecological modelling, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sciences exactes et naturelles
Abstract

12 pages; International audience; Studying the influence of changing environmental conditions on Antarctic marine benthic invertebrates is strongly constrained by limited access to the region, which poses difficulties to performing long-term experimental studies. Ecological modelling has been increasingly used as a potential alternative to assess the impact of such changes on species distribution or physiological performance.Among ecological models, the Dynamic Energy Budget (DEB) approach represents each individual through four energetic compartments (i.e. reserve, structure, maturation and reproduction) from which energy is allocated in contrasting proportions according to different life stages and to two forcing environmental factors (food resources and temperature).In this study, the example of an abundant coastal limpet, Nacella concinna (Strebel 1908), was studied. The species is known to have intertidal and subtidal morphotypes, genetically similar but physiologically and morphologically contrasting.The objectives of this paper are (1) to evaluate the potential of the DEB approach, and assess whether a DEB model can be separately built for the intertidal and subtidal morphotypes, based on a field experiment and data from literature and (2) to analyse whether models are contrasting enough to reflect the known physiological and morphological differences between the morphotypes.We found only minor differences in temperature-corrected parameter values between both populations, meaning that the observed differences can be only explained by differences in environmental conditions (i.e. DEB considered variables, food resources and temperature, but also other variables not considered by DEB). Despite the known morphological difference between the populations, the difference in shape coefficients was small.This study shows that even with the amount of data so far available in the literature, DEB models can already be applied to some Southern Ocean case studies, but, more data are required to accurately model the physiological and morphological differences between individuals.

Published
2020

5. Kappa free light chains is a valid tool in the diagnostics of MS: A large multicenter study

Author

Leurs, CE, Twaalfhoven, HAM, Lissenberg-Witte, BI, van Pesch, V, Dujmovic, I, Drulovic, J, Castellazzi, M, Bellini, T, Pugliatti, M, Kuhle, J, Villar, LM, Alvarez-Cermeño, JC, Alvarez-Lafuente, R, Hegen, H, Deisenhammer, F, Walchhofer, LM, Thouvenot, E, Comabella, M, Montalban, X, Vécsei, L, Rajda, C, Galimberti, D, Scarpini, E, Altintas, A, Rejdak, K, Frederiksen, JL, Pihl-Jensen, G, Jensen, PEH, Khalil, M, Voortman, MM, Fazekas, F, Saiz, Albert, La Puma, D, Vercammen, M, Vanopdenbosch, L, Uitdehaag, BMJ, Killestein, J, Bridel, C, Teunissen, Charlotte E, Universitat Autònoma de Barcelona, UCL - SSS/IONS/CEMO - Pôle Cellulaire et moléculaire, UCL - (SLuc) Service de neurologie, Basic (bio-) Medical Sciences, Ayşe, Altıntaş, Leurs, C.E., Twaalfhoven, H.A.M., Lissenberg-Witte, B.I., van Pesch, V., Dujmovic, I., Drulovic, J., Castellazzi, M., Bellini, T., Pugliatti, M., Kuhle, J., Villar, L.M., Alvarez-Cermeño, J.C., Alvarez-Lafuente, R., Hegen, H., Deisenhammer, F., Walchhofer, L.M., Thouvenot, E., Comabella, M., Montalban, X., Vécsei, L., Rajda, C., Galimberti, D., Scarpini, E., Rejdak, K., Frederiksen, J.L., Pihl-Jensen, G., Jensen, P.E.H., Khalil, M., Voortman, M.M., Fazekas, F., Saiz, A., La Puma, D., Vercammen, M., Vanopdenbosch, L., Uitdehaag, B.M.J., Killestein, J., Bridel, C., Teunissen, C., School of Medicine, Department of Neurology, Neurology, Laboratory Medicine, Epidemiology and Data Science, APH - Methodology, Amsterdam Neuroscience - Neuroinfection & -inflammation, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), Department of Anatomy and Neurosciences [Amsterdam, The Netherlands] (Amsterdam Neuroscience), Section Clinical Neuroanatomy [Amsterdam, The Netherlands], VU University Medical Center [Amsterdam]-VU University Medical Center [Amsterdam], Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU), Cliniques Universitaires Saint-Luc [Bruxelles], Clinical Centre of Serbia, Università degli Studi di Ferrara (UniFE), University Hospital Basel [Basel], Hospital Universitario Ramón y Cajal [Madrid], Universidad de Alcalá - University of Alcalá (UAH), Red Española de Esclerosis Múltiple (REEM), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos [Madrid, Spain] (IdISSC), Department of Neurology, Medical University of Innsbruck, Service de Neurologie [CHU Nimes] (Pôle NIRR), Hôpital Universitaire Carémeau [Nîmes] (CHU Nîmes), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Centre d'Esclerosi Múltiple de Catalunya (CemCat), Vall d'Hebron University Hospital [Barcelona], Centre de résonance magnétique biologique et médicale (CRMBM), Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Szeged [Szeged], Centro Dino Ferrari [Milano], Università degli Studi di Milano [Milano] (UNIMI)-Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Koç University, Medical University of Lublin, Rigshospitalet [Copenhagen], Copenhagen University Hospital, Danish Multiple Sclerosis Research Centre, Copenhagen University Hospital-Copenhagen University Hospital, Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz 8010, Austria, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Department of Neurology, AZ Sint Jan Brugge Oostende, Neuroscience Amsterdam, VU University Medical Centre, 1081HV 1117, Amsterdam, Amsterdam Neuroscience [Pays-Bas], and Vrije Universiteit Amsterdam [Amsterdam] (VU)-University of Amsterdam [Amsterdam] (UvA)-VU University Medical Center [Amsterdam]

Subjects
KFLC (kappa free light chain), Adult, Male, Multiple Sclerosis, Clinical Neurology, Esclerosi múltiple, CSF, CSF (cerebrospinal fluid), Immunoglobulin light chain, Sensitivity and Specificity, NO, Multiple sclerosis, Immunoglobulin kappa-Chains, 03 medical and health sciences, 0302 clinical medicine, Nuclear magnetic resonance, Immunoglobulin lambda-Chains, Humans, Medicine, Diagnostic biomarker, biomarkers, KFLC, OCB, 030304 developmental biology, 0303 health sciences, business.industry, Biochemical markers, Oligoclonal Bands, Reproducibility of Results, Middle Aged, OCB (oligoclonal IgG band), Free Light Chain, Biomarkers, Neurology, Multicenter study, Marcadors bioquímics, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Female, Neurology (clinical), business, Original Research Papers, 030217 neurology & neurosurgery, Kappa
Abstract

Objective: to validate kappa free light chain (KFLC) and lambda free light chain (LFLC) indices as a diagnostic biomarker in multiple sclerosis (MS). Methods: we performed a multicenter study including 745 patients from 18 centers (219 controls and 526 clinically isolated syndrome (CIS)/MS patients) with a known oligoclonal IgG band (OCB) status. KFLC and LFLC were measured in paired cerebrospinal fluid (CSF) and serum samples. Gaussian mixture modeling was used to define a cut-off for KFLC and LFLC indexes. Results: the cut-off for the KFLC index was 6.6 (95% confidence interval (CI) = 5.2–138.1). The cut-off for the LFLC index was 6.9 (95% CI = 4.5–22.2). For CIS/MS patients, sensitivity of the KFLC index (0.88; 95% CI = 0.85–0.90) was higher than OCB (0.82; 95%CI = 0.79–0.85; p < 0.001), but specificity (0.83; 95% CI = 0.78–0.88) was lower (OCB = 0.92; 95% CI = 0.89–0.96; p < 0.001). Both sensitivity and specificity for the LFLC index were lower than OCB. Conclusion: compared with OCB, the KFLC index is more sensitive but less specific for diagnosing CIS/MS. Lacking an elevated KFLC index is more powerful for excluding MS compared with OCB but the latter is more important for ruling in a diagnosis of CIS/MS., NA

Published
2020

6. Real-time imaging of multivesicular body-plasma membrane fusion to quantify exosome release from single cells

Author

Stephan Huveneers, Guillaume van Niel, Philippe Bun, Frederik J. Verweij, Maarten P. Bebelman, D. Michiel Pegtel, Pathology, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, CCA - Imaging and biomarkers, Medicinal chemistry, AIMMS, Department of Pathology [Amsterdam, The Netherlands] (Amsterdam Neuroscience ), VU University Medical Center [Amsterdam], Division of Medicinal Chemistry [Amsterdam, The Netherlands], Vrije Universiteit Amsterdam [Amsterdam] (VU)-Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Institut de psychiatrie et neurosciences de Paris (IPNP - U1266 Inserm - Paris Descartes), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU), Dupuis, Christine, Medical Biochemistry, ACS - Atherosclerosis & ischemic syndromes, ACS - Microcirculation, and AII - Inflammatory diseases

Subjects
Time Factors, Total internal reflection microscopy, Cellular homeostasis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Exosomes, Exosome, Membrane Fusion, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Tetraspanin, Live cell imaging, Plasma membrane fusion, Humans, Multivesicular Body, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, 0303 health sciences, Chemistry, Lipid bilayer fusion, Molecular Imaging, Cell biology, Exosomes/metabolism, Molecular Imaging/methods, Single-Cell Analysis, 030217 neurology & neurosurgery, HeLa Cells
Abstract

International audience; Exosomes are small extracellular vesicles with a diameter of 40-150 nm, and are implicated in cellular homeostasis and cell-cell communication. They can be secreted in bulk in response to cell-extrinsic and cell-intrinsic signals that cause multivesicular body (MVB) fusion with the plasma membrane (PM). However, research on the regulation of exosome release is hampered by the failure of current methods to capture the dynamics of exosome release. Here we describe how live imaging with tetraspanin-based pH-sensitive fluorescent reporters can quantify the MVB-PM fusion rate of single cells. Our approach enables identification of exogenous stimuli, signaling pathways, and fusion complexes, and can map subcellular sites of fusion events. In addition, dual-color imaging can be used to assess simultaneous release of different cargo by MVB exocytosis. This protocol describes the complete imaging experiment, consisting of transient expression of tetraspanin reporters (2 d), live-cell (dual-color) total internal reflection fluorescence microscopy (30-60 min per condition), and semiautomatic image analysis by using a newly developed ImageJ macro (±30 min per condition).

Published
2020

7. Making the field of computing more inclusive

Author

John \\'Scooter\\' Morris, Tovi Grossman, Jonathan Lazar, Gerrit C. van der Veer, Jennifer Mankoff, Elizabeth F. Churchill, Philippe Palanque, Towson University [Towson, MD, United States], University of Maryland System, Google Inc., Autodesk Research, University of Twente [Netherlands], Vrije Universiteit Amsterdam [Amsterdam] (VU), Open University of the Netherlands [Heerlen], Dalian Maritime University, Luxun Academy of Fine Arts - LAFA (Shenyang, Chine), Luxun Academy of Fine Arts (Shenyang) (LAFA), Interactive Critical Systems (IRIT-ICS), 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, University of California [San Francisco] (UCSF), University of California, Carnegie Mellon University [Pittsburgh] (CMU), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université Toulouse - Jean Jaurès - UT2J (FRANCE), Université Toulouse 1 Capitole - UT1 (FRANCE), Dalian Maritime University - DMU (CHINA), Google Inc. (USA), Luxun Academy of Fine Arts - LAFA (CHINA), Open Universiteit - OU (NETHERLANDS), University of California, San Francisco - UCSF (USA), University of Twente (NETHERLANDS), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Institut de recherche en informatique de Toulouse ( IRIT ), Institut National Polytechnique [Toulouse] ( INP ) -Université Toulouse 1 Capitole ( UT1 ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), University of California [San Francisco] ( UCSF ), Carnegie Mellon University [Pittsburgh] ( CMU ), Software and Sustainability (S2), Network Institute, Software & Services, and Institut National Polytechnique de Toulouse - INPT (FRANCE)

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, SDG 16 - Peace, General Computer Science, Computer science, [ INFO.INFO-CR ] Computer Science [cs]/Cryptography and Security [cs.CR], [ INFO.INFO-SE ] Computer Science [cs]/Software Engineering [cs.SE], 02 engineering and technology, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Interface homme-machine, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], Lead (geology), [ INFO.INFO-HC ] Computer Science [cs]/Human-Computer Interaction [cs.HC], Human–computer interaction, Architectures Matérielles, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Génie logiciel, 0501 psychology and cognitive sciences, [ INFO.INFO-ES ] Computer Science [cs]/Embedded Systems, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], 050107 human factors, ComputingMilieux_MISCELLANEOUS, ComputingMilieux_THECOMPUTINGPROFESSION, Field (Bourdieu), 05 social sciences, SDG 16 - Peace, Justice and Strong Institutions, Modélisation et simulation, Accessibility, Systèmes embarqués, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Justice and Strong Institutions, Emerging technologies, Human-centered computing, Cryptographie et sécurité, [INFO.INFO-ES]Computer Science [cs]/Embedded Systems, [ INFO.INFO-AR ] Computer Science [cs]/Hardware Architecture [cs.AR]
Abstract

People with disabilities are a potential source of ideas and additional membership for professional computing organizations. Including people with disabilities in the decision-making processes of professional computing organizations ensures the most important barriers are addressed first. SIGCHI is one of ACM's largest special interest groups, with approximately 3,500 members as of 2016. SIGCHI has three goals, underscore the importance of stakeholder engagement; offer broad suggestions for how large SIGs can improve the inclusiveness of physical events and digital content; and underscore that addressing physical and digital accessibility is an ongoing process that takes time, with involvement of many stakeholders. These stakeholders must work together to drive the creation of acceptable and accepted guidelines and resources, find individuals with expertise to work in an advisory capacity, and find volunteers to implement effective strategies and provide feedback regarding the policies and guidelines in action. SIGCHI's hope is that SIGCHI will be a community that is perceived as welcoming for all researchers and practitioners with disabilities. Large SIGs, when they educate others about digital and physical accessibility, can have significant influence on the conference locations they rent and the universities and companies that employ their members. ACM has a leading role to play by ensuring all SIGs strive to be inclusive and by thus being a role model for other professional associations. The best way to handle such responsibility would ultimately be to ensure there are professional staff supporting and centralizing the most vital accessibility needs and accessibility is included in contractual relationships.

Published
2017

8. Sarcopenia in older mice is characterized by a decreased anabolic response to a protein meal

Author

Jérôme Salles, Yvette C. Luiking, Miriam van Dijk, Jolanda Nagel, Stéphane Walrand, Francina J. Dijk, Sjors Verlaan, Klaske van Norren, Nutricia Research, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Department of Internal Medicine, section Gerontology and Geriatrics, Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Nutrition and Pharmacologie, Wageningen University and Research [Wageningen] (WUR), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Vrije University Medical Center, Wageningen University and Research Centre [Wageningen] (WUR), and Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Male, Aging, Sarcopenia, Health (social science), Anabolism, medicine.medical_treatment, Pilot Projects, Hindlimb, souris, medicine.disease_cause, chemistry.chemical_compound, 0302 clinical medicine, Anaerobiosis, senior citizens, [SDV.MHEP.GEG]Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, Malondialdehyde, Nutritional Biology, Anabolic resistance, Dietary Proteins, medicine.medical_specialty, mice, personne âgée, 03 medical and health sciences, Insulin resistance, sarcopenie, Internal medicine, medicine, Geriatric skeletal muscle, Animals, Muscle Strength, Muscle, Skeletal, VLAG, business.industry, Insulin, medicine.disease, Mice, Inbred C57BL, Disease Models, Animal, Oxidative Stress, Ageing, 030104 developmental biology, Endocrinology, chemistry, pathologie musculaire, Muscle function, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Geriatrics and Gerontology, business, Gerontology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Oxidative stress
Abstract

Ageing is associated with sarcopenia, a progressive decline of skeletal muscle mass, muscle quality and muscle function. Reduced sensitivity of older muscles to respond to anabolic stimuli, i.e. anabolic resistance, is part of the underlying mechanisms. Although, muscle parameters have been studied in mice of various ages/strains; the aim was to study if mice display similar deteriorating processes as human ageing. Therefore, 10,16,21 and 25 months-old C57BL6/6J male mice were studied to measure parameters of sarcopenia and factors contributing to its pathophysiology, with the aim of characterizing sarcopenia in old mice. Muscle mass of the hind limb was lower in 25 as compared to 10 month-old mice. A significant decrease in physical daily activity, muscle grip strength and ex vivo muscle maximal force production was observed in 25 compared to 10 month-old mice. The muscle anabolic response to a single protein meal showed increased muscle protein synthesis in young, but not in old mice, indicative to anabolic resistance. However, by increasing the protein content in meals, anabolic resistance could be overcome, similar as in human elderly. Additionally, aged mice showed higher fasted insulin and hepatic malondialdehyde (MDA) levels (=marker oxidative stress). This study shows clear characteristics of sarcopenia that coincide with anabolic resistance, insulin resistance and oxidative stress in 25 month-old C57/BL6 male mice, similar to human ageing. Furthermore, similar decline in muscle mass, strength and function was observed in this aged-mice-model. These observations offer potential for the future to explore in old mice the effects of interventions targeting sarcopenia

Published
2017

9. Correction: Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration

Author

Sylvain Monteux, James T. Weedon, Gesche Blume-Werry, Konstantin Gavazov, Vincent E. J. Jassey, Margareta Johansson, Frida Keuper, Carolina Olid, Ellen Dorrepaal, Systems Ecology, Climate Impacts Research Centre (CIRC), Umeå University, Department of Ecological Sciences, Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Plant and Vegetation Ecology (PLECO), University of Antwerp (UA), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Department of Physical Geography and Ecosystem Science [Lund], Lund University [Lund], Agroressources et Impacts environnementaux (AgroImpact), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, 03 medical and health sciences, SDG 16 - Peace, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030306 microbiology, SDG 16 - Peace, Justice and Strong Institutions, Microbiology, Justice and Strong Institutions, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

Since the publication of the original article, the authors noticed some errors in reference citation had been introduced throughout the paper. The following text contains excerpts from the original article and how they should appear with correct referencing. The publisher apologises for any inconvenience this has caused readers.

