39 results
Search Results
2. Mutated olfactomedin 1 in the interphotoreceptor matrix of the mouse retina causes functional deficits and vulnerability to light damage
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Barbara M. Braunger, Herbert Jägle, Johanna Hausberger, Marcus Koch, Walter Paper, Bernd Rosenhammer, Cornelia Volz, and Ernst R. Tamm
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0301 basic medicine ,Histology ,Light ,genetic structures ,Mutant ,Interphotoreceptor matrix ,Biology ,Retina ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,medicine ,Animals ,Photoreceptor Cells ,Outer nuclear layer ,Molecular Biology ,Glycoproteins ,Extracellular Matrix Proteins ,medicine.diagnostic_test ,Retinal ,Cell Biology ,Anatomy ,eye diseases ,Extracellular Matrix ,Cell biology ,Medical Laboratory Technology ,030104 developmental biology ,medicine.anatomical_structure ,chemistry ,Rhodopsin ,Mutation ,biology.protein ,Optic nerve ,sense organs ,030217 neurology & neurosurgery ,Electroretinography - Abstract
Olfactomedin 1 (OLFM1) is a secreted glycoprotein and member of the olfactomedin protein family, which is preferentially expressed in various areas throughout the central nervous system. To learn about the functional properties of OLFM1 in the eye, we investigated its localization in the mouse and pig eye. In addition, we analyzed the ocular phenotype of Olfm1 mutant mice in which 52 amino acids were deleted in the central part (M2 region) of OLFM1. OLFM1 was detected in cornea, sclera, retina, and optic nerve of both wild-type and Olfm1 mutant littermates. By immunohistochemistry and double labeling with the lectin peanut agglutinin, OLFM1 was found in the interphotoreceptor matrix (IPM) of mouse and pig retina where it was directly localized to the inner segments of photoreceptors. Western blotting confirmed the presence of the OLFM1 isoforms pancortin 1 (BMY) and pancortin 2 (BMZ) in the IPM. The retinal phenotype of Olfm1 mutant mice did not obviously differ from that of wild-type littermates. In addition, outer nuclear layer (ONL) and total retinal thickness were not different, and the same was true for the area of the optic nerve in cross sections. Functional changes were observed though by electroretinography, which showed significantly lower a- and b-wave amplitudes in Olfm1 mutant mice when compared to age-matched wild-type mice. When light damage experiments were performed as an experimental paradigm of photoreceptor apoptosis, significantly more TUNEL-positive cells were observed in Olfm1 mutant mice 30 h after light exposure. One week after light exposure, the ONL was significantly thinner in Olfm1 mutant mice than in wild-type littermates indicating increased photoreceptor loss. No differences were observed when rhodopsin turnover or ERK1/2 signaling was investigated. We conclude that OLFM1 is a newly identified IPM molecule that serves an important role for photoreceptor homeostasis, which is significantly compromised in the eyes of Olfm1 mutant mice.
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- 2016
3. Bioorthogonal click chemistry for fluorescence imaging of choline phospholipids in plants
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Kathrin Schrick, Janet M. Paper, and Thiya Mukherjee
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0106 biological sciences ,0301 basic medicine ,Cell signaling ,Arabidopsis thaliana ,Membrane lipids ,Phospholipid ,Fluorescence labeling ,Plant Science ,lcsh:Plant culture ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Phosphatidylcholine ,Genetics ,Propargylcholine ,Choline ,lcsh:SB1-1110 ,lcsh:QH301-705.5 ,Phospholipids ,Alexa Fluor ,Click chemistry ,fungi ,Methodology ,food and beverages ,Plant cell ,ESI-MS/MS ,030104 developmental biology ,Membrane ,lcsh:Biology (General) ,chemistry ,Biochemistry ,lipids (amino acids, peptides, and proteins) ,010606 plant biology & botany ,Biotechnology - Abstract
Background Phospholipids are important structural and signaling molecules in plant membranes. Some fluorescent dyes can stain general lipids of membranes, but labeling and visualization of specific lipid classes have yet to be developed for most components of the membrane. New techniques for visualizing membrane lipids are needed to further delineate their dynamic structural and signaling roles in plant cells. In this study we examined whether propargylcholine, a bioortholog of choline, can be used to label the major membrane lipid, phosphatidylcholine, and other choline phospholipids in plants. We established that propargylcholine is readily taken up by roots, and that its incorporation is not detrimental to plant growth. After plant tissue is harvested and fixed, a click-chemistry reaction covalently links the alkyne group of propargylcholine to a fluorescently-tagged azide, resulting in specific labeling of choline phospholipids. Results Uptake of propargylcholine, followed by click chemistry with fluorescein or Alexa Fluor 594 azide was used to visualize choline phospholipids in cells of root, leaf, stem, silique and seed tissues from Arabidopsis thaliana. Co-localization with various subcellular markers indicated coinciding fluorescent signals in cell membranes, such as the tonoplast and the ER. Among different cell types in the leaf epidermis, guard cells displayed strong labeling. Mass spectrometry-based lipidomic analysis of the various plant tissues revealed that incorporation of propargylcholine was strongest in roots with approximately 50% of total choline phospholipids being labeled, but it was also incorporated in the other tissues including seeds. Phospholipid profiling confirmed that, in each tissue analyzed, incorporation of the bioortholog had little impact on the pool of choline plus choline-like phospholipids or other lipid species. Conclusion We developed and validated a click-chemistry based method for fluorescence imaging of choline phospholipids using a bioortholog of choline, propargylcholine, in various cell-types and tissues from Arabidopsis. This click-chemistry method provides a direct way to metabolically tag and visualize specific lipid molecules in plant cells. This work paves the way for future studies addressing in situ localization of specific lipids in plants. Electronic supplementary material The online version of this article (10.1186/s13007-018-0299-2) contains supplementary material, which is available to authorized users.
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- 2018
4. Bioorthogonal click chemistry for fluorescence imaging of choline phospholipids in plants
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Paper, Janet M., primary, Mukherjee, Thiya, additional, and Schrick, Kathrin, additional
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- 2018
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5. α-Fucosidases with different substrate specificities from two species of Fusarium
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Jonathan D. Walton, Janet M. Paper, John S. Scott-Craig, Mareike Bongers, Richard E. Wiemels, Ahmed Faik, David Cavalier, and Melissa S. Borrusch
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alpha-L-Fucosidase ,Genetics ,Subfamily ,Sequence Homology, Amino Acid ,Sequence analysis ,Molecular Sequence Data ,Fungal genetics ,food and beverages ,Sequence alignment ,Sequence Analysis, DNA ,General Medicine ,Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Substrate Specificity ,Pichia pastoris ,Microbiology ,Fusarium ,Fusarium oxysporum ,Glycosides ,DNA, Fungal ,Sequence Alignment ,Gene ,Trichoderma reesei ,Biotechnology - Abstract
Two fungal-secreted α-fucosidases and their genes were characterized. FoFCO1 was purified from culture filtrates of Fusarium oxysporum strain 0685 grown on l-fucose and its encoding gene identified in the sequenced genome of strain 4287. FoFCO1 was active on p-nitrophenyl-α-fucoside (pNP-Fuc), but did not defucosylate a nonasaccharide (XXFG) fragment of pea xyloglucan. A putative α-fucosidase gene (FgFCO1) from Fusarium graminearum was expressed in Pichia pastoris. FgFCO1 was ∼1,800 times less active on pNP-Fuc than FoFCO1, but was able to defucosylate the XXFG nonasaccharide. Although FgFCO1 and FoFCO1 both belong to Glycosyl Hydrolase family 29, they share
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- 2012
6. Mutated olfactomedin 1 in the interphotoreceptor matrix of the mouse retina causes functional deficits and vulnerability to light damage
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Koch, Marcus A., primary, Rosenhammer, Bernd, additional, Paper, Walter, additional, Volz, Cornelia, additional, Braunger, Barbara M., additional, Hausberger, Johanna, additional, Jägle, Herbert, additional, and Tamm, Ernst R., additional
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- 2016
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7. α-Fucosidases with different substrate specificities from two species of Fusarium
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Paper, Janet M., primary, Scott-Craig, John S., additional, Cavalier, David, additional, Faik, Ahmed, additional, Wiemels, Richard E., additional, Borrusch, Melissa S., additional, Bongers, Mareike, additional, and Walton, Jonathan D., additional
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- 2012
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8. Inhibition of angiogenesis and murine tumour growth by laminarin sulphate
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Hoffman, R, primary, Paper, DH, additional, Donaldson, J, additional, and Vogl, H, additional
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- 1996
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9. Selective inhibition of cell proliferation and DNA synthesis by the polysulphated carbohydrate ι-carrageenan
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Hoffman, Richard, primary, Burns, Walter Woodrow, additional, and Paper, Dietrich H., additional
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- 1995
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10. Selective inhibition of cell proliferation and DNA synthesis by the polysulphated carbohydrate ?-carrageenan
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Hoffman, R., primary, Burns III, Walter Woodrow, additional, and Paper, Dietrich H., additional
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- 1995
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11. √-and λ-carrageenan as new angiogenesis inhibitors
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Vogl, H., primary, Hoffman, R., additional, Paper, D. H., additional, and Franz, G., additional
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- 1995
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12. Production of low molecular weight √-carrageenans and their effects on BFGF and on FBHE-cells
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Paper, D. H., primary, Hoffman, R., additional, Marchesan, M., additional, and Franz, G., additional
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- 1995
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13. A novel access to sulphated oligosaccharides with potential antiangiogenic effect
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Florian, G., primary, Paper, D. H., additional, Garna, A., additional, and Franz, G., additional
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- 1995
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14. Production of low molecular weight √-carrageenans and their effects on BFGF and on FBHE-cells
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Gerhard Franz, R. Hoffman, D. H. Paper, and M. Marchesan
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Cancer Research ,medicine.medical_specialty ,Hematology ,Oncology ,Chemistry ,Internal medicine ,medicine ,General Medicine ,Pharmacology - Published
- 1995
15. √-and λ-carrageenan as new angiogenesis inhibitors
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R. Hoffman, H. Vogl, D. H. Paper, and Gerhard Franz
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Cancer Research ,medicine.medical_specialty ,Hematology ,Oncology ,Angiogenesis ,Chemistry ,Internal medicine ,λ carrageenan ,medicine ,Cancer research ,General Medicine - Published
- 1995
16. A novel access to sulphated oligosaccharides with potential antiangiogenic effect
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D. H. Paper, A. Garna, Gerhard Franz, and G. Florian
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Cancer Research ,medicine.medical_specialty ,Hematology ,Oncology ,Antiangiogenic effect ,business.industry ,Internal medicine ,medicine ,Cancer research ,General Medicine ,business - Published
- 1995
17. Biotransformation of 5?H-pregnan-3?ol-20-one and cardenolides in cell suspension cultures of Nerium oleander L.
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Paper, Dietrich H., primary and Franz, Gerhard, additional
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- 1990
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18. Wet vibro-grinding of zircon with surfactants
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S. T. Balyuk, G. V. Kukolev, I. G. Orlova, Ts. E. Paper, E. D. Posokhova, E. D. Lisovaya, P. P. Arkhipov, and N. T. Dyrda
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Materials science ,Metallurgy ,Fineness ,Sintering ,chemistry.chemical_element ,Grinding ,chemistry ,Grind ,Triethanolamine ,Ceramics and Composites ,Materials Chemistry ,medicine ,Dispersion (chemistry) ,medicine.drug ,Titanium ,Zircon - Abstract
An investigation was carried out of the effect of various surfactants added during the wet vibrogrinding of zircon on the degree of dispersion of the powder and on the sintering of specimens molded from the powders. When added in proportions up to 0.2% all surfactants tested (naphthenate soap, Asidol, titanium soap, GKZh-94, GKZh-10, triethanolamine, and sugar) helped to reduce the time required to grind the zircon to a given fineness from 15–20 to 4 h, i.e., by a factor of about 2.5–4.