Published
2019

10. Relativistic equation of motion coupled cluster based on four-compoment Hamiltonians

Author

Bouchafra, Yassine, Halbert, Loïc, Réal, Florent, Vallet, Valérie, Virot, François, Shee, Avijit, Saue, Trond, Visscher, Lucas, Severo Pereira Gomes, André, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), PSN-RES/SEREX/L2EC, PSN-RES/SAG/LETR, Department of Chemistry, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), 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-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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 Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Faculty of Sciences, Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Laboratoire d'Etude du corium et du Transfert des radioélèments (IRSN/PSN-RES/SAG/LETR), Service des Accidents Graves (IRSN/PSN-RES/SAG), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

11. Panta Rhei benchmark dataset

Author

Heidi Kreibich, Kai Schröter, Giuliano Di Baldassarre, Anne F. Van Loon, Maurizio Mazzoleni, Guta Wakbulcho Abeshu, Svetlana Agafonova, Amir AghaKouchak, Hafzullah Aksoy, Camila Alvarez-Garreton, Blanca Aznar, Laila Balkhi, Marlies H. Barendrecht, Sylvain Biancamaria, Liduin Bos-Burgering, Chris Bradley, Yus Budiyono, Wouter Buytaert, Lucinda Capewell, Hayley Carlson, Yonca Cavus, Anaïs Couasnon, Gemma Coxon, Ioannis Daliakopoulos, Marleen C. de Ruiter, Claire Delus, Mathilde Erfurt, Giuseppe Esposito, Didier François, Frédéric Frappart, Jim Freer, Natalia Frolova, Animesh K. Gain, Manolis Grillakis, Jordi Oriol Grima, Diego A. Guzmán, Laurie S. Huning, Monica Ionita, Maxim Kharlamov, Dao Nguyen Khoi, Natalie Kieboom, Maria Kireeva, Aristeidis Koutroulis, Waldo Lavado-Casimiro, Hong-Yi Li, Maria Carmen LLasat, David Macdonald, Johanna Mård, Hannah Mathew-Richards, Andrew McKenzie, Alfonso Mejia, Eduardo Mario Mendiondo, Marjolein Mens, Shifteh Mobini, Guilherme Samprogna Mohor, Viorica Nagavciuc, Thanh Ngo-Duc, Huynh Thi Thao Nguyen, Pham Thi Thao Nhi, Olga Petrucci, Nguyen Hong Quan, Pere Quintana-Seguí, Saman Razavi, Elena Ridolfi, Jannik Riegel, Md Shibly Sadik, Nivedita Sairam, Elisa Savelli, Alexey Sazonov, Sanjib Sharma, Johanna Sörensen, Felipe Augusto Arguello Souza, Kerstin Stahl, Max Steinhausen, Michael Stoelzle, Wiwiana Szalińska, Qiuhong Tang, Fuqiang Tian, Tamara Tokarczyk, Carolina Tovar, Thi Van Thu Tran, Marjolein H. J. van Huijgevoort, Michelle T. H. van Vliet, Sergiy Vorogushyn, Thorsten Wagener, Yueling Wang, Doris E. Wendt, Elliot Wickham, Long Yang, Mauricio Zambrano-Bigiarini, Philip J. Ward, German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ), Uppsala University, Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Houston, Lomonosov Moscow State University (MSU), University of California [Irvine] (UC Irvine), University of California (UC), Istanbul Technical University (ITÜ), Center for Climate and Resilience Research [Conception] ((CR)2), Universidad de Concepción - University of Concepcion [Chile], Operations Department, Barcelona Cicle de l’Aigua, University of Saskatchewan [Saskatoon] (U of S), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Department of Groundwater Management, Deltares, Delft, University of Birmingham [Birmingham], Agency for the Assessment and Application of Technology, Imperial College London, Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Water and Climate Risk, and Amsterdam Sustainability Institute

Subjects
Oceanography, Hydrology and Water Resources, [SDE]Environmental Sciences, General Earth and Planetary Sciences, Oceanografi, hydrologi och vattenresurser, SDG 6 - Clean Water and Sanitation
Abstract

As the adverse impacts of hydrological extremes increase in many regions of the world, a better understanding of the drivers of changes in risk and impacts is essential for effective flood and drought risk management and climate adaptation. However, there is currently a lack of comprehensive, empirical data about the processes, interactions and feedbacks in complex human-water systems leading to flood and drought impacts. Here we present a benchmark dataset containing socio-hydrological data of paired events, i.e., two floods or two droughts that occurred in the same area. The 45 paired events occurred in 42 different study areas and cover a wide range of socio-economic and hydro-climatic conditions. The dataset is unique in covering both floods and droughts, in the number of cases assessed, and in the quantity of socio-hydrological data. The benchmark dataset comprises: 1) detailed review style reports about the events and key processes between the two events of a pair; 2) the key data table containing variables that assess the indicators which characterise management shortcomings, hazard, exposure, vulnerability and impacts of all events; 3) a table of the indicators-of-change that indicate the differences between the first and second event of a pair. The advantages of the dataset are that it enables comparative analyses across all the paired events based on the indicators-of-change and allows for detailed context- and location-specific assessments based on the extensive data and reports of the individual study areas. The dataset can be used by the scientific community for exploratory data analyses e.g. focused on causal links between risk management, changes in hazard, exposure and vulnerability and flood or drought impacts. The data can also be used for the development, calibration and validation of socio-hydrological models. The dataset is available to the public through the GFZ Data Services (Kreibich et al. 2023, link for review: https://dataservices.gfz-potsdam.de/panmetaworks/review/923c14519deb04f83815ce108b48dd2581d57b90ce069bec9c948361028b8c85/).

Published
2023

12. PROJECTION METHODS FOR NEURAL FIELD EQUATIONS

Author

Daniele Avitabile, Department of Mathematics [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU), Mathématiques pour les Neurosciences (MATHNEURO), 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), Mathematics, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, and Amsterdam Neuroscience - Systems & Network Neuroscience

Subjects
Numerical Analysis, Quantitative Biology::Neurons and Cognition, mathematical neuroscience, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Applied Mathematics, Numerical Analysis (math.NA), Dynamical Systems (math.DS), integro-differential equations, Computational Mathematics, FOS: Mathematics, projection methods, Mathematics - Numerical Analysis, Mathematics - Dynamical Systems, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract

International audience; Neural field models are nonlinear integro-differential equations for the evolution of neuronal activity, and they are a prototypical large-scale, coarse-grained neuronal model in continuum cortices. Neural fields are often simulated heuristically and, in spite of their popularity in mathematical neuroscience, their numerical analysis is not yet fully established. We introduce generic projection methods for neural fields, and derive a-priori error bounds for these schemes. We extend an existing framework for stationary integral equations to the time-dependent case, which is relevant for neuroscience applications. We find that the convergence rate of a projection scheme for a neural field is determined to a great extent by the convergence rate of the projection operator. This abstract analysis, which unifies the treatment of collocation and Galerkin schemes, is carried out in operator form, without resorting to quadrature rules for the integral term, which are introduced only at a later stage, and whose choice is enslaved by the choice of the projector. Using an elementary timestepper as an example, we demonstrate that the error in a time stepper has two separate contributions: one from the projector, and one from the time discretisation. We give examples of concrete projection methods: two collocation schemes (piecewise-linear and spectral collocation) and two Galerkin schemes (finite elements and spectral Galerkin); for each of them we derive error bounds from the general theory, introduce several discrete variants, provide implementation details, and present reproducible convergence tests.

Published
2023

13. Electronic states of (ultra) heavy halogen species with four-component based equation of motion coupled cluster methods

Author

Shee, Avijit, Saue, Trond, Visscher, Lucas, Severo Pereira Gomes, André, Physico-Chimie Moléculaire Théorique ( PCMT ), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 ( PhLAM ), Université de Lille-Centre National de la Recherche Scientifique ( CNRS ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Department of Chemistry - University of Michigan, University of Michigan [Ann Arbor], Méthodes et outils de la chimie quantique (LCPQ), Laboratoire de Chimie et Physique Quantiques ( LCPQ ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Theoretical Chemistry, Vrije Universiteit Amsterdam [Amsterdam] ( VU ), ANR-11-LABX-0005/11-LABX-0005,Cappa,Physiques et Chimie de l’Environnement Atmosphérique ( 2011 ), Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Department of Chemistry, University of Michigan, University of Michigan System-University of Michigan System, Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Vrije Universiteit Amsterdam [Amsterdam] (VU), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [ PHYS.PHYS.PHYS-CHEM-PH ] Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], [ CHIM.THEO ] Chemical Sciences/Theoretical and/or physical chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

14. Selection for associative learning of color stimuli reveals correlated evolution of this learning ability across multiple stimuli and rewards

Author

Liefting , Maartje, Hoedjes , Katja M, Lann , Cécile Le, Smid , Hans M, Ellers , Jacintha, Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Freie Universität Berlin [Berlin], Wageningen University and Research Centre [Wageningen] ( WUR ), Université de Lausanne ( UNIL ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Animal Ecology, Amsterdam, University of Amsterdam [Amsterdam] ( UvA ), Vrije Universiteit Amsterdam [Amsterdam] (VU), Freie Universität Berlin, Wageningen University and Research [Wageningen] (WUR), Université de Lausanne = University of Lausanne (UNIL), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), 820.01.023, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Animal Ecology

Subjects
[ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, colour, genetic structures, odor, Artificial selection, education, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Original Articles, associative learning, Laboratorium voor Erfelijkheidsleer, color, sensory modality, odour, Original Article, Laboratory of Genetics, Genetics, Ecology, Evolution, Behavior and Systematics, General Agricultural and Biological Sciences, Nasonia vitripennis, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; We are only starting to understand how variation in cognitive ability can result from local adaptations to environmental conditions. A major question in this regard is to what extent selection on cognitive ability in a specific context affects that ability in general through correlated evolution. To address this question we performed artificial selection on visual associative learning in female Nasonia vitripennis wasps. Using appetitive conditioning in which a visual stimulus was offered in association with a host reward, the ability to learn visual associations was enhanced within 10 generations of selection. To test for correlated evolution affecting this form of learning, the ability to readily form learned associations in females was also tested using an olfactory instead of a visual stimulus in the appetitive conditioning. Additionally, we assessed whether the improved associative learning ability was expressed across sexes by colour-conditioning males with a mating reward. Both females and males from the selected lines consistently demonstrated an increased associative learning ability compared to the control lines, independent of learning context or conditioned stimulus. No difference in relative volume of brain neuropils was detected between the selected and control lines. This article is protected by copyright. All rights reserved.

Published
2018

15. Extraordinary rocks from the peak ring of the Chicxulub impact crater: P-wave velocity, density, and porosity measurements from IODP/ICDP Expedition 364

Author

Jaime Urrutia-Fucugauchi, Axel Wittmann, C. Mellett, Kosei E. Yamaguchi, David A. Kring, Honami Sato, Ludovic Ferrière, Mario Rebolledo-Vieyra, Johanna Lofi, Rubén Ocampo-Torres, Cornelia Rasmussen, Auriol S. P. Rae, Marco J. L. Coolen, Heather L. Jones, Michael H. Poelchau, Long Xiao, Annemarie E. Pickersgill, Michael T. Whalen, Philippe Claeys, Kazuhisa Goto, Naotaka Tomioka, Ulrich Riller, Timothy J. Bralower, Chris Nixon, Christopher M. Lowery, S. Green, Elise Chenot, Jan Smit, Sonia M. Tikoo, Douglas R. Schmitt, Ligia Pérez-Cruz, E. Le Ber, Joanna Morgan, Sean P. S. Gulick, Charles S. Cockell, Gail L. Christeson, Catalina Gebhardt, Institute for Geophysics, University of Texas at Austin [Austin], Department of Geological Sciences, Department of Earth Science and Engineering, Imperial College London, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research ( AWI ), Lunar and Planetary Institute [Houston] ( LPI ), Department of Geology, University of Leicester, Géosciences Montpellier, Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Montpellier ( UM ) -Université des Antilles ( UA ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Physics, University of Alberta [Edmonton], University of Freiburg [Freiburg], Institut für Geologie, Universität Hamburg ( UHH ), Eyring Materials Center, Arizona State University [Tempe] ( ASU ), Department of Geosciences, PennState University [Pennsylvania] ( PSU ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Analytical, Environmental and Geo-Chemistry, Vrije Universiteit [Brussel] ( VUB ), School of Physics and Astronomy, University of Edinburgh, WA-Organic and Isotope Geochemistry Centre ( WA-OIGC ), Curtin University [Perth], Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), Natural History Museum [Vienna] ( NHM ), British Geological Survey [Edinburgh], International Research Institute of Disaster Science, Tohoku University [Sendai], United Kingdom Hydrographic Office, Institut de chimie et procédés pour l'énergie, l'environnement et la santé ( ICPEES ), Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ) -Matériaux et nanosciences d'Alsace, Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Instituto de Geofísica, Universidad Nacional Autónoma de México ( UNAM ), School of Geographical and Earth Sciences, University of Glasgow, Argon Isotope Facility, NERC/SUERC, Department of Geology and Geophysics, University of Utah, Japan Agency for Marine-Earth Science and Technology ( JAMSTEC ), Faculty of Earth and Life Sciences ( FALW ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Earth and Planetary Sciences, Rutgers, The State University of New Jersey [New Brunswick] ( RUTGERS ), Kochi Institute for Core Sample Research, University of Alaska Fairbanks ( UAF ), School of Earth Sciences, China University of Geosciences-Planetary Science Institute, Department of Chemistry, NASA Astrobiology Institute ( NAI ), Funding from the In-ternational Ocean Discovery Program (IODP) and the International Continental scientific Drilling Project (ICDP)., Analytical, Environmental & Geo-Chemistry, Chemistry, Earth System Sciences, Institute of Geophysics [Austin] (IG), Department of Geological Sciences [Austin], Jackson School of Geosciences (JSG), University of Texas at Austin [Austin]-University of Texas at Austin [Austin], Department of Earth Science and Engineering [Imperial College London], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Lunar and Planetary Institute [Houston] (LPI), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), University of Alberta, Universität Hamburg (UHH), Arizona State University [Tempe] (ASU), Pennsylvania State University (Penn State), Penn State System-Penn State System, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Analytical, Environmental and Geo- Chemistry, Vrije Universiteit Brussel (VUB), SUPA School of Physics and Astronomy [Edinburgh], WA-Organic and Isotope Geochemistry Centre (WA-OIGC), The Institute for Geoscience Research [Perth] (TIGeR), School of Earth and Planetary Science [Perth - Curtin university], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC)-Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC)-School of Earth and Planetary Science [Perth - Curtin university], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Natural History Museum [Vienna] (NHM), British Geological Survey (BGS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México (UNAM), NERC Argon Isotope Facility [Glasgow], Scottish Universities Environmental Research Centre (SUERC), University of Glasgow-University of Edinburgh-University of Glasgow-University of Edinburgh-Natural Environment Research Council (NERC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Earth and Planetary Sciences [Piscataway], Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), University of Alaska [Fairbanks] (UAF), School of Earth Sciences [Wuham], China University of Geosciences [Wuhan] (CUG), NASA Astrobiology Institute (NAI), and Geology and Geochemistry

Subjects
Geochemistry & Geophysics, 010504 meteorology & atmospheric sciences, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Lithology, 04 Earth Sciences, Borehole, Stratigraphic unit, 010502 geochemistry & geophysics, [ SDU.STU.ST ] Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, 01 natural sciences, physical properties, [ SDU.STU.GP ] Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Impact crater, Geochemistry and Petrology, Breccia, Earth and Planetary Sciences (miscellaneous), SDG 14 - Life Below Water, Petrology, Porosity, 0105 earth and related environmental sciences, Chicxulub peak ring physical properties impact crater, 02 Physical Sciences, Scientific drilling, impact crater, peak ring, Geophysics, Chicxulub, Space and Planetary Science, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Sedimentary rock, Geology
Abstract

Joint International Ocean Discovery Program and International Continental Scientific Drilling Program Expedition 364 drilled into the peak ring of the Chicxulub impact crater. We present P-wave velocity, density, and porosity measurements from Hole M0077A that reveal unusual physical properties of the peak-ring rocks. Across the boundary between post-impact sedimentary rock and suevite (impact melt-bearing breccia) we measure a sharp decrease in velocity and density, and an increase in porosity. Velocity, density, and porosity values for the suevite are 2900–3700 m/s, 2.06–2.37 g/cm3, and 20–35%, respectively. The thin (25 m) impact melt rock unit below the suevite has velocity measurements of 3650–4350 m/s, density measurements of 2.26–2.37 g/cm3, and porosity measurements of 19–22%. We associate the low velocity, low density, and high porosity of suevite and impact melt rock with rapid emplacement, hydrothermal alteration products, and observations of pore space, vugs, and vesicles. The uplifted granitic peak ring materials have values of 4000–4200 m/s, 2.39–2.44 g/cm3, and 8–13% for velocity, density, and porosity, respectively; these values differ significantly from typical unaltered granite which has higher velocity and density, and lower porosity. The majority of Hole M0077A peak-ring velocity, density, and porosity measurements indicate considerable rock damage, and are consistent with numerical model predictions for peak-ring formation where the lithologies present within the peak ring represent some of the most shocked and damaged rocks in an impact basin. We integrate our results with previous seismic datasets to map the suevite near the borehole. We map suevite below the Paleogene sedimentary rock in the annular trough, on the peak ring, and in the central basin, implying that, post impact, suevite covered the entire floor of the impact basin. Suevite thickness is 100–165 m on the top of the peak ring but 200 m in the central basin, suggesting that suevite flowed downslope from the collapsing central uplift during and after peak-ring formation, accumulating preferentially within the central basin.