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- 1977
19. Wet vibro-grinding of zircon with surfactants
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Orlova, I. G., primary, Posokhova, E. D., additional, Dyrda, N. T., additional, Balyuk, S. T., additional, Kukolev, G. V., additional, Lisovaya, E. D., additional, Arkhipov, P. P., additional, and Paper, Ts. E., additional
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- 1977
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20. A generic exact solver for vehicle routing and related problems
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Eduardo Uchoa, Artur Alves Pessoa, Ruslan Sadykov, François Vanderbeck, Universidade Federal Fluminense [Rio de Janeiro] (UFF), Reformulations based algorithms for Combinatorial Optimization (Realopt), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Atoptima, We would like to thank Teobaldo Bulhoes and Guillaume Marques for a large part of the implementation of the Julia–JuMP interface to the solver, Teobaldo Bulhoes, Guillaume Marques and Eduardo Queiroga for implementing, over that interface, the models corresponding to the examples of this paper, and Laurent Facq for a general support of the computing environment. Experiments presented in this paper were carried out using the PlaFRIM (Federative Platform for Research in Computer Science and Mathematics), created under the Inria PlaFRIM development action with support from Bordeaux INP, LABRI and IMB and other entities: Conseil Régional d’Aquitaine, Université de Bordeaux, CNRS and ANR in accordance to the 'Programme d’Investissements d’Avenir'. This study was financed in part by the Conselho Nacional de Científico e Tecnológico (CNPq), grant 313601/2018-6 (Produtividade 1B), and by the Funda¸c˜ao de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), grant E-26/202.887/2017 (Cientista do Estado)., Plafrim, 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)-Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, and Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)
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Mathematical optimization ,021103 operations research ,Bin packing problem ,General Mathematics ,Column generation ,0211 other engineering and technologies ,Integer programming ,Rule-based system ,[INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO] ,010103 numerical & computational mathematics ,02 engineering and technology ,Solver ,01 natural sciences ,Vehicle routing problem ,Path (graph theory) ,0101 mathematics ,Routing (electronic design automation) ,Software ,Routing ,Mathematics - Abstract
Major advances were recently obtained in the exact solution of vehicle routing problems (VRPs). Sophisticated branch-cut-and-price (BCP) algorithms for some of the most classical VRP variants now solve many instances with up to a few hundreds of customers. However, adapting and reimplementing those successful algorithms for other variants can be a very demanding task. This work proposes a BCP solver for a generic model that encompasses a wide class of VRPs. It incorporates the key elements found in the best existing VRP algorithms: ng-path relaxation, rank-1 cuts with limited memory, path enumeration, and rounded capacity cuts; all generalized through the new concepts of “packing set” and “elementarity set”. The concepts are also used to derive a branching rule based on accumulated resource consumption and to generalize the Ryan and Foster branching rule. Extensive experiments on several variants show that the generic solver has an excellent overall performance, in many problems being better than the best specific algorithms. Even some non-VRPs, like bin packing, vector packing and generalized assignment, can be modeled and effectively solved.
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- 2020
21. Improving hydrogeological understanding through well-test interpretation by diagnostic plot and modelling: a case study in an alluvial aquifer in France
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B. Dewandel, Julio Gonçalvès, Bernard Ladouche, Bruno Arfib, Thibaut Garin, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), This paper is part of the Karst-Huveaune project funded by Agence de l’Eau Rhône Méditerranée Corse, Région Sud-PACA, Conseil Départemental des Bouches-du-Rhône, Aix-Marseille Provence Métropole, BRGM (French Geological Survey), and Aix-Marseille University. The authors would like to thank the Antea Group Aubagne, HydroAssistance and the SPL Eau des Collines for field collaboration and access to the data., Karst-Huveaune 2018-2022, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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010504 meteorology & atmospheric sciences ,0207 environmental engineering ,Borehole ,Fluvial ,Aquifer ,Soil science ,02 engineering and technology ,Analytical solutions ,01 natural sciences ,Heterogenous alluvial aquifer ,Earth and Planetary Sciences (miscellaneous) ,[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology ,020701 environmental engineering ,[SDU.STU.AG]Sciences of the Universe [physics]/Earth Sciences/Applied geology ,0105 earth and related environmental sciences ,Water Science and Technology ,geography ,Multi-model approach ,geography.geographical_feature_category ,Hydrogeology ,Well test ,6. Clean water ,Alluvial plain ,Diagnostic plot ,Pumping test ,Drawdown (hydrology) ,Geology ,Test data - Abstract
As part of the Springer Nature Content Sharing Initiative, you can publicly share full-text access to a view-only version of your paper by using thefollowing SharedIt link: https://rdcu.be/cCd8u; International audience; The study of groundwater resources using pumping test data is usually carried out with the Theis solution, which enables the hydraulic parameters of porous aquifers such as the transmissivity and storage coefficient, to be estimated from the water-level drawdown. However, the data fitting can fail and provide only an indication that the pumped aquifer has a complex structure. Here, a diagnostic plot on log-derivative drawdown is used to identify flow regimes and thus aquifer heterogeneities, leading to plausible conceptual models. Nevertheless, the diagnostic plot is insufficient and must be accompanied by further modelling because of the nonuniqueness of the drawdown log-derivative signal. The proposed approach is applied to an alluvial plain in France, known to be complex because the deposition processes change over time, resulting in channel belts limited by low-permeability deposits in the floodplain or three-dimensional (3D) interconnected structures. Six analytical models were used to simulate drawdown and its derivatives during a three-day transient pumping test. The diagnostic performed on the pumping well showed that four conceptual models, with highly contrasted hydrodynamic behaviours, may correspond to the diagnostic. The joint use of pumping-well and observation-well data