Published
2018

16. Dietcoin: court-circuiter la vérification dans Bitcoin pour les téléphones mobiles

Author

Frey, Davide, Makkes, Marc, Roman, Pierre-Louis, Taïani, François, Voulgaris, Spyros, the World Is Distributed Exploring the tension between scale and coordination ( WIDE ), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -SYSTÈMES LARGE ÉCHELLE ( IRISA_D1 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Athens University of Economics and Business ( AUEB ), Region of Brittany, France, Doctoral school of the University of Brittany Loire (UBL), France, SIDN Fonds contract 172027, The Netherlands, Univ Rennes, Inria, CNRS, IRISA, France, Vrije Universiteit Amsterdam, The Netherlands, Athens University of Economics and Business, Greece, ANR-13-INFR-0003,SocioPlug,Cloud social sur des réseaux de plugs, pour un accès à l'information symétrique et respectueux de la vie privée ( 2013 ), the World Is Distributed Exploring the tension between scale and coordination (WIDE), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SYSTÈMES LARGE ÉCHELLE (IRISA-D1), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Vrije Universiteit Amsterdam [Amsterdam] (VU), Athens University of Economics and Business (AUEB), ANR-13-INFR-0003,SocioPlug,Cloud social sur des réseaux de plugs, pour un accès à l'information symétrique et respectueux de la vie privée(2013), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)

Subjects
blockchain, distributed ledger, mobile computing, UTXO, [ INFO.INFO-CR ] Computer Science [cs]/Cryptography and Security [cs.CR], informatique mobile, partitionnement, monnaie cryptographique, cryptocurrency, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], [INFO.INFO-MC]Computer Science [cs]/Mobile Computing, [ INFO.INFO-DC ] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [ INFO.INFO-MC ] Computer Science [cs]/Mobile Computing, sharding, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], registre distribué
Abstract

Blockchains have a storage scalability issue. Their size is not bounded and they grow indefinitely as time passes. As of August 2017, the Bitcoin blockchain is about 120 GiB big while it was only 75 GiB in August 2016. To benefit from Bitcoin full security model, a bootstrapping node has to download and verify the entirety of the 120 GiB. This poses a challenge for low-resource devices such as smartphones. Thankfully, an alternative exists for such devices which consists of downloading and verifying just the header of each block. This partial block verification enables devices to reduce their bandwidth requirements from 120 GiB to 35 MiB.However, this drastic decrease comes with a safety cost implied by a partial block verification. In this work, we enable low-resource devices to fully verify subchains of blocks without having to pay the onerous price of a full chain download and verification; a few additional MiB of bandwidth suffice. To do so, we propose the design of diet nodes that can securely query full nodes for shards of the UTXO set, which is needed to perform full block verification and can otherwise only be built by sequentially parsing the chain.; Les blockchains telles que Bitcoin passent mal à l’échelle, notamment du fait de leurs besoins important de stockage. Les besoins de stockage d’une blockchain typique ne sont pas limités et croissent indéfiniment. Par exemple, en août 2017, les données contenues dans la blockchainBitcoin représentaient environ 120 GiB, contre 75 GiB un an auparavant, en août 2016. Pour bénéficier des garanties complètes de sécurité apportées par Bitcoin, un noeud qui rejoint le réseau doit télécharger et vérifier l’intégralité des 120 GiB de données. Cette nécessité pose un défi pour les appareils à faibles ressources tels que les smartphones. Heureusement, une alternative existe pour de tels dispositifs qui consiste à télécharger et à vérifier seulement l’en-tête de chaque bloc de la blockchain. Cette vérification partielle des blocs permet aux appareils de réduire leurs besoins en bande passante de 120 GiB à 35 MiB, mais cette diminution drastique ne permet qu’une vérification partielle des blocs, et diminue grandement les garanties de sécurité offertes aux noeuds qui l’utilisent.Dans ce travail, nous proposons une approche qui permet aux appareils à faibles ressources de vérifier entièrement des sous-chaînes de blocs sans avoir à payer le prix onéreux d’un téléchargement et d’une vérification complète de la chaîne ; quelques MiB supplémentaires de bande passante suffisent. Pour ce faire, nous proposons d’introduire des noeuds Dietcoin qui sont capables en toute sécurité d’interroger des noeuds exécutant le protocole complet pour obtenir des fragments d’un ensemble appelé UTXO, nécessaire à la vérification complète des blocs.

Published
2018

17. Vertical distribution and diurnal migration of atlantid heteropods

Author

Christopher W. Smart, Hilary J. Sloane, Melanie J. Leng, Brett Metcalfe, P. N. Vinayachandran, Gerald Ganssen, Deborah Wall-Palmer, Earth and Climate, School of Geography, Earth and Environmental Sciences [Plymouth] (SoGEES), Plymouth University, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cluster Earth and Climate [Amsterdam], Department of Earth Sciences [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Nottingham, UK (UON), British Geological Survey [Keyworth], British Geological Survey (BGS), Centre for Atmospheric and Oceanic Sciences [Bangalore] (CAOS), Indian Institute of Science [Bangalore] (IISc Bangalore), European Project: 746186,H2020-MSCA-IF-2016,POSEIDoN(2017), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), VU University Amsterdam-VU University Amsterdam, and Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)-Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Climate change, Aquatic Science, engineering.material, 01 natural sciences, Isotopes of oxygen, Calcification, Diurnal cycle, 14. Life underwater, SDG 14 - Life Below Water, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Atlantidae, Gastropod, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Deep chlorophyll maximum, Ecology, biology, 010604 marine biology & hydrobiology, Aragonite, Ocean acidification, Vertical distribution, biology.organism_classification, Waves and shallow water, Oceanography, 13. Climate action, Diurnal migration, Oxygen isotopes, engineering, Environmental science
Abstract

Understanding the vertical distribution and migratory behaviour of shelled holoplanktonic gastropods is essential in determining the environmental conditions to which they are exposed. This is increasingly important in understanding the effects of ocean acidification and climate change. Here we investigated the vertical distribution of atlantid heteropods by collating data from publications and collections and using the oxygen isotope (?18O) composition of single aragonitic shells. Data from publications and collections show 2 patterns of migration behaviour: small species that reside in shallow water at all times, and larger species that make diurnal migrations from the surface at night to deep waters during the daytime. The ?18O data show that all species analysed (n = 16) calcify their shells close to the deep chlorophyll maximum. This was within the upper 110 m of the ocean for 15 species, and down to 146 m for a single species. These findings confirm that many atlantid species are exposed to large environmental variations over a diurnal cycle and may already be well adapted to face ocean changes. However, all species analysed rely on aragonite supersaturated waters in the upper 2.

Published
2018

18. Mechanosensitiviy of aged muscle stem cells

Author

Heleen E, Boers, Mohammad, Haroon, Fabien, Le Grand, Astrid D, Bakker, Jenneke, Klein-Nulend, Richard T, Jaspers, Laboratory for Myology [Amsterdam, The Netherlands] (Amsterdam Movement Sciences), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Faculty of Behavioural and Movement Sciences [Amsterdam, The Netherlands], Centre de recherche en myologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Oral Cell Biology [Amsterdam, The Netherlands] (Amsterdam Movement Sciences), Vrije Universiteit Amsterdam [Amsterdam] (VU)-University of Amsterdam [Amsterdam] (UvA)-Academic Centre for Dentistry Amsterdam [The Netherlands], HAL UPMC, Gestionnaire, Centre de recherche en Myologie – U974 SU-INSERM, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)

Subjects
muscle regeneration, [SDV]Life Sciences [q-bio], aging, mechanosensitivity, Mechanotransduction, Cellular, Weight-Bearing, [SDV] Life Sciences [q-bio], Adult Stem Cells, satellite cell, Animals, Humans, Muscle, Skeletal, Exercise, muscle stem cell, Perspectives, mechanotransduction
Abstract

During aging, skeletal muscle tissue progressively declines in mass, strength, and regenerative capacity. Decreased muscle stem cell (MuSC) number and impaired function might underlie the aging‐related muscle wasting and impaired regenerative capacity. As yet, the search for factors that regulate MuSC fate and function has revealed several biochemical factors within the MuSC niche that may be responsible for the decline in MuSC regenerative capacity. This decline cannot be explained by environmental factors solely, as the MuSC potential to regenerate muscle tissue is not reversed by changing the biochemical MuSC niche composition. Here we discuss the likeliness that during physical exercise, MuSCs within their niche are subjected to mechanical loads, in particular pressure and shear stress, as well as associated deformations. We postulate that these physical cues are involved in the activation and differentiation of MuSCs as these cells contain several transmembrane sensor proteins that have been shown to be mechanosensitive in other cell types, that is, endothelial cells and osteoprogenitors. We will specifically address age‐related changes in mechanosensing in MuSCs and their niche. Insight in the physical cues applied to the MuSCs in vivo, and how these cues affect MuSC fate and function, helps to develop new therapeutic interventions to counterbalance age‐related muscle loss. This requires an approach combining two‐ and three‐dimensional live cell imaging of MuSCs within contracting muscle tissue, mathematical finite element modeling, and cell biology. © 2017 The Authors. Journal of Orthopaedic Research® Published by Wiley Periodicals, Inc. on behalf of the Orthopaedic Research Society. J Orthop Res 36:632–641, 2018.

Published
2018

19. Is structural sensitivity a problem of oversimplified biological models? Insights from nested Dynamic Energy Budget models

Author

Clement Aldebert, Bob W. Kooi, Jean-Christophe Poggiale, David Nerini, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Universität Zürich [Zürich] ( UZH ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Theoretical Life Sciences, AIMMS, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Universität Zürich [Zürich] = University of Zurich (UZH), Vrije Universiteit Amsterdam [Amsterdam] (VU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Statistics and Probability, Scale (ratio), Model sensitivity, Computer science, Dynamic energy budget, Ecology (disciplines), Population Dynamics, Population, Models, Biological, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Functional response, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Bifurcations, 03 medical and health sciences, functional response, Animals, Statistical physics, Sensitivity (control systems), Logistic function, education, Ecosystem, SDG 15 - Life on Land, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, chemostat, General Immunology and Microbiology, Mathematical model, Applied Mathematics, Uncertainty, model sensitivity, General Medicine, Models, Theoretical, Metabolism, 030104 developmental biology, Chemostat, Research Design, Predatory Behavior, Modeling and Simulation, Social ecological model, General Agricultural and Biological Sciences, bifurcations, metabolism
Abstract

International audience; Many current issues in ecology require predictions made by mathematical models, which are built on somewhat arbitrary choices. Their consequences are quantified by sensitivity analysis to quantify how changes in model parameters propagate into an uncertainty in model predictions. An extension called structural sensitivity analysis deals with changes in the mathematical description of complex processes like predation. Such processes are described at the population scale by a specific mathematical function taken among similar ones, a choice that can strongly drive model predictions. However, it has only been studied in simple theoretical models. Here, we ask whether structural sensitivity is a problem of oversimplified models. We found in predator-prey models describing chemostat experiments that these models are less structurally sensitive to the choice of a specific functional response if they include mass balance resource dynamics and individual maintenance. Neglecting these processes in an ecological model (for instance by using the well-known logistic growth equation) is not only an inappropriate description of the ecological system, but also a source of more uncertain predictions.

Published
2018

20. Computational pan-genomics : Status, promises and challenges

Author

Lodewyk F. A. Wessels, Jan O. Korbel, Jasmijn A. Baaijens, Francesca Chiaromonte, Gunnar W. Klau, Kai Ye, Alexander Schönhuth, Francesca D. Ciccarelli, Tobias Marschall, Robin Cijvat, Matthias Schlesner, Adam M. Novak, Eleazar Eskin, Ashley D. Sanders, Sven Rahmann, Carl Shneider, Wigard P. Kloosterman, Knut Reinert, Eric-Wubbo Lameijer, Sandra Smit, Benedict Paten, Mohammed El-Kebir, Valentina Boeva, Evan E. Eichler, Cornelia M. van Duijn, Can Alkan, Jeroen de Ridder, Benjamin Langmead, Dick de Ridder, Jiayin Wang, David Porubsky, Fabio Vandin, Erwin Datema, Ben Raphael, Paul Kersey, Nadia Pisanti, Corinna Ernst, Klaasjan G. Ouwens, Y. Zhang, Thomas Abeel, Erik Garrison, Veli Mäkinen, Paul I.W. de Bakker, Victor Guryev, Siavash Sheikhizadeh, Manja Marz, Marcel Martin, Ole Schulz-Trieglaff, Pieter B. Neerincx, Rayan Chikhi, Eric Rivals, John C. Mu, Raoul J. P. Bonnal, Bas E. Dutilh, Paul Medvedev, Louis Dijkstra, Pierre Peterlongo, Ali Ghaffaari, Daniel Valenzuela, Epidemiology, Gastroenterology & Hepatology, Erasmus MC other, Alkan, Can, Saarland University [Saarbrücken], Max Planck Institute for Informatics [Saarbrücken], Karlsruhe Institute of Technology (KIT), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Delft Bioinformatics Lab [Delft], Delft University of Technology (TU Delft), Computational Science Lab [Amsterdam], University of Amsterdam [Amsterdam] (UvA), Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Universidade Federal do Rio de Janeiro (UFRJ), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Section genetics [Utrecht], Center for Molecular medicine [Utrecht], University Medical Center [Utrecht]-University Medical Center [Utrecht], Helsinki Institute for Information Technology, Department of Computer Science [Helsinki], Falculty of Science [Helsinki], University of Helsinki-University of Helsinki, Howard Hughes Medical Institute [Santa Cruz] (HHMI), Center for Biomolecular Science & Engineering, European Research Institute for the Biology of Ageing [Groningen] (ERIBA), University Medical Center Groningen [Groningen] (UMCG), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), 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), Department of Computer Engineering (Bilkent-CS), Bilkent, Life Sciences [Amsterdam] (MAC4), Centrum Wiskunde & Informatica (CWI), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL), Centre de Bioinformatique (CBIO), MINES ParisTech - École nationale supérieure des mines de Paris-PSL Research University (PSL), Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Integrative Biology Program [Milano], Istituto Nazionale Genetica Molecolare [Milano] (INGM), Department of Statistics [Pennsylvania], Pennsylvania State University (Penn State), Penn State System-Penn State System, Bioinformatics and Sequence Analysis (BONSAI), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 (CRIStAL), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Monet DB Solutions [Amsterdam], KeyGene [Wageningen], Department of Epidemiology [Rotterdam], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Howard Hughes Medical Institute [Berkeley], University of California [Berkeley], University of California-University of California, Genome Informatics [Duisburg], Universität Duisburg-Essen [Essen], Departement of human genetics [Los Angeles], Computer Science Department [Los Angeles] (UCLA), University of California [Los Angeles] (UCLA), University of California-University of California-University of California [Los Angeles] (UCLA), The Wellcome Trust Sanger Institute [Cambridge], Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universiteit Leiden [Leiden], Department of Computer Science [Baltimore], Johns Hopkins University (JHU), Centre de Physique des Particules de Marseille (CPPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Aix Marseille Université (AMU), University of Pennsylvania [Philadelphia], China Agricultural University (CAU), University of Groningen [Groningen], Department of Biological Psychology [Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Dipartimento di Informatica [Pisa] (DI), University of Pisa - Università di Pisa, Faculty of Computer Science [Dortmund], Technische Universität Dortmund [Dortmund] (TU), Service de Pneumologie A [Paris], AP-HP - Hôpital Bichat - Claude Bernard [Paris], Department of Mathematics and Computer Science (Freie Universität Berlin), Freie Universität Berlin, Wageningen University and Research Centre [Wageningen] (WUR), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Division of Theoretical Bioinformatics [Heidelberg], German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Illumina Cambridge, Illumina, Terry Fox Laboratory, BC Cancer Agency (BCCRC)-British Columbia Cancer Agency Research Centre, Bioinformatics Group [Wageningen], Leiden Observatory [Leiden], Regeneron Pharmaceuticals [Tarrytown], Shaanxi University of Science and Technology, Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, Universita degli Studi di Padova, The Netherlands Organization for Scientific Research (NWO) Vidi (639.072.309 to A.S., 864.14.004 to B.E.D.), CAPES/BRASIL (to B.E.D.), the Academy of Finland (284598 [CoECGR] to V.M. and D.V.), the Russian Scientific Foundation (14–11–00826 to L.D.), Institut de Biologie Computationnelle (ANR-11-BINF- 0002 to E.R.), and the French Colib’read project (ANR–12– BS02–0008 to E.R.). NSFC 31671372 (to K. Y.), the Dutch Graduate School for Experimental Plant Sciences (054EPS15 to S.S.), the EMGO Institute for Health and Care Research (EMGO+) to K.O., the National Human Genome Research Institute (1U54HG007990 [BD2K] to B.P. and A.M.N., 5U41HG007234 [GENCODE] to B.P.), the W. M. Keck Foundation (DT06172015 to B.P. and A.M.N.), the Simons Foundation (SFLIFE# 351901 to B.P. and A.M.N.), the ARCS Foundation (2014–15 ARCS fellowship to A.M.N.), Edward Schulak (Edward Schulak Fellowship in Genomics to A.M.N.), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-12-BS02-0008,Colib'read,Méthodes d'extraction d'information biologique dans les données HTS non assemblées(2012), Karlsruhe Institute of Technology ( KIT ), Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Harvard Medical School [Boston] ( HMS ) -Massachusetts General Hospital [Boston] ( MGH ) -Massachusetts Institute of Technology ( MIT ), Delft University of Technology ( TU Delft ), University of Amsterdam [Amsterdam] ( UvA ), Universidade Federal do Rio de Janeiro ( UFRJ ), European Bioinformatics Institute [Hinxton] ( EMBL-EBI ), European Molecular Biology Laboratory [Hinxton], Department of Computer Science, Howard Hughes Medical Institute [Santa Cruz] ( HHMI ), European Research Institute for the Biology of Ageing [Groningen] ( ERIBA ), University Medical Center Groningen [Groningen] ( UMCG ), Institut de Biologie Computationnelle ( IBC ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Méthodes et Algorithmes pour la Bioinformatique ( MAB ), 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 ), Department of Computer Engineering ( Bilkent-CS ), Life Sciences [Amsterdam] ( MAC4 ), Centrum Wiskunde & Informatica ( CWI ), Institut Cochin ( UM3 (UMR 8104 / U1016) ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), PSL Research University ( PSL ), Centre de Bioinformatique ( CBIO ), MINES ParisTech - École nationale supérieure des mines de Paris-PSL Research University ( PSL ), MINES ParisTech - École nationale supérieure des mines de Paris-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -INSTITUT CURIE, Istituto Nazionale Genetica Molecolare [Milano] ( INGM ), PennState University [Pennsylvania] ( PSU ), Bioinformatics and Sequence Analysis ( BONSAI ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 ( CRIStAL ), Ecole Centrale de Lille-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut Mines-Télécom [Paris]-Université de Lille-Centre National de la Recherche Scientifique ( CNRS ) -Ecole Centrale de Lille-Institut Mines-Télécom [Paris]-Université de Lille-Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Erasmus University Medical Center [Rotterdam], Computer Science Department [Los Angeles] ( UCLA ), University of California at Los Angeles [Los Angeles] ( UCLA ) -University of California at Los Angeles [Los Angeles] ( UCLA ), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale ( ERABLE ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ), Johns Hopkins University ( JHU ), Centre de Physique des Particules de Marseille ( CPPM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Aix Marseille Université ( AMU ), China Agricultural University ( CAU ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA_D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Université de Bretagne Sud ( UBS ) -École normale supérieure - Rennes ( ENS Rennes ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -IMT Atlantique Bretagne-Pays de la Loire ( IMT Atlantique ), Dipartimento di Informatica [Pisa] ( DI ), University of Pisa [Pisa], Technische Universität Dortmund [Dortmund] ( TU ), Department of Mathematics and Computer Science ( Freie Universität Berlin ), Freie Universität Berlin [Berlin], Wageningen University and Research Centre [Wageningen] ( WUR ), K.U.Leuven, German Cancer Research Center [Heidelberg] ( DKFZ ), Helmholtz-Gemeinschaft-Helmholtz-Gemeinschaft, BC Cancer Agency ( BCCRC ) -British Columbia Cancer Agency Research Centre, Netherlands Cancer Institute ( NKI ), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier ( 2011 ), ANR-12-BS02-0008,Colib'read,Méthodes d'extraction d'information biologique dans les données HTS non assemblées ( 2012 ), Helsinki Institute for Information Technology (HIIT), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Aalto University, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Bilkent University [Ankara], Université Paris sciences et lettres (PSL), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Statistics [PennState], Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], Howard Hughes Medical Institute (HHMI), Universität Duisburg-Essen = University of Duisburg-Essen [Essen], University of California (UC)-University of California (UC)-University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Universiteit Leiden, Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Mathematics and Computer Science, Wageningen University and Research [Wageningen] (WUR), Università degli Studi di Padova = University of Padua (Unipd), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), Aalto University-University of Helsinki, University of California [Santa Cruz] (UCSC), University of California, Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), MINES ParisTech - École nationale supérieure des mines de Paris, Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Université de Lille-Centrale Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centrale Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Groningen Research Institute for Asthma and COPD (GRIAC)

Subjects
0301 basic medicine, Data structures, Computer science, Medizin, 02 engineering and technology, computer.software_genre, Genome, Computational and Statistical Genetics, data structures, haplotypes, pan-genome, read mapping, sequence graph, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], 0303 health sciences, education.field_of_study, Point (typography), Genomics, Papers, Data mining, Sequence graph, Computational problem, Construct (philosophy), Algorithms, Human, Information Systems, Bioinformatics, 0206 medical engineering, Population, Pan-genome, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Bioinformatica, Humans, Haplotypes, Read mapping, Computational Biology, Genome, Human, Software, Molecular Biology, education, Representation (mathematics), 030304 developmental biology, Computational genomics, Data structure, Data science, Human genetics, 030104 developmental biology, Paradigm shift, ddc:004, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], EPS, computer, 020602 bioinformatics
Abstract

Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case ofHomo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension ofcomputational pan-genomics, a new sub-area of research in computational biology. In this paper, we generalize existing definitions and understand apan-genomeas any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies, and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.

Published
2018

21. Theoretical study of the I++ I- mutual neutralization reaction

Author

Badin, Sylvain, Yuan, Xiang, Bourgeois, Pierre-Louis, Gomes, Andre Severo Pereira, Sisourat, Nicolas, Theoretical Chemistry, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Chemistry and Amsterdam Centre for Multiscale Modeling (ACMM) VU University Amsterdam (ACMM), Vrije Universiteit Amsterdam [Amsterdam] (VU), French national supercomputing facilities (Grants No. DARI A0090801859 and No. A0110801859), ANR-19-CE29-0019,CompRIXS,Calcul de la diffusion inélastique résonante de rayons X pour toute la classification périodique(2019), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), and ANR-16-IDEX-0004,ULNE,ULNE(2016)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Atomic Physics (physics.atom-ph), FOS: Physical sciences, SDG 7 - Affordable and Clean Energy, Physics - Atomic Physics
Abstract

International audience; We have computed the cross sections of the mutual neutralization reaction between I+ and I- for a collision energy varying from 0.001 eV to 50 eV. These cross sections were obtained using the adiabatic potential energy curves of the I2 system computed with a direct relativistic Multi-Reference Configuration Interaction method and a semi-classical approach (i.e. Landau Zener Surface Hopping). We report the cross sections towards the following neutral sates : I(2P3/2)+I(2P3/2), I(2P3/2) + I(2P1/2), I(2P1/2) + I(2P1/2) and I(5p46s) + I(2P3/2). We also discuss the cross sections towards the two following excited ionic states : I- (1S0) + I+ (3P0) and I- (1S0) + I+ (3D2). The results of these calculations are in accordance with recent experimental measurements conducted in the double ion ring DESIREE in Stockholm. These results can be used to model iodine plasma kinetics and thus to improve our understanding of the latter.

Published
2023

22. Simulations of the Holocene climate in Europe using an interactive downscaling within the iLOVECLIM model (version 1.1)

Author

Frank Arthur, Didier M. Roche, Ralph Fyfe, Aurélien Quiquet, Hans Renssen, Earth Sciences, University of South-Eastern Norway (USN), Vrije Universiteit Amsterdam [Amsterdam] (VU), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), School of Geography, Earth and Environmental Sciences [Plymouth] (SoGEES), and Plymouth University

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, Stratigraphy, SDG 13 - Climate Action, Paleontology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment
Abstract

This study presents the application of an interactive downscaling in Europe using iLOVECLIM (a model of intermediate complexity), increasing its atmospheric resolution from 5.56 to 0.25∘ kilometric. A transient simulation using the appropriate climate forcings for the entire Holocene (11.5–0 ka BP) was done for both the standard version of the model and with an interactive downscaling applied. Our results show that simulations from downscaling present spatial variability that agrees better with proxy-based reconstructions and other climate models as compared to the standard model. The downscaling scheme simulates much higher (by at least a factor of 2) precipitation maxima and provides detailed information in mountainous regions. We focus on examples from the Scandes mountains, the Alps, the Scottish Highlands, and the Mediterranean. The higher spatial resolution of the downscaling provides a more realistic overview of the topography and gives local climate information, such as precipitation and temperature gradient, that is important for paleoclimate studies. With downscaling, we simulate similar trends and spatial patterns of the precipitation changes reconstructed by other proxy studies (for example in the Alps) as compared to the standard version. Our downscaling tool is numerically cheap, implying that our model can perform kilometric, multi-millennial simulations and is suitable for future studies.

Published
2023

23. Many parasitoids lack adult fat accumulation, despite fatty acid synthesis

Author

Bertanne Visser, Cécile Le Lann, Daniel A. Hahn, Mark Lammers, Caroline M. Nieberding, Hans T. Alborn, Thomas Enriquez, Mathilde Scheifler, Jeffrey A. Harvey, Jacintha Ellers, Université de Liège, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville] (UF), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Université Catholique de Louvain = Catholic University of Louvain (UCL), United States Department of Agriculture (USDA), Netherlands Institute of Ecology (NIOO-KNAW), Vrije Universiteit Amsterdam [Amsterdam] (VU), and BV and MS were funded by the Fonds National de Recherche Scientifique. TE was funded by the Fondation Fyssen and the University of Liège. DAH was funded by US National Science Foundation grant 1639005.

Subjects
Nutrient metabolism, Parasitic wasp, Insect Science, Lipogenesis, Life histories, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Hymenoptera, Lipids, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Fat reserves, specifically the accumulation of triacylglycerols, are a major energy source and play a key role for life histories. Fat accumulation is a conserved metabolic pattern across most insects, yet in most parasitoid species adults do not gain fat mass, even when nutrients are readily available and provided ad libitum. This extraordinary physiological phenotype has evolved repeatedly in phylogenetically dispersed parasitoid species. This poses a conundrum because it could lead to significant constraints on energy allocation toward key adult functions such as survival and reproduction. Recent work on the underlying genetic and biochemical mechanisms has spurred a debate on fat accumulation versus fat production, because of incongruent interpretation of results obtained using different methodologies. This debate is in part due to semantics, highlighting the need for a synthetic perspective on fat accumulation that reconciles previous debates and provides new insights and terminology. In this paper, we propose updated, unambiguous terminology for future research in the field, including "fatty acid synthesis" and "lack of adult fat accumulation", and describe the distinct metabolic pathways involved in the complex process of lipogenesis. We then discuss the benefits and drawbacks of the main methods available to measure fatty acid synthesis and adult fat accumulation. Most importantly, gravimetric/colorimetric and isotope tracking methods give complementary information, provided that they are applied with appropriate controls and interpreted correctly. We also compiled a comprehensive list of fat accumulation studies performed during the last 25 years. We present avenues for future research that combine chemistry, ecology, and evolution into an integrative approach, which we think is needed to understand the dynamics of fat accumulation in parasitoids.

Published
2023

24. Randomness in Local Optima Network Sampling

Author

Thomson, Sarah, Veerapen, Nadarajen, Ochoa, Gabriela, van den Berg, Daan, University of Stirling, Operational Research, Knowledge And Data (ORKAD), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Amsterdam [Amsterdam] (VU), and ACM

Subjects
Quadratic Assignment Problem, Local Optima Networks, Iterated Local Search, [INFO]Computer Science [cs], Fitness Landscapes
Abstract

We consider statistical randomness in the construction of local optima networks (LONs) and conduct a preliminary and exploratory study into this. LONs capture a fitness landscape into network format: the nodes are local optima, and edges are heuristic search transitions between them. Problem instances from the benchmark quadratic assignment problem library are used in the analysis. LONs are constructed using an iterated local search (ILS) and several different random seeds. Metrics are computed from the networks and visualised to assess the effect of randomness. Algorithm performance models for ILS runtime are built using metrics of LONs constructed using different seeds and the results compared. The results show that some LON metrics seem consistent across seeds, while others vary substantially. Additionally, the quality of algorithm performance models using LON metrics as predictors can differ depending on randomness. Finally, LON metrics associated with separate seeds can lead to different algorithm configuration recommendations for the same instance.

Published
2023

25. Global Atmospheric δ13CH4 and CH4 Trends for 2000–2020 from the Atmospheric Transport Model TM5 Using CH4 from Carbon Tracker Europe–CH4 Inversions

Author

Mannisenaho, Vilma, Tsuruta, Aki, Backman, Leif, Houweling, Sander, Segers, Arjo, Krol, Maarten, Saunois, Marielle, Poulter, Benjamin, Zhang, Zhen, Lan, Xin, Dlugokencky, Edward, Michel, Sylvia, White, James, Aalto, Tuula, Finnish Meteorological Institute (FMI), SRON Netherlands Institute for Space Research (SRON), Vrije Universiteit Amsterdam [Amsterdam] (VU), The Netherlands Organisation for Applied Scientific Research (TNO), Wageningen University and Research [Wageningen] (WUR), Institute for Marine and Atmospheric Research [Utrecht] (IMAU), Utrecht University [Utrecht], Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation INVerse pour les mesures atmosphériques et SATellitaires (SATINV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), NASA Goddard Space Flight Center (GSFC), Earth Science System Interdisciplinary Center [College Park] (ESSIC), College of Computer, Mathematical, and Natural Sciences [College Park], University of Maryland [College Park], University of Maryland System-University of Maryland System-University of Maryland [College Park], University of Maryland System-University of Maryland System, ESRL Global Monitoring Laboratory [Boulder] (GML), NOAA Earth System Research Laboratory (ESRL), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), University of Colorado [Boulder], University of North Carolina [Chapel Hill] (UNC), and University of North Carolina System (UNC)

Subjects
S, A. Krol, M. Saunois, M, Poulter, M. Poulter, Backman, A, X. et al methane isotopes atmospheric modelling, Krol, Z, X, atmospheric modelling, isotopes, Segers, V, Saunois, Houweling, L, et al methane, V. Tsuruta, S. Segers, A. Backman, B, Zhang, Mannisenaho, Lan, [SDU]Sciences of the Universe [physics], Z. Lan, B. Zhang, Tsuruta, L. Houweling
Abstract

This study investigates atmospheric δ 13 CH 4 trends, as produced by a global atmospheric transport model using CH 4 inversions from CarbonTracker-Europe CH 4 for 2000-2020, and compares them to observations. The CH 4 inversions include the grouping of the emissions both by δ 13 CH 4 isotopic signatures and process type to investigate the effect, and to estimate the CH 4 magnitudes and model CH 4 and δ 13 CH 4 trends. In addition to inversion results, simulations of the global atmospheric transport model were performed with modified emissions. The estimated global CH 4 trends for oil and gas were found to increase more than coal compared to the priors from 2000-2006 to 2007-2020. Estimated trends for coal emissions at 30 • N-60 • N are less than 50% of those from priors. Estimated global CH 4 rice emissions trends are opposite to priors, with the largest contribution from the EQ to 60 • N. The results of this study indicate that optimizing wetland emissions separately produces better agreement with the observed δ 13 CH 4 trend than optimizing all biogenic emissions simultaneously. This study recommends optimizing separately biogenic emissions with similar isotopic signature to wetland emissions. In addition, this study suggests that fossil-based emissions were overestimated by 9% after 2012 and biogenic emissions are underestimated by 8% in the inversion using EDGAR v6.0 as priors.

Published
2023

26. Exploration of excited, electron attachment and detachment states of (ultra)heavy halogen species with relativistic 4-component EOM-CC methods

Author

Shee, Avijit, Saue, Trond, Visscher, Lucas, Severo Pereira Gomes, André, Physico-Chimie Moléculaire Théorique (PCMT), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Faculty of Sciences, Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

27. Supplementing Breakfast with a Vitamin D and Leucine-Enriched Whey Protein Medical Nutrition Drink Enhances Postprandial Muscle Protein Synthesis and Muscle Mass in Healthy Older Men

Author

Adeline Blot, Christophe Giraudet, N. Farigon, Audrey Chanet, Yves Boirie, Yvette Luiking, Sjors Verlaan, Corinne Pouyet, Jérôme Salles, Véronique Patrac, Noël Cano, Stéphane Walrand, Marion Jourdan, Véronique Pidou, Anke Bongers, Noureddine Hafnaoui, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Nutricia Research, Gerontology and Geriatrics, Vrije University Medical Center, Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), nutrition clinique, Centre Hospitalier Universitaire de Clermont-Ferrand, Nutricia Research, Nutricia Advanced Medical Nutrition, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), and CHU Clermont-Ferrand

Subjects
0301 basic medicine, Male, vitamine D, Medicine (miscellaneous), Muscle Proteins, chemistry.chemical_compound, Food science, Vitamin D, senior citizens, 2. Zero hunger, Nutrition and Dietetics, apport nutritionnel, Postprandial Period, 3. Good health, Postprandial, Before Breakfast, muscle mass, protéine, Vitamin, medicine.medical_specialty, masse musculaire, nutritional support, sarcopenia, personne âgée, Beverages, 03 medical and health sciences, Double-Blind Method, Leucine, Internal medicine, medicine, Vitamin D and neurology, Humans, Muscle, Skeletal, Aged, Breakfast, 030109 nutrition & dietetics, business.industry, medicine.disease, protein intake, Diet, Endocrinology, Whey Proteins, chemistry, Gene Expression Regulation, Sarcopenia, Lean body mass, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Cholecalciferol, protein, Energy Intake, Body mass index, muscle protein synthesis, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Analysis
Abstract

Background: A promising strategy to help older adults preserve or build muscle mass is to optimize muscle anabolism through providing an adequate amount of high-quality protein at each meal.Objective: This "proof of principle" study investigated the acute effect of supplementing breakfast with a vitamin D and leucine-enriched whey protein medical nutrition drink on postprandial muscle protein synthesis and longer-term effect on muscle mass in healthy older adults.Methods: A randomized, placebo-controlled, double-blind study was conducted in 24 healthy older men [mean ± SD: age 71 ± 4 y; body mass index (in kg/m2) 24.7 ± 2.8] between September 2012 and October 2013 at the Unit of Human Nutrition, University of Auvergne, Clermont-Ferrand, France. Participants received a medical nutrition drink [test group; 21 g leucine-enriched whey protein, 9 g carbohydrates, 3 g fat, 800 IU cholecalciferol (vitamin D3), and 628 kJ] or a noncaloric placebo (control group) before breakfast for 6 wk. Mixed muscle protein fractional synthesis rate (FSR) was measured at week 0 in the basal and postprandial state, after study product intake with a standardized breakfast with the use of l-[2H5]-phenylalanine tracer methodology. The longer-term effect of the medical nutrition drink was evaluated by measurement of appendicular lean mass, representing skeletal muscle mass at weeks 0 and 6, by dual-energy X-ray absorptiometry.Results: Postprandial FSR (0-240 min) was higher in the test group than in the control group [estimate of difference (ED): 0.022%/h; 95% CI: 0.010%/h, 0.035%/h; ANCOVA, P = 0.001]. The test group gained more appendicular lean mass than the control group after 6 wk (ED: 0.37 kg; 95% CI: 0.03, 0.72 kg; ANCOVA, P = 0.035), predominantly as leg lean mass (ED: 0.30 kg; 95% CI: 0.03, 0.57 kg; ANCOVA, P = 0.034).Conclusions: Supplementing breakfast with a vitamin D and leucine-enriched whey protein medical nutrition drink stimulated postprandial muscle protein synthesis and increased muscle mass after 6 wk of intervention in healthy older adults and may therefore be a way to support muscle preservation in older people. This trial was registered at www.trialregister.nl as NTR3471.