allowed the only appropriate model to be identified—a dual-permeability model characterizing a multilayer aquifer. The conceptual model matched the geological observations in boreholes and corroborates the fluvial sequence stratigraphy of the alluvial plain. The pumping test used here is a tool to explore the 3D architecture of the fluvial reservoir at the scale of the depositional sequence in the floodplain.; El estudio de los recursos hídricos subterráneos a partir de los datos de los ensayos de bombeo suele realizarse con la solución de Theis, que permite estimar los parámetros hidráulicos de los acuíferos porosos, como la transmisividad y el coeficiente de almacenamiento, a partir del descenso del nivel del agua. Sin embargo, el ajuste de los datos puede no funcionar y proporcionar sólo una indicación de que el acuífero bombeado tiene una estructura compleja. En este caso, se utiliza un diagrama de diagnóstico de la depresión logarítmica derivada para identificar los regímenes de flujo y, por tanto, las heterogeneidades del acuífero, lo que conduce a modelos conceptuales plausibles. Sin embargo, el diagrama de diagnóstico es insuficiente y debe ir acompañado de una modelización adicional debido a la no unicidad de la señal log-derivada de la depresión. El enfoque propuesto se aplica a una llanura aluvial en Francia, conocida por su complejidad debido a que los procesos de deposición cambian con el tiempo, dando lugar a franjas de canales limitadas por depósitos de baja permeabilidad en la llanura de inundación o a estructuras tridimensionales (3D) interconectadas. Se utilizaron seis modelos analíticos para simular la depresión y sus derivados durante un ensayo de bombeo transitorio de tres días. El diagnóstico realizado en el pozo de bombeo mostró que pueden corresponder cuatro modelos conceptuales, con comportamientos hidrodinámicos muy contrastados. La utilización conjunta de los datos del pozo de bombeo y del pozo de observación permitió identificar el único modelo apropiado: un modelo de doble permeabilidad que caracteriza un acuífero multicapa. El modelo conceptual coincidió con las observaciones geológicas en pozos de sondeo y corrobora la estratigrafía de la secuencia fluvial de la llanura aluvial. El ensayo de bombeo utilizado aquí es una herramienta para explorar la arquitectura 3D del depósito fluvial a escala de la secuencia deposicional en la llanura aluvial.; L’étude des ressources en eau souterraine à partir de données d’essais de pompage est généralement réalisée avec la solution de Theis, qui permet d’estimer les paramètres hydrauliques des aquifères poreux, tels que la transmissivité et le coefficient d’emmagasinement, à partir du rabattement du niveau d’eau. Cependant, l’ajustement des données peut échouer et fournir seulement une indication relative à la complexité de la structure de l’aquifère sollicité par pompage. Ici, un tracé de diagnostic de la dérivé du rabattement selon une échelle logarithmique est utilisé pour identifier les régimes d’écoulement et donc les hétérogénéités de l’aquifère, conduisant à des modèles conceptuels plausibles. Néanmoins, le diagnostic de puits est insuffisant et doit être accompagné d’une modélisation plus poussée en raison de la non-unicité du signal de la dérivée du rabattement selon une échelle logarithmique. L’approche proposée est appliquée à une plaine alluviale en France, connue pour être complexe car les processus de dépôt ont évolué au cours du temps, donnant lieu à des zones de chenaux limitées par des dépôts peu perméables dans la plaine d’inondation ou à des structures tridimensionnelles (3D) interconnectées. Six modèles analytiques ont été utilisés pour simuler le rabattement et ses dérivés pendant un essai de pompage transitoire de trois jours. Le diagnostic réalisé sur le puits de pompage a montré que quatre modèles conceptuels, aux comportements hydrodynamiques très contrastés, peuvent correspondre au diagnostic. L’utilisation conjointe des données des puits de pompage et des puits d’observation a permis d’identifier le seul modèle approprié - un modèle à double perméabilité caractérisant un aquifère multicouche. Le modèle conceptuel correspond aux observations géologiques dans les forages et corrobore la stratigraphie séquentielle fluviale de la plaine alluviale. L’essai de pompage utilisé ici est un outil permettant d’explorer l’architecture 3D du réservoir fluvial à l’échelle de la séquence de dépôt dans la plaine d’inondation.; O estudo dos recursos hídricos subterrâneos utilizando dados de teste de vazão é comumente resolvido por meio da equação de Theis, o que permite que os parâmetros hidráulicos dos aquíferos porosos, como a transmissividade e o coeficiente de armazenamento, possam ser estimados a partir do rebaixamento do nível d’água. Porém, o ajuste dos dados pode falhar, indicando apenas que o aquífero bombeado apresenta uma estrutura complexa. Aqui, um gráfico de diagnóstico da derivada logarítmica do rebaixamento é usado para identificar o regime de fluxo e, portanto, a heterogeneidade do aquífero, levando a modelos conceituais plausíveis. Ainda assim, o gráfico de diagnóstico é insuficiente e deve ser acompanhado de mais modelos, devido ao sinal não único da derivada logarítmica do rebaixamento. A abordagem proposta foi utilizada em uma planície aluvial na França, conhecida por ser complexa, pois os processos de deposição mudam com o tempo, o que resulta em um cinturão de canais limitados por depósitos de baixa permeabilidade na planície de inundação ou por estruturas tridimensionais (3D) interconectadas. Seis modelos analíticos foram utilizados para simular o rebaixamento, e suas funções derivadas, durante um teste de bombeamento transiente de 3 dias. O diagnóstico simulado para o poço de bombeamento mostrou que quatro modelos conceituais, cada um com comportamento hidrodinâmico contrastante, podem corresponder ao diagnóstico. A junção dos dados do poço de bombeamento e dos dados de poço de observação permitiu a identificação do único modelo apropriado – um modelo de permeabilidade dual caracterizando um aquífero multicamadas. O modelo conceitual coincide com as observações da geologia dos poços e corrobora com a sequência estratigráfica fluvial da planície aluvial. O teste de bombeamento utilizado é uma ferramenta para explorar a arquitetura 3D do reservatório fluvial na escala da sequência deposicional da planície de inundação.; 利用抽水试验数据研究地下水资源通常采用 Theis 解, 它可以根据水位降深估算多孔介质含水层的水力参数, 如传导系数和蓄水系数。然而, 数据拟合可能会失败, 并且只能表明抽水含水层具有复杂的结构。在这里, 对数导数降深的诊断图用于识别流态, 从而识别含水层的异质性, 由此可形成合理的概念模型。然而, 由于降深对数导数信号的非唯一性, 仅用诊断图是不够的, 必须再建模分析。所提出的方法应用于法国众所周知复杂的冲积平原, 由于沉积过程随时间变化, 导致河岸带受到漫滩中低渗透性沉积物或三维 (3D) 互连结构的影响。在为期三天的非稳定抽水测试期间, 六个解析解模型用于模拟降深及其导数。抽水井上进行的诊断表明, 具有高度异质的水动力行为的四个概念模型可能与诊断相符。抽水井和观测井数据的联合使用可确定唯一合适的模型, 即表征多层含水层的双渗透模型。概念模型与钻孔中的地质观察相匹配, 并证实了冲积平原的河流相地层。此处使用的抽水试验是在漫滩沉积相尺度上探索冲积相储层 3D 结构的工具。
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- 2021
22. Uses and perceptions of medications among French older adults: results from the 2020 French Health Barometer survey
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Anh Thi-Quynh Tran, Noémie Soullier, Joël Ankri, Marie Herr, Laure Carcaillon-Bentata, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Hôpital Raymond Poincaré [Garches], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National de la Santé et de la Recherche Médicale, Inserm, The authors are grateful to the French Health Barometer team of the French National Public Health Agency for their work and support. They also thank Solène Drusch, PhD Candidate at Université Paris-Saclay, UVSQ, INSERM, CESP, Anti-infective evasion and pharmacoepidemiology, for reviewing preliminary version of this paper., This study received no external funding. The French Health Barometer survey was funded by the French National Public Health Agency., and HAL UVSQ, Équipe
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[SDV]Life Sciences [q-bio] ,Self Medication ,Health survey ,Health Surveys ,[SDV] Life Sciences [q-bio] ,Cross-Sectional Studies ,Older adults ,Polypharmacy ,Humans ,Perceptions ,Female ,France ,Self-medication ,Geriatrics and Gerontology ,Aged - Abstract
Background There are few studies reporting on self-medication, perceptions or difficulties older adults have with their medications. This study aimed to describe the uses and the perceptions of medications among older adults in France and to identify patient groups based on that information. Methods We used data from the 2020 ‘French Health Barometer’ – a nationally-representative cross-sectional survey. We assessed polypharmacy (five or more medications), self-medication, and patient perceptions of medications. Robust Poisson regression was used to investigate socio-demographic and health-related factors associated with the outcomes. Latent class analysis was used to identify patient groups classified by the use and the perceptions of medications. Factors associated with group assignment were investigated by multinomial logistic regression. All analyses were weighted. Results The study sample comprised 1,623 respondents aged 70–85 years. Polypharmacy and self-medication were reported in 23.5 and 48.7% of the older population, respectively. Polypharmacy was associated with increasing age, low education, and impaired health status. Self-medication was associated with female sex and high education. Among individuals taking at least 1 medication, 8.2% reported not to understand all their medications, and 9.7% having difficulty taking medications as prescribed. Among individuals taking at least 2 medications, 23.2% thought that they took too many medications. Three patient groups were identified: ‘Non-polypharmacy, positive perceptions’ (62.5%), ‘Polypharmacy, positive perceptions’ (28.0%), and ‘Negative perceptions’ (9.5%). Conclusions Polypharmacy and self-medication are common in French older adults. One segment of people reported negative perceptions of their medications regardless of their polypharmacy status. This underlines the difference between the objective and perceived measures of polypharmacy.
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- 2022
23. The association between objective vision impairment and mild cognitive impairment among older adults in low- and middle-income countries
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Hans Oh, Ai Koyanagi, Guillermo F. López-Sánchez, Jae Il Shin, Yvonne Barnett, Lee Smith, Pinar Soysal, Louis Jacob, Laurie T. Butler, Nicola Veronese, Shahina Pardhan, Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), National Institute on Aging, NIA: 08-CN-0020, OGHA 04034785, R01-AG034479, R21-AG034263, Y1-AG-1005, YA1323, This paper uses data from WHO?s Study on Global Ageing and Adult Health (SAGE). SAGE is supported by the U.S. National Institute on Aging through Interagency Agreements OGHA 04034785, YA1323?08-CN-0020, Y1-AG-1005?01 and through research grants R01-AG034479 and R21-AG034263., Smith, L., Shin, J.I., Jacob, L., López-Sánchez, G.F., Oh, H., Barnett, Y., Pardhan, S., Butler, L., Soysal, P., Veronese, N., Koyanagi, A., and SOYSAL, PINAR
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Male ,Gerontology ,China ,Aging ,medicine.medical_specialty ,Visual acuity ,genetic structures ,Epidemiology ,[SDV]Life Sciences [q-bio] ,Visual impairment ,Vision impairment ,Logistic regression ,Odds ,03 medical and health sciences ,0302 clinical medicine ,Prevalence ,Humans ,Medicine ,Dementia ,Cognitive Dysfunction ,030212 general & internal medicine ,Association (psychology) ,Developing Countries ,Aged ,Low- and middle-income countries ,business.industry ,Mild cognitive impairment ,medicine.disease ,eye diseases ,Smith L., Shin J. I. , Jacob L., López-Sánchez G. F. , Oh H., Barnett Y., Pardhan S., Butler L., Soysal P., Veronese N., et al., -The association between objective vision impairment and mild cognitive impairment among older adults in low- and middle-income countries.-, Aging clinical and experimental research, 2021 ,Vision impairment, Mild cognitive impairment, Older adults, Low- and middle-income countries, Epidemiology ,Cross-Sectional Studies ,Ageing ,Older adults ,Female ,Geriatrics and Gerontology ,medicine.symptom ,business ,030217 neurology & neurosurgery - Abstract
Aim: The association between visual impairment and mild cognitive impairment (MCI) has not been investigated to date. Thus, we assessed this association among older adults from six low- and middle-income countries (LMICs) (China, India, Ghana, Mexico, Russia, and South Africa) using nationally representative datasets. Methods: Cross-sectional, community-based data from the WHO Study on global AGEing and adult health (SAGE) were analyzed. Visual acuity was measured using the tumbling ElogMAR chart, and vision impairment (at distance and near) was defined as visual acuity worse than 6/18 (0.48 logMAR) in the better-seeing eye. The definition of MCI was based on the National Institute on Aging-Alzheimer’s Association criteria. Multivariable logistic regression was conducted. Results: Data on 32,715 individuals aged ≥ 50years [mean (SD) age 62.1 (15.6) years; 51.2% females] were analyzed. Compared to those without far or near vision impairment, those with near vision impairment but not far vision impairment (OR = 1.33; 95% CI = 1.16–1.52), and those with both far and near vision impairment (OR = 1.70; 95% CI = 1.27–2.29) had significantly higher odds for MCI. Only having far vision impairment was not significantly associated with MCI. Conclusions: Visual impairment is associated with increased odds for MCI among older adults in LMICs with the exception of far vision impairment only. Future longitudinal and intervention studies should examine causality and whether improvements in visual acuity, or early intervention, can reduce risk for MCI and ultimately, dementia. © 2021, The Author(s), under exclusive licence to Springer Nature Switzerland AG part of Springer Nature.