Published
2017

28. To boldly go where no one has gone before: integrating in site location analysis and predictive modelling, the hierarchical types map

Author

Nüsslein, Antonin, Nuninger, Laure, Verhagen, Philip, Archéologie et histoire ancienne : Méditerranée - Europe ( ARCHIMEDE ), Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Ministère de la Culture et de la Communication ( MCC ) -Institut national de recherches archéologiques préventives ( Inrap ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux ( MSHE ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Cultural Landscape and Urban Environment ( CLUE ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), CNRS - MENESR - Université de Strasbourg, Jeffrey Glover Georgia State University, Dept. Anthropolgy, IHAPMA Introducing the human factor in predictive modelling, Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux (UAR 3124) (MSHE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Cultural Landscape and Urban Environment (CLUE), Vrije Universiteit Amsterdam [Amsterdam] (VU), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), and Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux (MSHE)

Subjects
[SHS.STAT]Humanities and Social Sciences/Methods and statistics, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, socio-cultural factors, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, [ SHS ] Humanities and Social Sciences, site location analysis, predictive modelling, temporal factors, [ SHS.STAT ] Humanities and Social Sciences/Methods and statistics, [SHS]Humanities and Social Sciences, Roman period
Abstract

International audience; Over the years, predictive modelling has been characterized as being environmentally deterministic, a-temporal, or even as a way of ‘effectively de-humanising the past’. Over the past ten years, however, spatial analysis of settlement patterns has progressed substantially, paying much more attention to the role of socio-cultural factors and the analysis of settlement pattern dynamics. In this paper, we will present an approach to site location analysis and predictive modelling that can be characterized as essentially data driven, yet is very much theoretically informed, and which has focused primarily on facilitating comparisons between various chrono-cultural contexts. Our experiments, that have been carried out since 2010, have mainly used data from the Roman period in various regions of France, but the general ideas and workflow can easily be transferred to other settings. To enrich the approach new developments were tested to understand the role of settlement hierarchy and its influence on the subsequent development and structuring of settlement patterns. These new developments were applied to three case study carried out in the north-east of France.

Published
2017

29. Strain analysis in CRT candidates using the novel segment length in cine (SLICE) post-processing technique on standard CMR cine images

Author

Cornelis P. Allaart, Alwin Zweerink, Albert C. van Rossum, Robin Nijveldt, Mathias Meine, Pierre Croisille, Patrick Clarysse, Joost P.A. Kuijer, Aernout M. Beek, Peter M. van de Ven, Li Na Wu, ICaR-VU, VU University Medical Center [Amsterdam], Department of Physics and Medical Technology, Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Clinical Epidemiology and Biostatistics, Department of Cardiology, Utrecht University [Utrecht], RMN et optique : De la mesure au biomarqueur, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagerie et modélisation Vasculaires, Thoraciques et Cérébrales (MOTIVATE), Vrije Universiteit Medical Centre ( VUMC ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ) -Vrije Universiteit Amsterdam [Amsterdam] ( VU ), 5 - RMN et optique : De la mesure aux biomarqueurs, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé ( CREATIS ), Hospices Civils de Lyon ( HCL ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Hospices Civils de Lyon ( HCL ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), 1 - Imagerie et modélisation Vasculaires, Thoraciques et Cérébrales ( MOTIVATE ), Cardiology, ACS - Heart failure & arrhythmias, Amsterdam Neuroscience - Brain Imaging, Radiology and nuclear medicine, APH - Methodology, Epidemiology and Data Science, ACS - Atherosclerosis & ischemic syndromes, and ACS - Microcirculation

Subjects
Male, Intraclass correlation, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, medicine.medical_treatment, Vascular damage Radboud Institute for Health Sciences [Radboudumc 16], Bundle-Branch Block, Cardiac resynchronization therapy, Magnetic Resonance Imaging, Cine, Cardiac Resynchronization Therapy (CRT), Myocardial tagging (CMR-TAG), [ SPI.SIGNAL ] Engineering Sciences [physics]/Signal and Image processing, 030204 cardiovascular system & hematology, Ventricular Function, Left, 030218 nuclear medicine & medical imaging, Cardiac Resynchronization Therapy, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Radiology, Nuclear Medicine and imaging, Segment length in cine (SLICE) technique, cardiovascular diseases, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, Aged, Reproducibility, Strain (chemistry), Myocardial strain analysis, Left bundle branch block, business.industry, Patient Selection, Ultrasound, Segment length, Reproducibility of Results, General Medicine, Gold standard (test), Middle Aged, medicine.disease, Prognosis, Myocardial Contraction, cardiovascular system, Female, business, Nuclear medicine, Cardiac, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Biomarkers, circulatory and respiratory physiology, Cardiovascular magnetic resonance (CMR)
Abstract

Objectives Although myocardial strain analysis is a potential tool to improve patient selection for cardiac resynchronization therapy (CRT), there is currently no validated clinical approach to derive segmental strains. We evaluated the novel segment length in cine (SLICE) technique to derive segmental strains from standard cardiovascular MR (CMR) cine images in CRT candidates. Methods Twenty-seven patients with left bundle branch block underwent CMR examination including cine imaging and myocardial tagging (CMR-TAG). SLICE was performed by measuring segment length between anatomical landmarks throughout all phases on short-axis cines. This measure of frame-to-frame segment length change was compared to CMR-TAG circumferential strain measurements. Subsequently, conventional markers of CRT response were calculated. Results Segmental strains showed good to excellent agreement between SLICE and CMR-TAG (septum strain, intraclass correlation coefficient (ICC) 0.76; lateral wall strain, ICC 0.66). Conventional markers of CRT response also showed close agreement between both methods (ICC 0.61–0.78). Reproducibility of SLICE was excellent for intra-observer testing (all ICC ≥0.76) and good for interobserver testing (all ICC ≥0.61). Conclusions The novel SLICE post-processing technique on standard CMR cine images offers both accurate and robust segmental strain measures compared to the ‘gold standard’ CMR-TAG technique, and has the advantage of being widely available. Key Points • Myocardial strain analysis could potentially improve patient selection for CRT. • Currently a well validated clinical approach to derive segmental strains is lacking. • The novel SLICE technique derives segmental strains from standard CMR cine images. • SLICE-derived strain markers of CRT response showed close agreement with CMR-TAG. • Future studies will focus on the prognostic value of SLICE in CRT candidates. Electronic supplementary material The online version of this article (doi:10.1007/s00330-017-4890-0) contains supplementary material, which is available to authorized users.

Published
2017

30. Sustainable computational science: the ReScience initiative

Author

Rougier, Nicolas P, Hinsen, Konrad, Alexandre, Frederic, Arildsen, Thomas, Barba, Lorena A, Benureau, Fabien C.Y, Brown, C. Titus, deBuy, Pierre, Caglayan, Ozan, Davison, Andrew P., Delsuc, Marc-Andre, Detorakis, Georgios, Diem, Alexandra, Drix, Damien, Enel, Pierre, Girard, Benoit, Guest, Olivia, Hall, Matt G, Henriques, Rafael N, Hinaut, Xavier, Jaron, Kamil S, Khamassi, Mehdi, Klein, Almar, Manninen, Tiina, Marchesi, Pietro, McGlinn, Daniel, Metzner, Christoph, Petchey, Owen, Plesser, Hans Ekkehard, Poisot, Timothee, Ram, Karthik, Ram, Yoav, Roesch, Etienne, Rossant, Cyrille, Rostami, Vahid, Shifman, Aaron, Stachelek, Joseph, Stimberg, Marcel, Stollmeier, Frank, Vaggi, Federico, Viejo, Guillaume, Vitay, Julien, Vostinar, Anya E, Yurchak, Roman, Zito, Tiziano, Mnemonic Synergy ( Mnemosyne ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut des Maladies Neurodégénératives [Bordeaux] ( IMN ), Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de biophysique moléculaire ( CBM ), Université d'Orléans ( UO ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Electronic Systems - Aalborg University, Aalborg University [Denmark] ( AAU ), Washington State University ( WSU ), CIM - Communication, Information, Médias - EA 1484 ( CIM ), Université Sorbonne Nouvelle - Paris 3, Université Libre de Bruxelles [Bruxelles] ( ULB ), Laboratoire d'Informatique de l'Université du Mans ( LIUM ), Le Mans Université ( UM ), Ecole des Neurosciences de Paris Île de France ( ENP ), Ecole des Neurosciences de Paris, Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des signaux et systèmes ( L2S ), Université Paris-Sud - Paris 11 ( UP11 ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), University of Southampton [Southampton], Humboldt Universität zu Berlin, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute ( SBRI ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Physiologie de la Perception et de l'Action ( LPPA ), Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des Systèmes Intelligents et de Robotique ( ISIR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), University of Oxford [Oxford], University College of London [London] ( UCL ), Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Knowledge Technology group [Hamburg] ( KT ), Department of Informatics [Hamburg], Universität Hamburg ( UHH ) -Universität Hamburg ( UHH ), Université de Lausanne ( UNIL ), National Coalition of Independent Scholar ( NCIS ), Finnish Meteorological Institute ( FMI ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Department of Biology [Charleston], College of Charleston, Universität Zürich [Zürich] ( UZH ), University of Zürich [Zürich] ( UZH ), Institute of Neuroscience and Medicine [Jülich] ( INM-1 ), Université de Montréal, University of California [Berkeley], Department of Biological Sciences [Stanford], Stanford University [Stanford], Department of Psychology, University of Geneva [Switzerland], Swiss Center for Affective Sciences, University of Ottawa [Ottawa], Michigan State University [East Lansing], Institut de la Vision, 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 ), Institut d'études de la cognition ( IEC ), Département d'Etudes Cognitives - ENS Paris ( DEC ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ), Max Planck Institute of Experimental Medicine [Göttingen] ( MPI ), Statistical Machine Learning and Parsimony ( SIERRA ), Département d'informatique de l'École normale supérieure ( DI-ENS ), École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria de Paris, Institut National de Recherche en Informatique et en Automatique ( Inria ), Chemnitz University of Technology, Grinnell College, Laboratoire pour l'utilisation des lasers intenses ( LULI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -École polytechnique ( X ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Eberhard Karls Universität Tübingen, Mnemonic Synergy (Mnemosyne), Laboratoire Bordelais de Recherche en Informatique (LaBRI), 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, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aalborg University [Denmark] (AAU), Washington State University (WSU), University of California [Davis] (UC Davis), University of California (UC), Université libre de Bruxelles (ULB), Laboratoire d'Informatique de l'Université du Mans (LIUM), Le Mans Université (UM), Ecole des Neurosciences de Paris Île de France (ENP), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des signaux et systèmes (L2S), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), University of Southampton, Humboldt University Of Berlin, Institut cellule souche et cerveau (SBRI), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Physiologie de la Perception et de l'Action (LPPA), Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Intelligents et de Robotique (ISIR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), AMAC, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, University College of London [London] (UCL), Instituto de Medicina Molecular (iMM), Faculdade de Medicina [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA)-Universidade de Lisboa = University of Lisbon (ULISBOA), Knowledge Technology group [Hamburg] (KT), University of Hamburg-University of Hamburg, Université de Lausanne = University of Lausanne (UNIL), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Coalition of Independent Scholar (NCIS), Finnish Meteorological Institute (FMI), Vrije Universiteit Amsterdam [Amsterdam] (VU), Universität Zürich [Zürich] = University of Zurich (UZH), Institute of Neuroscience and Medicine [Jülich] (INM-1), Université de Montréal (UdeM), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biology [Stanford], Stanford University, Université de Genève = University of Geneva (UNIGE), Swiss Center for Affective Sciences (CISA), Michigan State University System, 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), Labex Institut d'étude de la cognition (IEC), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Max Planck Institute of Experimental Medicine [Göttingen] (MPI), Max-Planck-Gesellschaft, Statistical Machine Learning and Parsimony (SIERRA), Département d'informatique - ENS Paris (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria), Chemnitz University of Technology / Technische Universität Chemnitz, Laboratoire pour l'utilisation des lasers intenses (LULI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, 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, Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of California, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humboldt-Universität zu Berlin, Institut cellule souche et cerveau (U846 Inserm - UCBL1), Universidade de Lisboa (ULISBOA)-Universidade de Lisboa (ULISBOA), Université de Lausanne (UNIL), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Département d'informatique de l'École normale supérieure (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Rougier, Nicolas P.

Subjects
FOS: Computer and information sciences, Technology, Journal, lcsh:QA75.5-76.95, Computational Science, GitHub, Scientific Computing and Simulation, Social Computing, Open Science, Replicability, REPRODUCIBLE RESEARCH, [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], Open peer-review, Digital Libraries (cs.DL), Computational science, Open science, Publication, Reproducible, Replicable, Sustainable, GitHub, Open peer-review, [ INFO.INFO-DL ] Computer Science [cs]/Digital Libraries [cs.DL], Science & Technology, Computer Science, Information Systems, Data Science, Computational science, bepress|Physical Sciences and Mathematics|Computer Sciences, Computer Science - Digital Libraries, Sustainable, Reproducibility, Networking and Information Technology R&D (NITRD), Digital Libraries, Computer Science, Reproducible, Publication, Open science, lcsh:Electronic computers. Computer science, [INFO.INFO-DL] Computer Science [cs]/Digital Libraries [cs.DL], Replicable
Abstract

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests., 8 pages, 1 figure

Published
2017

31. On Rectangle-Decomposable 2-Parameter Persistence Modules

Author

Botnan, Magnus Bakke, Lebovici, Vadim, Oudot, Steve, Cabello, Sergio, Chen, Danny Z., Mathematics, Vrije Universiteit Amsterdam [Amsterdam] (VU), 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), Sergio Cabello, Danny Z. Chen, Schloss Dagstuhl--Leibniz-Zentrum für Informatik, La Géometrie au Service du Numérique (GEOMERIX), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Paris (IP Paris), Cabello, Sergio, and Chen, Danny Z.

Subjects
Computational Geometry (cs.CG), FOS: Computer and information sciences, Topological data analysis, SDG 10 - Reduced Inequalities, Multiparameter persistence, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], Theoretical Computer Science, Computational Theory and Mathematics, [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], FOS: Mathematics, Computer Science - Computational Geometry, Discrete Mathematics and Combinatorics, Algebraic Topology (math.AT), Mathematics - Algebraic Topology, Geometry and Topology, rank invaria, Rank invariant
Abstract

This paper addresses two questions: (a) can we identify a sensible class of 2-parameter persistence modules on which the rank invariant is complete? (b) can we determine efficiently whether a given 2-parameter persistence module belongs to this class? We provide positive answers to both questions, and our class of interest is that of rectangle-decomposable modules. Our contributions include: on the one hand, a proof that the rank invariant is complete on rectangle-decomposable modules, together with an inclusion-exclusion formula for counting the multiplicities of the summands; on the other hand, algorithms to check whether a module induced in homology by a bifiltration is rectangle-decomposable, and to decompose it in the affirmative, with a better complexity than state-of-the-art decomposition methods for general 2-parameter persistence modules. Our algorithms are backed up by a new structure theorem, whereby a 2-parameter persistence module is rectangle-decomposable if, and only if, its restrictions to squares are. This local characterization is key to the efficiency of our algorithms, and it generalizes previous conditions derived for the smaller class of block-decomposable modules. It also admits an algebraic formulation that turns out to be a weaker version of the one for block-decomposability. By contrast, we show that general interval-decomposability does not admit such a local characterization, even when locality is understood in a broad sense. Our analysis focuses on the case of modules indexed over finite grids, the more general cases are left as future work., Comment: This is the final version to be published in DCG. Changed the algorithm in Section 3 for computing the rank invariant, which was incorrect. The new algorithm reduces to computing 1-parameter vineyards along a family of paths in the grid. It was first proposed in the PhD thesis of D. Morozov

Published
2022

32. Metabolic acceleration in the pond snail Lymnaea stagnalis?

Author

Elke I. Zimmer, Virginie Ducrot, Tjalling Jager, Joris M. Koene, Sebastiaan A.L.M. Kooijman, Laurent Lagadic, Biosphere Impact Studies, Belgian Nuclear Research Centre, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Ecological Science [Amsterdam], European Union PITN-GA-2009-238148, French funds under the Program 'Environnement-Sante-Travail' from ANSES (project acronym MODENDO) EST 2011/1/153, Jaap van der Meer, Sebastiaan Kooijman, Chris Klok, Kearney Michael, Jeroen Wijsman, European Project: 238148, Theoretical Life Sciences, Animal Ecology, and Amsterdam Global Change Institute

Subjects
0106 biological sciences, Ontogeny, Dynamic energy budget, Acceleration (differential geometry), Lymnaea stagnalis, Snail, Aquatic Science, Biology, Oceanography, simultaneous hermaphroditism, 010603 evolutionary biology, 01 natural sciences, SDG 17 - Partnerships for the Goals, biology.animal, Juvenile, Ecology, Evolution, Behavior and Systematics, food limitation, Hatching, Ecology, 010604 marine biology & hydrobiology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Growth curve (biology), mollusk, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, metabolic acceleration, dynamic Energy Budget
Abstract

Under constant environmental conditions, most animals tend to grow following the von Bertalanffy growth curve. Deviations from this curve can point to changes in the environment that the animals experience, such as food limitation when the available food is not sufficient or suitable. However, such deviations can also point to a phenomenon called metabolic acceleration, which is receiving increasing attention in the field of Dynamic Energy Budget (DEB) modeling. Reasons for such an acceleration are usually changes in shape during ontogeny, which cause changes in the surface area to volume ratio of the organism. Those changes, in turn, lead to changes in some of the model parameters that have length in their dimension. The life-history consequences of metabolic acceleration as implemented in the DEB theory are an s-shaped growth curve (when body size is expressed as a length measure) and a prolongation of the hatching time. The great pond snail . Lymnaea stagnalis was earlier found to be food limited during the juvenile phase in laboratory experiments conducted under classical ecotoxicity test protocols. The pond snail has isomorphic shell growth but yet does not exhibit the expected von Bertalanffy growth curve under food limitation. When applying the standard DEB model to data from such life-cycle experiments, we also found that the hatching time is consistently underestimated, which could be a sign of metabolic acceleration. We here present an application of the DEB model including metabolic acceleration to the great pond snail. We account for the simultaneous hermaphroditism of the snail by including a model extension that describes the relative investment into the male and female function. This model allowed us to adequately predict the life history of the snail over the entire life cycle. However, the pond snail does not change in shape substantially after birth, so the original explanation for the metabolic acceleration does not hold. Since the change in shape is not the only explanation for metabolic acceleration in animals, we discuss the possible other explanations for this pattern in . L. stagnalis.