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- 2021
24. Bayesian optimization using deep Gaussian processes with applications to aerospace system design
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Nouredine Melab, El-Ghazali Talbi, Mathieu Balesdent, Loïc Brevault, Ali Hebbal, DTIS, ONERA, Université Paris Saclay [Palaiseau], ONERA-Université Paris-Saclay, Optimisation de grande taille et calcul large échelle (BONUS), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), 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), and This work is co-funded by ONERA-The French Aerospace Lab and Université de Lille, in the context of a joint PhD thesis. Discussions with Hugh Salimbeni and Zhenwen Dai were very helpful for this work, special thanks to them. The Experiments presented in this paper were carried out using the Grid’5000 testbed, supported by a scientific interest group hosted by Inria and including CNRS, RENATER and several Universities as well as other organizations (see https://www.grid5000.fr).
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Mathematical optimization ,021103 operations research ,Control and Optimization ,Optimization problem ,Covariance function ,Computer science ,Mechanical Engineering ,Bayesian optimization ,0211 other engineering and technologies ,Aerospace Engineering ,Context (language use) ,02 engineering and technology ,symbols.namesake ,Test case ,[STAT.ML]Statistics [stat]/Machine Learning [stat.ML] ,symbols ,Systems design ,[MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC] ,021108 energy ,Electrical and Electronic Engineering ,Representation (mathematics) ,Gaussian process ,ComputingMilieux_MISCELLANEOUS ,Software ,Civil and Structural Engineering - Abstract
Bayesian Optimization using Gaussian Processes is a popular approach to deal with optimization involving expensive black-box functions. However, because of the assumption on the stationarity of the covariance function defined in classic Gaussian Processes, this method may not be adapted for non-stationary functions involved in the optimization problem. To overcome this issue, Deep Gaussian Processes can be used as surrogate models instead of classic Gaussian Processes. This modeling technique increases the power of representation to capture the non-stationarity by considering a functional composition of stationary Gaussian Processes, providing a multiple layer structure. This paper investigates the application of Deep Gaussian Processes within Bayesian Optimization context. The specificities of this optimization method are discussed and highlighted with academic test cases. The performance of Bayesian Optimization with Deep Gaussian Processes is assessed on analytical test cases and aerospace design optimization problems and compared to the state-of-the-art stationary and non-stationary Bayesian Optimization approaches.
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- 2020
25. A general global-local modelling framework for the deterministic optimisation of composite structures
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Marco Picchi Scardaoni, Marco Montemurro, Institut de Mécanique et d'Ingénierie de Bordeaux (I2M), École Nationale Supérieure d'Arts et Métiers (ENSAM), Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Arts et Métiers Sciences et Technologies, HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), University of Pisa - Università di Pisa, and This paper presents part of the activities carried out within the research project PARSIFAL ('PrandtlPlane ARchitecture for the Sustainable Improvement of Future AirpLanes'), which has been funded by the European Union under the Horizon 2020 Research and Innovation Program (Grant Agreement n.723149)
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Mathematical optimization ,Control and Optimization ,Cantilever ,Local modelling approach ,Computer science ,0211 other engineering and technologies ,02 engineering and technology ,Marsaglia polar method ,Design strategy ,[SPI.MECA.SOLID]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Solid mechanics [physics.class-ph] ,01 natural sciences ,Polar method ,021105 building & construction ,Mécanique: Mécanique des structures [Sciences de l'ingénieur] ,0101 mathematics ,Anisotropy ,Composites ,Buckling ,Deterministic optimisation ,Global/local modelling approach ,Deterministic Optimisation ,Mécanique: Mécanique des solides [Sciences de l'ingénieur] ,Global ,Optimisation et contrôle [Mathématique] ,Computer Graphics and Computer-Aided Design ,Computer Science Applications ,Design for manufacturability ,010101 applied mathematics ,[SPI.MECA.STRU]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Structural mechanics [physics.class-ph] ,Control and Systems Engineering ,Macroscopic scale ,[MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC] ,Engineering design process ,Software - Abstract
International audience; This work deals with the multi-scale optimisation of composite structures by adopting a general global-local (GL) modelling strategy to assess the structure responses at different scales. The GL modelling approach is integrated into the multi-scale two-level optimisation strategy (MS2LOS) for composite structures. The resulting design strategy is, thus, called GL-MS2LOS and aims at proposing a very general formulation of the design problem, without introducing simplifying hypotheses on the laminate stack and by considering, as design variables, the full set of geometric and mechanical parameters defining the behaviour of the composite structure at each pertinent scale. By employing a GL modelling approach, most of the limitations of well-established design strategies, based on analytical or semi-empirical models, are overcome. The GL-MS2LOS makes use of the polar formalism to describe the anisotropy of the composite at the macroscopic scale (where it is modelled as an equivalent homogeneous anisotropic plate). In this work, deterministic algorithms are exploited during the solution search phase. The challenge, when dealing with such a design problem, is to develop a suitable formulation and dedicated operators, to link global and local models physical responses and their gradients. Closed-form expressions of structural responses gradients are rigorously derived by taking into account for the coupling effects when passing from global to local models. The effectiveness of the GL-MS2LOS is proven on a meaningful benchmark: the least-weight design of a cantilever wing subject to different design requirements. Constraints include maximum allowable displacements, maximum allowable strains, blending, manufacturability requirements and buckling factor.; This work deals with the multi-scale optimisation of composite structures by adopting a general global-local (GL) modelling strategy to assess the structure responses at different scales. The GL modelling approach is integrated into the multi-scale two-level optimisation strategy (MS2LOS) for composite structures. The resulting design strategy is, thus, called GL-MS2LOS and aims at proposing a very general formulation of the design problem, without introducing simplifying hypotheses on the laminate stack and by considering, as design variables, the full set of geometric and mechanical parameters defining the behaviour of the composite structure at each pertinent scale. By employing a GL modelling approach, most of the limitations of well-established design strategies, based on analytical or semi-empirical models, are overcome. The GL-MS2LOS makes use of the polar formalism to describe the anisotropy of the composite at the macroscopic scale (where it is modelled as an equivalent homogeneous anisotropic plate). In this work, deterministic algorithms are exploited during the solution search phase. The challenge, when dealing with such a design problem, is to develop a suitable formulation and dedicated operators, to link global and local models physical responses and their gradients. Closed-form expressions of structural responses gradients are rigorously derived by taking into account for the coupling effects when passing from global to local models. The effectiveness of the GL-MS2LOS is proven on a meaningful benchmark: the least-weight design of a cantilever wing subject to different design requirements. Constraints include maximum allowable displacements, maximum allowable strains, blending, manufacturability requirements and buckling factor.