Published
2014

33. The formation of peak rings in large impact craters

Author

Cornelia Rasmussen, Jaime Urrutia-Fucugauchi, Honami Sato, Timothy J. Bralower, Xiao Long, Sonia M. Tikoo, David A. Kring, Douglas R. Schmitt, Mario Rebolledo-Vieyra, Philippe Claeys, C.L. Mellett, Johanna Lofi, W. Zylberman, Kosei E. Yamaguchi, Michael T. Whalen, Sean P. S. Gulick, Ludovic Ferrière, Elise Chenot, Gail L. Christeson, Gareth S. Collins, Kazuhisa Goto, Ulrich Riller, Rubén Ocampo-Torres, Naotaka Tomioka, Annemarie E. Pickersgill, Charles S. Cockell, Joanna Morgan, Axel Wittmann, Ligia Pérez-Cruz, Heather L. Jones, Erwan Le Ber, Michael H. Poelchau, Gordon R. Osinski, Jan Smit, Catalina Gebhardt, Christopher M. Lowery, Auriol S. P. Rae, Marco J. L. Coolen, Department of Earth Science and Technology [Imperial College London], Imperial College London, Institute of Geophysics [Austin] (IG), University of Texas at Austin [Austin], Department of Geosciences, Pennsylvania State University (Penn State), Penn State System-Penn State System, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Analytical, Environmental and Geo- Chemistry, Vrije Universiteit [Brussels] (VUB), SUPA School of Physics and Astronomy [Edinburgh], University of Edinburgh, WA-Organic and Isotope Geochemistry Centre (WA-OIGC), Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Natural History Museum [Vienna] (NHM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), International Research Institute of Disaster Science, Tohoku University [Sendai], Lunar and Planetary Institute [Houston] (LPI), Department of Geology [Leicester], University of Leicester, Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), School of Earth Sciences [Wuham], China University of Geosciences [Wuham] (CUG), The Lyell Centre, British Geological Survey (BGS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [London, ON], University of Western Ontario (UWO), Centre for Planetary Science and Exploration [London, ON] (CPSX), Instituto de Geofísica, Universidad Nacional Autónoma de México (UNAM), School of Geographical and Earth Sciences, University of Glasgow, Geology, University of Freiburg [Freiburg], Department of Geology and Geophysics, University of Utah, Unidad de Ciencias del Agua, Centro de Investigación Científica de Yucatán, Institut für Geologie, Universität Hamburg (UHH), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Physics [Edmonton], University of Alberta, Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Earth and Planetary Sciences [Piscataway], Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Kochi Institute for Core Sample Research, University of Alaska [Fairbanks] (UAF), Physical Sciences, Arizona State University [Tempe] (ASU)-LeRoy Eyring Center for Solid State Science, Department of Chemistry, Toho University, NASA Astrobiology Institute (NAI), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Work funded by the European Consortium for Ocean Research Drilling (ECORD) and the International Continental Scientific Program, with contributions and logistical support from the Yucatan State Government and Universidad Nacional Autónoma de México (UNAM)., Institute for Geophysics, University of Texas at Austin [Austin]-Jackson School of Geosciences, PennState University [Pennsylvania] ( PSU ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Analytical, Environmental and Geo-Chemistry, Vrije Universiteit [Brussel] ( VUB ), School of Physics and Astronomy [Edinburgh], WA-Organic and Isotope Geochemistry Centre ( WA-OIGC ), Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), Natural History Museum [Vienna] ( NHM ), Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research ( AWI ), Lunar and Planetary Institute [Houston] ( LPI ), Université des Antilles et de la Guyane ( UAG ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), School of Earth Sciences, China University of Geosciences-Planetary Science Institute, British Geological Survey, Institut de chimie et procédés pour l'énergie, l'environnement et la santé ( ICPEES ), Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ) -Matériaux et nanosciences d'Alsace, Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), University of Western Ontario ( UWO ), Centre for Planetary Science and Exploration [London, ON] ( CPSX ), Universidad Nacional Autónoma de México ( UNAM ), Universität Hamburg ( UHH ), Japan Agency for Marine-Earth Science and Technology ( JAMSTEC ), University of Alberta [Edmonton], Faculty of Earth and Life Sciences ( FALW ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Rutgers, The State University of New Jersey [New Brunswick] ( RUTGERS ), University of Alaska Fairbanks ( UAF ), Arizona State University [Tempe] ( ASU ) -LeRoy Eyring Center for Solid State Science, NASA Astrobiology Institute ( NAI ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Analytical, Environmental & Geo-Chemistry, Chemistry, Earth System Sciences, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Vrije Universiteit Brussel (VUB), The Institute for Geoscience Research [Perth] (TIGeR), School of Earth and Planetary Science [Perth - Curtin university], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC)-Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC)-School of Earth and Planetary Science [Perth - Curtin university], China University of Geosciences [Wuhan] (CUG), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Science and Technology Facilities Council (STFC), Natural Environment Research Council (NERC), BG International Limited, ConocoPhillips, Particle Physics and Astronomy Research Council (PPARC), The Leverhulme Trust, Penn State Department of Geosciences, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), and Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Dike, 010504 meteorology & atmospheric sciences, General Science & Technology, BASIN FORMATION, Mineralogy, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, GRAVITY, Impact crater, Planet, impact cratering, Impact structure, Petrology, CRUSTAL STRUCTURE, BASIN, 0105 earth and related environmental sciences, geography, Science & Technology, Multidisciplinary, geography.geographical_feature_category, Felsic, Drilling, Crust, [ SDU.STU ] Sciences of the Universe [physics]/Earth Sciences, terrestrial analog, CHICXULUB CRATER, Multidisciplinary Sciences, MODEL, 13. Climate action, DENSITY, ASYMMETRY, Science & Technology - Other Topics, QUARTZ, Shear zone, Geology
Abstract

The Chicxulub impact crater, known for its link to the demise of the dinosaurs, also provides an opportunity to study rocks from a large impact structure. Large impact craters have “peak rings” that define a complex crater morphology. Morgan et al. looked at rocks from a drilling expedition through the peak rings of the Chicxulub impact crater (see the Perspective by Barton). The drill cores have features consistent with a model that postulates that a single over-heightened central peak collapsed into the multiple-peak-ring structure. The validity of this model has implications for far-ranging subjects, from how giant impacts alter the climate on Earth to the morphology of crater-dominated planetary surfaces.Science, this issue p. 878; see also p. 836Large impacts provide a mechanism for resurfacing planets through mixing near-surface rocks with deeper material. Central peaks are formed from the dynamic uplift of rocks during crater formation. As crater size increases, central peaks transition to peak rings. Without samples, debate surrounds the mechanics of peak-ring formation and their depth of origin. Chicxulub is the only known impact structure on Earth with an unequivocal peak ring, but it is buried and only accessible through drilling. Expedition 364 sampled the Chicxulub peak ring, which we found was formed from uplifted, fractured, shocked, felsic basement rocks. The peak-ring rocks are cross-cut by dikes and shear zones and have an unusually low density and seismic velocity. Large impacts therefore generate vertical fluxes and increase porosity in planetary crust.

Published
2016

34. Estimating 'land use heritage' to model changes in archaeological settlement patterns

Author

Angelo Castrorao Barba, Philip Verhagen, Frédérique Bertoncello, Laure Nuninger, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux ( MSHE ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Cultural Landscape and Urban Environment ( CLUE ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age ( CEPAM ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), PHC IHAPMAUMR 6249 Chrono-Environnement - USR 3124 MSHE C.N. Ledoux - UMR 7264NWO (the Netherlands Organisation for Scientific Research) under the VIDI Innovational Research Incentives Scheme (project number 276-61-005), Internship of the fourth author at VU University Amsterdam as part of a II level University Master in GIS and Remote Sensing at the Centre for GeoTechnologies (University of Siena), funded by a scholarship for postgraduate studies from the Sicilian Region (Sovvenzione Globale PO FSE SICILIA 2007-2013)., Art and Culture, History, Antiquity, CLUE+, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux (UAR 3124) (MSHE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Cultural Landscape and Urban Environment (CLUE), Vrije Universiteit Amsterdam [Amsterdam] (VU), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), and Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux (MSHE)

Subjects
010506 paleontology, Index (economics), [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, 01 natural sciences, [ SHS.GEO ] Humanities and Social Sciences/Geography, socio-cultural variables, Order (exchange), memory of landscape, 0601 history and archaeology, Rural settlement, [ SHS.STAT ] Humanities and Social Sciences/Methods and statistics, 0105 earth and related environmental sciences, heritage map, [SHS.STAT]Humanities and Social Sciences/Methods and statistics, 060102 archaeology, Land use, Predictive modelling, 06 humanities and the arts, [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, Archaeology, Preference, Variable (computer science), Geography, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, settlement pattern analysis, Settlement (trust)
Abstract

International audience; In this paper, we present a method to calculate a “land use heritage map” based on the concept of “memory of landscape”. Such a map can be seen as one variable among others influencing site location preference, and can be used as input for predictive models. The computed values equate to an index of long-term land use intensity. We will first discuss the method used for creating the land use heritage map, for which kernel density estimates are used.We will then present the use of these land use heritage maps for site location analysis in two study areas in SE France. Earlier analyses showed that the influence of the natural environment on settlement location choice in the Roman period is limited. In contrast, land use heritage seems to have a stronger influence on the placement of new settlements. We will discuss the implications for predictive modelling of settlement patterns.

Published
2016

35. Approximation algorithms for replenishment problems with fixed turnover times

Author

Yang Jiao, R. Ravi, Thomas Bosman, Martijn van Ee, Leen Stougie, Alberto Marchetti-Spaccamela, Centrum Wiskunde & Informatica, Amsterdam (CWI), The Netherlands, Vrije Universiteit Amsterdam [Amsterdam] (VU), Tepper School of Business, Carnegie Mellon University [Pittsburgh] (CMU), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centrum Wiskunde & Informatica (CWI), University of Amsterdam [Amsterdam] (UvA), Netherlands Defence Academy, Boeing Research and Technology Europe, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria), The research of YJ and RR was supported in part by the U. S. National Science Foundation under award numbers CCF-1527032 and CCF-1655442, and the U. S. Office of Naval Research under award number N00014-18-1-2099. The research of LS was supported by the Netherlands Organisation for Scientific Research (NWO) through the Gravitation Programme Networks (024.002.003), Bender, Michael A., Farach-Colton, Martin, Mosteiro, Miguel A., Econometrics and Operations Research, Tinbergen Institute, Amsterdam Business Research Institute, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], and Operations Analytics

Subjects
FOS: Computer and information sciences, Schedule, Mathematical optimization, Optimization problem, Computational complexity theory, General Computer Science, Computer science, 0211 other engineering and technologies, Time horizon, G.2.2, 0102 computer and information sciences, 02 engineering and technology, 01 natural sciences, Theoretical Computer Science, Traveling salesman, Computer Science - Data Structures and Algorithms, Inventory routing, Data Structures and Algorithms (cs.DS), [INFO]Computer Science [cs], Approximation algorithms, F.2.2, 021103 operations research, Applied Mathematics, Approximation algorithm, SDG 8 - Decent Work and Economic Growth, Pinwheel scheduling, Computer Science Applications, Periodic maintenance, 010201 computation theory & mathematics, Replenishment problem, Node (circuits), Routing (electronic design automation), Constant (mathematics)
Abstract

We introduce and study a class of optimization problems we call replenishment problems with fixed turnover times: a very natural model that has received little attention in the literature. Clients with capacity for storing a certain commodity are located at various places; at each client the commodity depletes within a certain time, the turnover time, which is constant but can vary between locations. Clients should never run empty. The natural feature that makes this problem interesting is that we may schedule a replenishment (well) before a client becomes empty, but then the next replenishment will be due earlier also. This added workload needs to be balanced against the cost of routing vehicles to do the replenishments. In this paper, we focus on the aspect of minimizing routing costs. However, the framework of recurring tasks, in which the next job of a task must be done within a fixed amount of time after the previous one is much more general and gives an adequate model for many practical situations. Note that our problem has an infinite time horizon. However, it can be fully characterized by a compact input, containing only the location of each client and a turnover time. This makes determining its computational complexity highly challenging and indeed it remains essentially unresolved. We study the problem for two objectives: min–avg minimizes the average tour cost and min–max minimizes the maximum tour cost over all days. For min–max we derive a logarithmic factor approximation for the problem on general metrics and a 6-approximation for the problem on trees, for which we have a proof of NP-hardness. For min–avg we present a logarithmic factor approximation on general metrics, a 2-approximation for trees, and a pseudopolynomial time algorithm for the line. Many intriguing problems remain open.

Published
2022

36. The Role of Different Types of Actors In The Future of Sustainable Agriculture In a Dutch Peri-urban Area

Author

Catharina J. E. Schulp, Franziska Komossa, Laura Scherer, Emma H. van der Zanden, Marta Debolini, Annette Piorr, Vrije Universiteit Amsterdam [Amsterdam] (VU), Universiteit Leiden, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), European Project: 9723391(1997), European Project: 817949,CONSOLE, Environmental Geography, and Earth and Climate

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, Global and Planetary Change, Farms, Ecology, the Netherlands, Regional agri-food system, Agriculture, Bayes Theorem, Sustainable Development, Bayesian Belief Network, Pollution, Europe, SDG 17 - Partnerships for the Goals, Stakeholder participation, Sustainable Intensification, Local supply chains, City Planning, Forecasting, Netherlands
Abstract

Peri-urban areas support a broad range of multifunctional demands for public goods. In northwest Europe, peri-urban areas tend to overlap with intensive agricultural land, resulting in conflicts between agricultural use and the public good demands of residents. Sustainable intensification (SI) of agriculture might help reconcile agricultural and well-being goals, but it is unclear how the mix of actors in a peri-urban setting can trigger or restrain SI. In a Dutch case study, we explored how SI of agriculture can contribute to making peri-urban areas more sustainable, and which actors are key enabling factors for implementing SI. We used interviews, surveys, workshops, and empirical analysis to obtain insight into the stakeholder’s vision of a sustainable future for the case study area, the farming system and actor network. We integrated these insights in a Bayesian Belief Network, where we linked the actor network to implementation of three SI measures (farm-level efficiency measures, small landscape elements, and direct sales), and used sensitivity analysis to model effects of support for implementation by different groups of actors. The case study has a dense stakeholder network, where, dependent on the SI measure, farmers are triggered by all actors to implement SI, or have a stronger role in uptake themselves. The sensitivity analysis suggested that the future preferred by the stakeholders requires broad support of all actors involved, with local actors without a formal role being essential for uptake. Overall, trade-offs among public goods are almost inevitable when taking up SI measures.

Published
2022

37. Tracking Hunter-Gatherer Impact on Vegetation in Last Interglacial and Holocene Europe

Author

Nikulina, Anastasia, Macdonald, Katharine, Scherjon, Fulco, A. Pearce, Elena, Davoli, Marco, Svenning, Jens-Christian, Vella, Emily, Gaillard, Marie-José, Zapolska, Anhelina, Arthur, Frank, Martinez, Alexandre, Hatlestad, Kailin, Mazier, Florence, Serge, Maria Antonia, Lindholm, Karl-Johan, Fyfe, Ralph, Renssen, Hans, Roche, Didier, Kluiving, Sjoerd, Roebroeks, Wil, Serge, Maria, Universiteit Leiden, Aarhus University [Aarhus], Uppsala University, Linnaeus University, Vrije Universiteit Amsterdam [Amsterdam] (VU), University of South-Eastern Norway (USN), Géographie de l'environnement (GEODE), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Plymouth University, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Earth and Climate, CLUE+, Art and Culture, History, Antiquity, Earth Sciences, Amsterdam Sustainability Institute, Leiden University, Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 010506 paleontology, Archeology, 010504 meteorology & atmospheric sciences, Holocene, 15. Life on land, Human-environment interaction, Mesolithic, Neanderthal, Last Interglacial, Hunter-gatherers, 01 natural sciences, Archaeology, 13. Climate action, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Arkeologi, 0105 earth and related environmental sciences
Abstract

We review palaeoenvironmental proxies and combinations of these relevant for understanding hunter-gatherer niche construction activities in pre-agricultural Europe. Our approach consists of two steps: (1) identify the possible range of hunter-gatherer impacts on landscapes based on ethnographic studies; (2) evaluate proxies possibly reflecting these impacts for both the Eemian (Last Interglacial, Middle Palaeolithic) and the Early–Middle Holocene (Mesolithic). We found these paleoenvironmental proxies were not able to unequivocally establish clear-cut differences between specific anthropogenic, climatic and megafaunal impacts for either time period in this area. We discuss case studies for both periods and show that published evidence for Mesolithic manipulation of landscapes is based on the interpretation of comparable data as available for the Last Interglacial. If one applies the ‘Mesolithic’ interpretation schemes to the Neanderthal record, three common niche construction activities can be hypothesised: vegetation burning, plant manipulation and impact on animal species presence and abundance. Our review suggests that as strong a case can be made for a Neanderthal impact on landscapes as for anthropogenic landscape changes during the Mesolithic, even though the Neanderthal evidence comes from only one high-resolution site complex. Further research should include attempts (e.g. by means of modelling studies) to establish whether hunter-gatherer impact on landscapes played out at a local level only versus at a larger scale during both time periods, while we also need to obtain comparative data on the population sizes of Last Interglacial and Holocene hunter-gatherers, as these are usually inferred to have differed significantly.