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- 2020
26. Production-based pollution versus deforestation: optimal policy with state-independent and-dependent environmental absorption efficiency restoration process
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Marc Leandri, Eugene Khmelnitsky, Fouad El Ouardighi, ESSEC Business School [Cergy-Pontoise], Tel Aviv University [Tel Aviv], Centre d'études sur la mondialisation, les conflits, les territoires et les vulnérabilités (Cemotev), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Tel Aviv University, TAU, and The authors acknowledge helpful comments from one anonymous referee. This research was supported by ESSEC Business School (France) and Tel Aviv University (Israel). The first author dedicates this paper to the memory of Mohamed El Houari, a wonderful mentor and friend.
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Pollution ,Natural resource economics ,Process (engineering) ,media_common.quotation_subject ,0211 other engineering and technologies ,General Decision Sciences ,Social Welfare ,02 engineering and technology ,Management Science and Operations Research ,History dependence ,Deforestation ,11. Sustainability ,Restoration process ,Production (economics) ,10. No inequality ,Environmental absorption efficiency ,media_common ,021103 operations research ,[INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO] ,15. Life on land ,13. Climate action ,Sustainability ,Environmental science ,Optimal pollution ,Absorption efficiency - Abstract
International audience; An important yet largely unexamined issue is how the interaction between deforestation and pollution affects economic and environmental sustainability.This article seeks to bridge the gap by introducing a dynamic model of pollution accumulation where polluting emissions can be mitigated and the absorption efficiency of pollution sinks can be restored. We assume that emissions are due to a production activity, and we include deforestation both as an additional source of emissions and as a cause of the exhaustion of environmental absorption efficiency. To account for the fact that the switching of natural sinks to a pollution source can be either possible, and in such a case even reversible, or impossible, we consider that restoration efforts can be either independent from or dependent on environmental absorption efficiency, i.e., state-independent versus state-dependent restoration efforts. We determine (i) whether production or deforestation is the most detrimental from environmental and social welfare perspectives, and (ii) how state-dependent restoration process affects pollution accumulation and deforestation policies and the related environmental and social welfare consequences.
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- 2020
27. Single-molecule localization microscopy
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Markus Sauer, Florian Schueder, Melike Lakadamyali, Gerti Beliu, Melina Theoni Gyparaki, Suliana Manley, Ralf Jungmann, Juliette Griffié, Mickaël Lelek, Christophe Zimmer, Imagerie et Modélisation - Imaging and Modeling, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, University of Würzburg = Universität Würzburg, Ludwig Maximilian University [Munich] (LMU), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), C.Z. acknowledges funding by Institut Pasteur, Fondation pour la Recherche Médicale (grant DEQ 20150331762), Région Ile de France, Agence Nationale de la Recherche and Investissement d’Avenir grant ANR-16-CONV-0005. M.La. acknowledges funding from the National Institutes of Health/National Institutes of General Medical Sciences (NIH/NIGMS) under grant RO1 GM133842-01. G.B. and M.S. acknowledge funding by the German Research Foundation (DFG) (SA829/19-1) and the European Regional Development Fund (EFRE project ‘Center for Personalized Molecular Immunotherapy’). F.S. and R.J. acknowledge support by the DFG through SFB1032 (project A11) and the Max Planck Society. J.G. and S.M. acknowledge funding by the European Union’s H2020 programme under the Marie Skłodowska-Curie grant BALTIC (to J.G.) and ERC Piko (to S.M.)., The authors apologize to the authors of numerous papers that could not be cited owing to limited space. M.Le. and C.Z. thank B. Lelandais for excellent comments on the manuscript and M. Singh for acquiring the image shown in Fig. 3b., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania [Philadelphia], Max Planck Institute of Biochemistry (MPIB), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)
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Single molecule localization ,light-microscopy ,Computer science ,business.industry ,General Medicine ,Article ,General Biochemistry, Genetics and Molecular Biology ,optical reconstruction microscopy ,diffraction-limit ,Fluorescent labelling ,3-dimensional superresolution ,live-cell ,correlative superresolution fluorescence ,Microscopy ,Time course ,Image acquisition ,colocalization analysis ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,Computer vision ,Artificial intelligence ,business ,living cells ,intramolecular spirocyclization ,Image resolution ,electron-microscopy - Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM. This Primer explains the central concepts of single-molecule localization microscopy (SMLM) before discussing experimental considerations regarding fluorophores, optics and data acquisition, processing and analysis. The Primer further describes recent high-impact discoveries made by SMLM techniques and concludes by discussing emerging methodologies.
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- 2021
28. Accounting for competition in multi-environment tree genetic evaluations: a case study with hybrid pines
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Nuno Borralho, Eduardo P. Cappa, Ector Belaber, Maria Elena Gauchat, Cristian Damián Schoffen, Facundo Muñoz, Leopoldo Sanchez, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), RAIZ – Forestry & Paper Research Institut, Instituto Superior Técnico, Universidade Técnica de Lisboa, Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This study was funded by the National Institute of Agricultural Technology (INTA) (grant numbers PNFOR-01104062, MSNES-1242204/5). E.P.C.’s research was partially supported by the National Agency for the Promotion of Science and Technology of Argentina (ANPCYT, PICT-2016 1048). F.M.’s research is partially supported by research grant MTM2016-77501-P from the State Research Agency of the Spanish Ministry of Science, Innovation and Universities jointly with the European Regional Development Fund, FEDER.