Published
2022

38. Role of host cell traversal by the malaria sporozoite during liver infection

Author

Rogerio Amino, Joana Tavares, Nico van Rooijen, Elodie Mordelet, Robert Ménard, Alexander Medvinsky, Sabine Thiberge, Pauline Formaglio, Biologie et Génétique du Paludisme, Institut Pasteur [Paris], Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal] (IBMC), Macrophages et Développement de l'Immunité, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Cell Biology [Amsterdam UMC], Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Edinburgh, This work was supported by funds from Pasteur Institute, the French National Research Agency (grant no. ANR-10-JCJC-1302-PlasmoPEP), the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant no. ANR-10-LABX-62-IBEID), the European Community’s Seventh Framework Programme (Evimalar, FP7/2007-2013, grant no. 242095), Natixis, and the Leukaemia and Lymphoma Research Funding (UK). J. Tavares was supported by a fellowship from the Fundação para Ciência e Tecnologia (SFRH/BPD/48340/2008) and P. Formaglio by a Ph.D. fellowship from the Direction Générale de l’Armement, We thank S. Shorte and the Dynamic Imaging Platform (PFID-Institut Pasteur) for the support with confocal microscopy, C. Bourgouin and the Center of Production and Infection of Anopheles (CEPIA-Institut Pasteur) for mosquito rearing, and G. Milon, G. Lauvau, and T. Graf for providing the lys-gfp mice., ANR-10-JCJC-1302,PlasmoPEP,Imagerie in vivo de la phase pre-erythrocitaire du paludisme(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Molecular cell biology and Immunology, CCA - Immuno-pathogenesis, Institut Pasteur [Paris] (IP), Universidade do Porto = University of Porto, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, MESH: Cell Death, sporozoites, Plasmodium berghei, MESH: Endothelial Cells/pathology, Plasmodium, Mice, MESH: Anopheles/parasitology, Cell Movement, Immunology and Allergy, Parasite hosting, MESH: Animals, MESH: Endothelial Cells/parasitology, 0303 health sciences, MESH: Sporozoites/cytology, Liver infection, Cell Death, biology, Anopheles, MESH: Malaria/parasitology, 3. Good health, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Hepatocyte, Female, MESH: Plasmodium berghei/physiology, Antibody, host (organism), Programmed cell death, MESH: Cell Movement, Kupffer Cells, diagnostic imaging, Green Fluorescent Proteins, Immunology, malaria, MESH: Green Fluorescent Proteins/metabolism, MESH: Host-Parasite Interactions/immunology, parasites, liver, Article, Host-Parasite Interactions, MESH: Malaria/pathology, drug clearance, 03 medical and health sciences, MESH: Mice, Inbred C57BL, parasitic diseases, medicine, Animals, MESH: Mice, 030304 developmental biology, 030306 microbiology, MESH: Liver/pathology, Endothelial Cells, biology.organism_classification, Virology, infection, MESH: Male, Mice, Inbred C57BL, plasmodium, MESH: Plasmodium berghei/cytology, biology.protein, MESH: Liver/parasitology, MESH: Female, keratoconjunctivitis sicca, MESH: Sporozoites/physiology, MESH: Kupffer Cells/parasitology, MESH: Kupffer Cells/pathology
Abstract

Malaria sporozoites cross the liver sinusoidal barrier, target Kupffer cells and endothelial cells with cell traversal inhibiting sporozoite clearance., Malaria infection starts when the sporozoite stage of the Plasmodium parasite is injected into the skin by a mosquito. Sporozoites are known to traverse host cells before finally invading a hepatocyte and multiplying into erythrocyte-infecting forms, but how sporozoites reach hepatocytes in the liver and the role of host cell traversal (CT) remain unclear. We report the first quantitative imaging study of sporozoite liver infection in rodents. We show that sporozoites can cross the liver sinusoidal barrier by multiple mechanisms, targeting Kupffer cells (KC) or endothelial cells and associated or not with the parasite CT activity. We also show that the primary role of CT is to inhibit sporozoite clearance by KC during locomotion inside the sinusoid lumen, before crossing the barrier. By being involved in multiple steps of the sporozoite journey from the skin to the final hepatocyte, the parasite proteins mediating host CT emerge as ideal antibody targets for vaccination against the parasite.

Published
2013
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39. Stable Vectorization of Multiparameter Persistent Homology using Signed Barcodes as Measures

Author

Loiseaux, David, Scoccola, Luis, Carrière, Mathieu, Botnan, Magnus Bakke, Oudot, Steve, 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), Northeastern University [Boston], Vrije Universiteit Amsterdam [Amsterdam] (VU), La Géometrie au Service du Numérique (GEOMERIX), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Paris (IP Paris), and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)

Subjects
Computational Geometry (cs.CG), FOS: Computer and information sciences, Computer Science - Machine Learning, Statistics - Machine Learning, [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], FOS: Mathematics, Algebraic Topology (math.AT), Computer Science - Computational Geometry, Machine Learning (stat.ML), [INFO]Computer Science [cs], Mathematics - Algebraic Topology, Machine Learning (cs.LG)
Abstract

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data., 23 pages, 3 figures, 8 tables

Published
2023

40. From fossils to mind

Author

de Sousa, A., Beaudet, A., Calvey, T., Bardo, A., Benoit, J., Charvet, C., Dehay, C., Gómez-Robles, A., Gunz, P., https://orcid.org/0000-0002-2350-4450, Heuer, K., van den Heuvel, M., Hurst, S., Lauters, P., Reed, D., Salagnon, M., Sherwood, C., Ströckens, F., Tawane, M., Todorov, O., Toro, R., Wei, Y., de Sousa, Alexandra A [0000-0003-2379-3894], Beaudet, Amélie [0000-0002-9363-5966], Calvey, Tanya [0000-0002-7540-2130], Bardo, Ameline [0000-0003-1840-6423], Gómez-Robles, Aida [0000-0002-8719-2660], Gunz, Philipp [0000-0002-2350-4450], Heuer, Katja [0000-0002-7237-0196], van den Heuvel, Martijn P [0000-0003-1570-1195], Hurst, Shawn [0000-0002-1458-759X], Lauters, Pascaline [0000-0003-3664-3182], Sherwood, Chet C [0000-0001-6711-449X], Todorov, Orlin S [0000-0002-0295-7557], Apollo - University of Cambridge Repository, Bath Spa University, Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), University of Cape Town, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), University of Kent [Canterbury], University of the Witwatersrand [Johannesburg] (WITS), Auburn University (AU), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (SBRI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Neuroanatomie Appliquée et Théorique / Applied and Theoretical Neuroanatomy (NAAT), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Vrije Universiteit Amsterdam [Amsterdam] (VU), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Institut Royal des Sciences Naturelles de Belgique (IRSNB), University of Texas at Austin [Austin], Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), The George Washington University (GW), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Ditsong National Museum of Natural History [Pretoria, South Africa] (DNMNH), Macquarie University [Sydney], Beijing University of Posts and Telecommunications (BUPT), A.Ba. was funded by the Agence Nationale de la Recherche (grant number: ANR-20-CE27-0009-01). A.Be. was funded by the National Research Foundation of South Africa (Research Development Grants for Y-Rated Researchers (grant number 129336) and the South Africa/France (PROTEA) Joint Research Programme (grant number 129923). C.C.S. was funded by NSF (EF-2021785, DRL-2219759) and NIH (NS092988, AG067419, HG011641). C.J.C. was funded by NIGMS COBRE (grant number 5P20GM103653). J.B. was funded by the NRF African Origins Platform. K.H. and R.T. were supported by the French Agence Nationale de la Recherche, projects NeuroWebLab (ANR-19-DATA-0025) and DMOBE (ANR-21-CE45-0016). K.H. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No101033485 (Individual Fellowship). O.S.T was funded by a Discovery Project Award (project number: DP210101324) funded by the Australian Government. P.G. was funded by the Max Planck Society (grant number M.IF.A.XXXX8103)., ANR-20-CE27-0009,PaleoBRAIN,Ressusciter le cerveau d'Homo erectus et des Néandertaliens(2020), ANR-19-DATA-0025,NeuroWebLab,Un laboratoire de neuroscience collectif: Au delà de FAIR(2019), and ANR-21-CE45-0016,DMOBE,Méchanique dévelopemental de l'évolution du cerveau(2021)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Archaeology, Fossils, Brain, Artifacts, Phylogeny, [SHS]Humanities and Social Sciences
Abstract

International audience; Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology’s approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.

Published
2023

41. New approach methods to improve human health risk assessment of thyroid hormone system disruption–a PARC project

Author

Ramhøj, Louise, Axelstad, Marta, Baert, Yoni, Cañas-Portilla, Ana I, Chalmel, Frédéric, Dahmen, Lars, De La Vieja, Antonio, Evrard, Bertrand, Haigis, Ann-Cathrin, Hamers, Timo, Heikamp, Kim, Holbech, Henrik, Iglesias-Hernandez, Patricia, Knapen, Dries, Marchandise, Lorna, Morthorst, Jane E, Nikolov, Nikolai Georgiev, Nissen, Ana C V E, Oelgeschlaeger, Michael, Renko, Kostja, Rogiers, Vera, Schüürmann, Gerrit, Stinckens, Evelyn, Stub, Mette H, Torres-Ruiz, Monica, Van Duursen, Majorie, Vanhaecke, Tamara, Vergauwen, Lucia, Wedebye, Eva Bay, Svingen, Terje, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Vrije Universiteit Brussel (VUB), Instituto de Salud Carlos III [Madrid] (ISC), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), German Federal Institute for Risk Assessment [Berlin] (BfR), University of Antwerp (UA), Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Southern Denmark (SDU), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), This project is part of the Partnership for the Assessment of Risk from Chemicals (PARC), funding by the European Union’s Horizon Europe research and innovation programme under Grant Agreement No 101057014. Additional co-funders are acknowledged, including the Danish Environmental Protection Agency (DK EPA), the German Federal Institute for Risk Assessment (BfR), the University of Antwerp Research Fund (project ID 44602), the Spanish Government (Grant Number: MCIN/AEI/10.13039/501100011033/PID 2021-125948OB-I00/FEDER, UE), and Chair Mireille Aerens for the Development of Alternative Methods, Vrije Universiteit Brussel., European Project: 101057014,Horizon Europe,PARC(2022), Pharmaceutical and Pharmacological Sciences, Experimental in vitro toxicology and dermato-cosmetology, Basic (bio-) Medical Sciences, Biology of the Testis, Biology, Faculty of Medicine and Pharmacy, and Vriendenkring VUB

Subjects
Adverse outcome pathways, Thyroid disruption, regulatory toxicology, Endocrine disruption, Pharmacology. Therapy, Non-animal test methods, thyroid disruption, chemicals, endocrine disruption, General Medicine, adverse outcome pathways, SDG 3 - Good Health and Well-being, non-animal test methods, [SDV.TOX]Life Sciences [q-bio]/Toxicology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Chemicals, Regulatory toxicology, PARC, Biology, PARC endocrine disruption thyroid disruption non-animal test methods regulatory toxicology adverse outcome pathways chemicals
Abstract

Current test strategies to identify thyroid hormone (TH) system disruptors are inadequate for conducting robust chemical risk assessment required for regulation. The tests rely heavily on histopathological changes in rodent thyroid glands or measuring changes in systemic TH levels, but they lack specific new approach methodologies (NAMs) that can adequately detect TH-mediated effects. Such alternative test methods are needed to infer a causal relationship between molecular initiating events and adverse outcomes such as perturbed brain development. Although some NAMs that are relevant for TH system disruption are available–and are currently in the process of regulatory validation–there is still a need to develop more extensive alternative test batteries to cover the range of potential key events along the causal pathway between initial chemical disruption and adverse outcomes in humans. This project, funded under the Partnership for the Assessment of Risk from Chemicals (PARC) initiative, aims to facilitate the development of NAMs that are specific for TH system disruption by characterizing in vivo mechanisms of action that can be targeted by in embryo/in vitro/in silico/in chemico testing strategies. We will develop and improve human-relevant in vitro test systems to capture effects on important areas of the TH system. Furthermore, we will elaborate on important species differences in TH system disruption by incorporating non-mammalian vertebrate test species alongside classical laboratory rat species and human-derived in vitro assays.

Published
2023

42. Efficient Computation of General Modules for ALC Ontologies (Extended Version)

Author

Yang, Hui, Koopmann, Patrick, Ma, Yue, Bidoit, Nicole, Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Vrije Universiteit Amsterdam [Amsterdam] (VU)

Subjects
FOS: Computer and information sciences, Computer Science - Logic in Computer Science, Artificial Intelligence (cs.AI), Computer Science - Artificial Intelligence, Logic in Computer Science (cs.LO), [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

We present a method for extracting general modules for ontologies formulated in the description logic ALC. A module for an ontology is an ideally substantially smaller ontology that preserves all entailments for a user-specified set of terms. As such, it has applications such as ontology reuse and ontology analysis. Different from classical modules, general modules may use axioms not explicitly present in the input ontology, which allows for additional conciseness. So far, general modules have only been investigated for lightweight description logics. We present the first work that considers the more expressive description logic ALC. In particular, our contribution is a new method based on uniform interpolation supported by some new theoretical results. Our evaluation indicates that our general modules are often smaller than classical modules and uniform interpolants computed by the state-of-the-art, and compared with uniform interpolants, can be computed in a significantly shorter time. Moreover, our method can be used for, and in fact improves, the computation of uniform interpolants and classical modules., Comment: This is the extended version of a paper accepted at IJCAI 2023

Published
2023

43. Tracking pan-continental trends in environmental contamination using sentinel raptors—what types of samples should we use?

Author

Paola Movalli, Antonio J. García-Fernández, Silvia Espín, Michael Coeurdassier, Oliver Krone, Richard F. Shore, B. van Hattum, Veerle L.B. Jaspers, Christian Sonne, Emma Martínez-López, N.W. van den Brink, Pilar Gómez-Ramírez, Igor Eulaers, Clémentine Fritsch, Dorte Herzke, Rafael Mateo, Björn Helander, Guy Duke, European Science Foundation, Section of Ecology, Department of Biology, University of Turku, Department of Toxicology, Faculty of Veterinary Medicine, University of Murcia, FRAM—High North Research Centre for Climate and the Environment, Norwegian Institute for Air Research (NILU), NERC Centre for Ecology and Hydrology, Natural Environment Research Council (NERC), Institute for Environmental Studies, VU University, Vrije Universiteit Amsterdam [Amsterdam] (VU), DELTARES - Marine and Coastal Systems, Deltares system, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Department of Bioscience, Artic Research Centre (ARC), Aarhus University [Aarhus], Behavioural Ecology and Ecophysiology Group, Department of Biology, UA, University of Antwerp (UA), Department of Biology [Trondheim] (IBI NTNU), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, Centre for the Environment, Oxford University Environmental Change Institute, University of Oxford [Oxford], Environmental Research & Monitoring, Swedish Museum of Natural History, Swedish Museum of Natural History (NRM), Instituto de Investigación en Recursos Cinegéticos (IREC), Department of Collections, Naturalis Biodiversity Center, Naturalis Biodiversity Center [Leiden], Division of Toxicology, Wageningen University, Wageningen University and Research [Wageningen] (WUR), Research Networking Programme funded through European Science Foundation (ESF), Norwegian Institute for Air Research ( NILU ), NERC Centre for Ecology and Hydrology Lancaster Environment Centre, Centre for Ecology and Hydrology ( NERC ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Deltares system (NETHERLANDS), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Department of Bioscience, Artic Research Centre ( ARC ), University of Antwerp ( UA ), Department of Biology ( Norwegian University of Science and Technology ), Norwegian University of Science and Technology [Trondheim] ( NTNU ), Leibniz Institute for Zoo and Wildlife Research, Oxford University, Swedish Museum of Natural History, Instituto de Investigacion en Recursos Cinegeticos ( IREC CSIC UCLM JCCM ), and Wageningen University and Research Centre [Wageningen] ( WUR )

Subjects
010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Environmental pollution, 010501 environmental sciences, Toxicology, 01 natural sciences, Diagnostics & Crisis Organization, Environmental monitoring, Biomonitoring, media_common, Trophic level, Diagnostiek & Crisisorganisatie, Ecology, Pharmacology. Therapy, Contaminación, Environmental resource management, General Medicine, Bird of prey, Matrix, Sample type, Contaminant, Monitoring, Contamination, Europe, Chemistry, Dierecologie, Environmental Pollutants, Animal Ecology, Environmental Monitoring, Sentinel species, Biology, Management, Monitoring, Policy and Law, Article, Ecology and Environment, media_common.cataloged_instance, Animals, European Union, European union, Toxicologie, 0105 earth and related environmental sciences, WIMEK, Raptors, business.industry, Ave de rapiña, Feathers, [SDE.ES]Environmental Sciences/Environmental and Society, 13. Climate action, business, Environmental Pollution, Zoology, [ SDE.ES ] Environmental Sciences/Environmental and Society, Bird of prey, Contaminant, Monitoring, Sample type, Matrix
Abstract

This article is an output from a workshop on Setting Best Practices on Raptor Contaminant Monitoring Activities in Europe, one of the activities of the EURAPMON network (http:// www.eurapmon.net) hosted in Murcia in May–June 2013.-- et al., Biomonitoring using birds of prey as sentinel species has been mooted as a way to evaluate the success of European Union directives that are designed to protect people and the environment across Europe from industrial contaminants and pesticides. No such pan-European evaluation currently exists. Coordination of such large scale monitoring would require harmonisation across multiple countries of the types of samples collected and analysed-matrices vary in the ease with which they can be collected and the information they provide. We report the first ever pan-European assessment of which raptor samples are collected across Europe and review their suitability for biomonitoring. Currently, some 182 monitoring programmes across 33 European countries collect a variety of raptor samples, and we discuss the relative merits of each for monitoring current priority and emerging compounds. Of the matrices collected, blood and liver are used most extensively for quantifying trends in recent and longer-term contaminant exposure, respectively. These matrices are potentially the most effective for pan-European biomonitoring but are not so widely and frequently collected as others. We found that failed eggs and feathers are the most widely collected samples. Because of this ubiquity, they may provide the best opportunities for widescale biomonitoring, although neither is suitable for all compounds. We advocate piloting pan-European monitoring of selected priority compounds using these matrices and developing read-across approaches to accommodate any effects that trophic pathway and species differences in accumulation may have on our ability to track environmental trends in contaminants., The work undertaken for this review was also supported by EURAPMON.

Published
2016

44. Dynamics of stable isotope ratios (d13c and d15n) in different organs of crassostrea gigas at two contrasted ecosystems : insights from growth and food sources

Author

Emmery, A., Alunno-Bruscia, M., Bataille, M. P., Kooijman, S. A. L. M., Sébastien Lefebvre, Université de Caen Normandie (UNICAEN), Normandie Université (NU), VU University Amsterdam, Université du Littoral Côte d'Opale (ULCO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Region Basse-Normandie and Ifremer, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord])

Subjects
trophic ecology, crepidula-fornicata, mytilus-edulis, cerastoderma-edule, ACL, [SDV]Life Sciences [q-bio], coastal ecosystems, marennes-oleron bay, carbon isotopes, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, reproductive-cycle, suspension-feeders, seasonal-variation
Abstract

WOS:000401091600004; International audience; We studied the influence of food availability on the growth (whole body and organs) of the oyster Crassostrea gigas and on the dynamics of their delta C-13 and delta N-15 respective values. Juvenile oysters originating from Arcachon Bay were transplanted to two contrasting ecosystems, Baie des Veys (BDV) and Rade de Brest (RDB), for a 1-yr growth survey. In BDV, chlorophyll-a concentrations ([Chl-a]) was 3 times higher than in RDB on average, which accounts for the differences in oyster growth between BDV and RDB. Differences in trophic conditions could also explain the differences in C/N ratios and delta C-13 values between sites partly due to higher investment in gametogenesis for the oysters in BDV than in RDB; these differences widened when lipid normalized delta C-13 values were used. Oysters clearly selected microalgae as the main food source, and especially phytoplankton. Gi (Gills), Mu (Muscle) and Re (remaining organs) clearly exhibited different isotopic enrichment levels, with delta(Mu) \textgreater delta(Gi) \textgreater delta(Re) regardless of C or N elements, culture sites and seasons. delta N-15 discrimination between organs was rather equivalent between sites. These results would benefit from an experiment under controlled conditions along a calibration of the lipid normalization to correct delta C-13 values in bivalves.

Published
2016

45. Human FcγRIIA induces anaphylactic and allergic reactions

Author

Nico van Rooijen, Friederike Jönsson, Lawrence B. Schwartz, Takao Shimizu, Wei Zhao, Marc Daëron, David A. Mancardi, Yoshihiro Kita, Bruno Iannascoli, Pierre Bruhns, Huot Khun, Allergologie Moléculaire et Cellulaire, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Virginia Commonwealth University (VCU), The University of Tokyo (UTokyo), Histopathologie humaine et Modèles animaux, Institut Pasteur [Paris], Department of Molecular Cell Biology [Amsterdam UMC], Vrije Universiteit Medical Centre (VUMC), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), This work was supported by the Institut Pasteur, Inserm, the Agence Nationale de la Recherche (ANR, grant GENOPAT-09-GENO-014-01), the Société Française d'Allergologie (SFA, Soutien de la recherche en allergologie 2010), and the Balsan company. F.J. is a recipient of a fellowship from the Fondation pour la Recherche Médicale (FRM). D.A.M. is a recipient of a fellowship from the Institut Pasteur (Bourse Roux). W.Z. and L.B.S. were funded in part by U19AI077435 from the National Institutes of Health., ANR-09-GENO-0014,InflammAbs,Contrôle de l'inflammation par les RFc humains dans des modèles murins d'allergie et d'autoimmunité.(2009), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), Molecular cell biology and Immunology, and CCA - Immuno-pathogenesis

Subjects
MESH: Inflammation, Allergy, Respiratory System, mast cells, airway inflammation, MESH: Neutrophils, Immunoglobulin E, MESH: Mice, Knockout, Biochemistry, 0302 clinical medicine, neutrophils, MESH: Animals, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Receptor, Cells, Cultured, MESH: Respiratory System, Mice, Knockout, 0303 health sciences, biology, Passive Cutaneous Anaphylaxis, Airway inflammation, MESH: Mast Cells, Hematology, immunoglobulin e, macrophages, 3. Good health, immunoglobulin g, [SDV.IMM]Life Sciences [q-bio]/Immunology, hypersensitivity, monocytes, MESH: Passive Cutaneous Anaphylaxis, MESH: Cells, Cultured, mice, MESH: Mice, Transgenic, MESH: Hypersensitivity, Immunology, Mice, Transgenic, MESH: Receptors, IgG, 03 medical and health sciences, MESH: Eosinophils, MESH: Mice, Inbred C57BL, In vivo, anaphylaxis, medicine, Animals, Humans, MESH: Mice, 030304 developmental biology, Inflammation, MESH: Humans, Passive anaphylaxis, business.industry, Receptors, IgG, Anaphylactic reactions, Cell Biology, medicine.disease, Eosinophils, Mice, Inbred C57BL, biology.protein, business, 030215 immunology
Abstract

IgE and IgE receptors (FcϵRI) are well-known inducers of allergy. We recently found in mice that active systemic anaphylaxis depends on IgG and IgG receptors (FcγRIIIA and FcγRIV) expressed by neutrophils, rather than on IgE and FcϵRI expressed by mast cells and basophils. In humans, neutrophils, mast cells, basophils, and eosinophils do not express FcγRIIIA or FcγRIV, but FcγRIIA. We therefore investigated the possible role of FcγRIIA in allergy by generating novel FcγRIIA-transgenic mice, in which various models of allergic reactions induced by IgG could be studied. In mice, FcγRIIA was sufficient to trigger active and passive anaphylaxis, and airway inflammation in vivo. Blocking FcγRIIA in vivo abolished these reactions. We identified mast cells to be responsible for FcγRIIA-dependent passive cutaneous anaphylaxis, and monocytes/macrophages and neutrophils to be responsible for FcγRIIA-dependent passive systemic anaphylaxis. Supporting these findings, human mast cells, monocytes and neutrophils produced anaphylactogenic mediators after FcγRIIA engagement. IgG and FcγRIIA may therefore contribute to allergic and anaphylactic reactions in humans.

Published
2012

46. Bursting in a next generation neural mass model with synaptic dynamics: a slow–fast approach

Author

Halgurd Taher, Daniele Avitabile, Mathieu Desroches, Mathématiques pour les Neurosciences (MATHNEURO), 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), Vrije Universiteit Amsterdam [Amsterdam] (VU), Mathematics, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, and Amsterdam Neuroscience - Systems & Network Neuroscience

Subjects
Bursting, Quantitative Biology::Neurons and Cognition, Astrophysics::High Energy Astrophysical Phenomena, [SCCO.NEUR]Cognitive science/Neuroscience, Applied Mathematics, Mechanical Engineering, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], FOS: Physical sciences, Aerospace Engineering, Ocean Engineering, Dynamical Systems (math.DS), Nonlinear Sciences - Adaptation and Self-Organizing Systems, Canards, Control and Systems Engineering, Spiking neural network, FOS: Mathematics, Mathematics - Dynamical Systems, Electrical and Electronic Engineering, Mean-field theory, Slow–fast dynamics, Adaptation and Self-Organizing Systems (nlin.AO)
Abstract

We report a detailed analysis on the emergence of bursting in a recently developed neural mass model that includes short-term synaptic plasticity. Neural mass models can mimic the collective dynamics of large-scale neuronal populations in terms of a few macroscopic variables like mean membrane potential and firing rate. The present one is particularly important, as it represents an exact meanfield limit of synaptically coupled quadratic integrate and fire (QIF) neurons. Without synaptic dynamics, a periodic external current with slow frequency$$\varepsilon $$εcan lead to burst-like dynamics. The firing patterns can be understood using singular perturbation theory, specifically slow–fast dissection. With synaptic dynamics, timescale separation leads to a variety of slow–fast phenomena and their role for bursting becomes inordinately more intricate. Canards are crucial to understand the route to bursting. They describe trajectories evolving nearby repelling locally invariant sets of the system and exist at the transition between subthreshold dynamics and bursting. Near the singular limit$$\varepsilon = 0$$ε=0, we report peculiarjump-on canards, which block a continuous transition to bursting. In the biologically more plausible$$\varepsilon $$ε-regime, this transition becomes continuous and bursts emerge via consecutive spike-adding transitions. The onset of bursting is complex and involvesmixed-type-like torus canards, which form the very first spikes of the burst and follow fast-subsystem repelling limit cycles. We numerically evidence the same mechanisms to be responsible for bursting emergence in the QIF network with plastic synapses. The main conclusions apply for the network, owing to the exactness of the meanfield limit.

Published
2022

47. Consumption and release of dissolved organic %%CONV_ERR%%carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling

Author

Marie Eichinger, Dominique Lefèvre, Sebastiaan A.L.M. Kooijman, Bruno Charrière, Richard Sempéré, Jean-Christophe Poggiale, Gérald Grégori, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Vrije Universiteit, Faculty of Earth and Life Science, and Theoretical Life Sciences

Subjects
[ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, 010504 meteorology & atmospheric sciences, Dynamic energy budget, Biomass, Mineralogy, Aquatic Science, Bacterial growth, 01 natural sciences, Carbon cycle, Bacterial dynamics, DEB theory, Marine bacteriophage, Dissolved organic carbon, SDG 14 - Life Below Water, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, DOC degradation, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Chemistry, 010604 marine biology & hydrobiology, Substrate (marine biology), Environmental chemistry, Mechanistic model, Degradation (geology), DOC release
Abstract

To investigate the effects of episodic occurrence of dissolved organic carbon(DOC) in the natural environment, bacterial degradation of labile DOC was studied under laboratory-controlled conditions followed by modelling. A single labile DOC compound was periodically added to the experimental culture and its degradation by a monospecific marine bacterial strain was followed. The measured variables were DOC and bacterial biomass determined from the particulate organic carbon values. Experimental dynamics showed a repetition of 2 successive patterns after each DOC pulse:(1) substrate consumption and bacterial growth in the first few hours after substrate addition, followed by(2) bacterial reduction(organic carbon-related) and associated non-labile DOC release within the next few hours. Based on these experimental results, the Dynamic Energy Budget theory was applied for the first time to such conditions to develop a mechanistic model that comprised 7 parameters and 4 state variables in which bacterial biomass was fractionated into reserve and structure compartments. The model was constructed by accounting for a constant specific maintenance rate and comprised 2 different cell maintenance fluxes, one fuelled from cell reserves when substrate was abundant and one from reserves and cell structures when starvation occurred. This new model of bacterial degradation adequately matched experimental measurements and accurately reproduced the accumulation of non-labile DOC in the culture during the experiment. This model can easily be implemented in an aquatic biogeochemical model and could provide better understanding of the role of bacteria in carbon cycling in fluctuating environments. © Inter-Research 2009.

Published
2009

48. Risk of SARS-CoV-2 infection, severe COVID-19 illness and COVID-19 mortality in people with pre-existing mental disorders: an umbrella review

Author

Cadorin, Camilla, Bertolini, Federico, Witteveen, Anke, Young, Susanne, Cuijpers, Pim, Ayuso-Mateos, Jose, Barbui, Corrado, Cabello, María, Downes, Naomi, Franzoi, Daniele, Gasior, Michael, Gray, Brandon, John, Ann, Melchior, Maria, van Ommeren, Mark, Palantza, Christina, Purgato, Marianna, van der Waerden, Judith, Wang, Siyuan, Sijbrandij, Marit, Clinical Psychology, APH - Mental Health, World Health Organization (WHO) Collaborating Center, APH - Global Health, Clinical, Neuro- & Developmental Psychology, Università degli studi di Verona = University of Verona (UNIVR), Department of Clinical, Neuro and Developmental Psychology, Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Psychiatry, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Department of Psychiatry, Universidad Autónoma de Madrid, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Department of Mental Health and Substance Use, World Health Organization, Swansea University, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), and Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
Umbrella review, Psychiatry and Mental health, Sars-CoV-2, SDG 3 - Good Health and Well-being, [SDV]Life Sciences [q-bio], Mental health, Pre-existing mental health disorders, Mortality, Covid-19
Abstract

Introduction The COVID-19 pandemic has posed a serious health risk, especially in vulnerable populations. Even before the pandemic, people with mental disorders had worse physical health outcomes compared to the general population. This umbrella review investigated whether having a pre-pandemic mental disorder was associated with worse physical health outcomes due to the COVID-19 pandemic. Methods Following a pre-registered protocol available on the Open Science Framework platform, we searched Ovid MEDLINE All, Embase (Ovid), PsycINFO (Ovid), CINAHL, and Web of Science up to the 6th of October 2021 for systematic reviews on the impact of COVID-19 on people with pre-existing mental disorders. The following outcomes were considered: risk of contracting the SARS-CoV-2 infection, risk of severe illness, COVID-19 related mortality risk, risk of long-term physical symptoms after COVID-19. For meta-analyses, we considered adjusted odds ratio (OR) as effect size measure. Screening, data extraction and quality assessment with the AMSTAR 2 tool have been done in parallel and duplicate. Results We included five meta-analyses and four narrative reviews. The meta-analyses reported that people with any mental disorder had an increased risk of SARS-CoV-2 infection (OR: 1.71, 95% CI 1.09–2.69), severe illness course (OR from 1.32 to 1.77, 95%CI between 1.19–1.46 and 1.29–2.42, respectively) and COVID-19 related mortality (OR from 1.38 to 1.52, 95%CI between 1.15–1.65 and 1.20–1.93, respectively) as compared to the general population. People with anxiety disorders had an increased risk of SAR-CoV-2 infection, but not increased mortality. People with mood and schizophrenia spectrum disorders had an increased COVID-19 related mortality but without evidence of increased risk of severe COVID-19 illness. Narrative reviews were consistent with findings from the meta-analyses. Discussion and conclusions As compared to the general population, there is strong evidence showing that people with pre-existing mental disorders suffered from worse physical health outcomes due to the COVID-19 pandemic and may therefore be considered a risk group similar to people with underlying physical conditions. Factors likely involved include living accommodations with barriers to social distancing, cardiovascular comorbidities, psychotropic medications and difficulties in accessing high-intensity medical care.

Published
2023

49. Deep-UV Rayleigh scattering of N2, CH4 and SF6

Author

Wim Ubachs, Harold Linnartz, Dmitry Ityaksov, Atoms, Molecules, Lasers, Physical Chemistry, Physics and Astronomy, Laser Centre Vrije Universiteit Amsterdam (LCVU), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Raymond and Sackler Laboratory for Astrophysics, Leiden Observatory [Leiden], and Universiteit Leiden [Leiden]-Universiteit Leiden [Leiden]

Subjects
Scattering, Chemistry, business.industry, Biophysics, Scattering length, Condensed Matter Physics, Molecular physics, Cavity ring-down spectroscopy, Physics::Fluid Dynamics, Condensed Matter::Materials Science, Cross section (physics), symbols.namesake, Wavelength, Optics, Physical Sciences, Rayleigh length, symbols, SDG 7 - Affordable and Clean Energy, Physical and Theoretical Chemistry, Rayleigh scattering, business, Spectroscopy, Molecular Biology, Computer Science::Information Theory
Abstract

International audience; Rayleigh scattering room temperature cross-section values of N2, CH4 and SF6 have been obtained between 198 and 270 nm by combining cavity ring-down spectroscopy (CRDS) and pressure ramp measurements. The experimental data have been fitted to a functional representation, describing the ~1/λ4 like behavior of the Rayleigh scattering cross section over a wide wavelength range. The resulting values are compared to numerical predictions, based on refractive indices and molecular anisotropy data as available from literature. From this, values of molecular volume polarizability αvol and depolarization ratios are derived. It is found that the optical extinction for all three gases is governed by Rayleigh scattering for wavelengths down to 200 nm. No absorption onsets in the specified deep-UV region have been observed.

Published
2008

50. Un modèle de champ neuronal pour l'allumage et la propagation de la dépression corticale propagée

Author

Baspinar, E, Avitabile, D, Desroches, M, Mantegazza, M, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Amsterdam [Amsterdam] (VU), Mathématiques pour les Neurosciences (MATHNEURO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and 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)

Subjects
spreading depression, [SCCO.NEUR]Cognitive science/Neuroscience, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], neural field, dynamical systems, Migraine
Abstract

We propose a new neural field model for migraine-related cortical spreading depression (CSD). The model follows the Wilson-Cowan-Amari formalism. It is based on an excitatory-inhibitory neuron population pair which is coupled to a potassium concentration variable. This model is spatially extended to a cortical layer. Therefore, it can model both the ignition and propagation of CSD. It controls the propagation speed via connection weights and contribution weight of each population activity to the potassium accumulation in the extracellular matrix. The simulation results regarding the propagation speed are in coherence with the experiment results provided in Chever et al. (2021).

Published
2023

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