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Additive and competition genotype–environment interaction ,0106 biological sciences ,Mixed model ,[SDV]Life Sciences [q-bio] ,media_common.quotation_subject ,Accounting ,Tree breeding ,010603 evolutionary biology ,01 natural sciences ,Genetic correlation ,Competition (biology) ,Competition model ,Genetic variation ,Gene–environment interaction ,media_common ,Mathematics ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,Ecology ,business.industry ,Diameter at breast height ,Forestry ,15. Life on land ,Total heritable variance ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,business ,010606 plant biology & botany - Abstract
International audience; Key message: A novel multi-environment competition individual-tree mixed model resulted in better fit, and greater individual narrow- and broad-sense heritabilities than the model without competition, notably for traits showing competition. In multi-environment tests, the proposed model would allow tree breeders to select genotypes with the best performance in both additive direct and competition breeding values, increasing forest productivity. Context: Genetic merit of trees is known to be affected and interact with local competition effects as well as changes across environmental conditions. Recent studies showed that competition genetic effects can affect the genetic variance and bias the tree breeding values, and its covariance with direct breeding values has been variable across traits. Aims: The present paper extends a mixed-model methodology to the problem of accounting for competition in a multi-environment set of forest genetic trials and exploring its impact on genetic variances as well as the multi-environment genetic correlation. Methods: The proposed model is illustrated using data from two full-sib trials of Pinus elliottii var. elliottii × Pinus caribaea var. hondurensis F1. Dispersion parameters and (co)variance of total breeding values were estimated for diameter at breast height, total tree height, and stem straightness at age 10. Results: For traits showing competition effects (diameter at breast height and total tree height), the proposed multi-environment competition model gave better fit than the simpler model. Accounting for competition increased the direct additive variance, reduced the residual variances, and did not change significantly the across-site additive genetic correlation. However, for diameter at breast height, top 5% best genetic rankings showed differences. Conclusion: When traits are strongly affected by inter-tree competition, the use of the proposed model in multi-environment analyses can efficiently identify the phenomenon with general benefits in the fitting of genetic components and open the door to select on the basis of competitiveness.
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- 2021
29. Combining probability with qualitative degree-of-certainty metrics in assessment
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Richard Bradley, Brian Hill, Casey Helgeson, Groupement de Recherche et d'Etudes en Gestion à HEC (GREGH), Ecole des Hautes Etudes Commerciales (HEC Paris)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), Department of Archaeology, University of Reading (UOR), HEC Research Paper Series, and Hill, Brian
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Atmospheric Science ,010504 meteorology & atmospheric sciences ,Operations research ,Computer science ,[SDE.MCG]Environmental Sciences/Global Changes ,media_common.quotation_subject ,Climate change ,B Philosophy (General) ,050905 science studies ,01 natural sciences ,[SHS.PHIL] Humanities and Social Sciences/Philosophy ,Consistency (database systems) ,Degree of certainty ,[SHS.ECO] Humanities and Social Sciences/Economics and Finance ,0105 earth and related environmental sciences ,media_common ,Global and Planetary Change ,business.industry ,05 social sciences ,[SHS.PHIL]Humanities and Social Sciences/Philosophy ,Usability ,Ambiguity ,Certainty ,[SHS.ECO]Humanities and Social Sciences/Economics and Finance ,[SDE.MCG] Environmental Sciences/Global Changes ,climate change ,uncertainty reporting ,[SHS.GESTION]Humanities and Social Sciences/Business administration ,confidence ,0509 other social sciences ,business ,GE Environmental Sciences ,Decision analysis - Abstract
International audience; Reports of the Intergovernmental Panel on Climate Change (IPCC) employ an evolving framework of calibrated language for assessing and communicating degrees of certainty in findings. A persistent challenge for this framework has been ambiguity in the relationship between multiple degree-of-certainty metrics. We aim to clarify the relationship between the likelihood and confidence metrics used in the Fifth Assessment Report (2013), with benefits for mathematical consistency among multiple findings and for usability in downstream modeling and decision analysis. We discuss how our proposal meshes with current and proposed practice in IPCC uncertainty assessment.
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- 2018
30. Energy-efficient joint video encoding and transmission framework for WVSN
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Youssef Fakhri, Patrick Corlay, Driss Aboutajdine, François-Xavier Coudoux, Othmane Alaoui-Fdili, Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Laboratoire de Recherche en Informatique et Télécommunications [Rabat] (GSCM-LRIT), University of Mohammed V, COMmunications NUMériques - IEMN (COMNUM - IEMN), Institut d’Électronique, de Microélectronique et de Nanotechnologie - Département Opto-Acousto-Électronique - UMR 8520 (IEMN-DOAE), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France)-Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-INSA Institut National des Sciences Appliquées Hauts-de-France (INSA Hauts-De-France), Faculté des Sciences [Kenitra], Université Ibn Tofaïl (UIT), Université Mohammed V de Rabat [Agdal] (UM5), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), and Acknowledgements This research was supported by the excellence fellowships program of the National Center for Scientific and Technical Research (CNRST) of Morocco (G01/003) and the Franco-Moroccan cooperation program in STICs for the research project 'RECIF'. The authors would also like to thank the editorial office Christian Malan, the editor-in-chief, the guest editors as well as the anonymous reviewers for their efforts and valuable comments and suggestions that have led to improvements in this paper.
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Computer Networks and Communications ,Computer science ,Real-time computing ,02 engineering and technology ,Video quality ,[INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI] ,[INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI] ,[SPI]Engineering Sciences [physics] ,Packet loss ,Video encoding ,Region of interest ,0202 electrical engineering, electronic engineering, information engineering ,Media Technology ,[INFO]Computer Science [cs] ,Block-matching algorithm ,"Energy-efficiency in WVSN" ,business.industry ,020206 networking & telecommunications ,Scalable Video Coding ,[SPI.TRON]Engineering Sciences [physics]/Electronics ,"Video distortion prediction" ,Rate–distortion optimization ,Transmission (telecommunications) ,Hardware and Architecture ,"Cross-layer design" ,020201 artificial intelligence & image processing ,"Energy consumption prediction" ,business ,[SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing ,Wireless sensor network ,Encoder ,"Energy-efficient reliable routing" ,Software ,Computer network - Abstract
JIF=2.101; International audience; In this paper, we propose an energy-efficient joint video encoding and transmission framework for network lifetime extension, under an end-to-end video quality constraint in the Wireless Video Sensor Networks (WVSN). This framework integrates an energy-efficient and adaptive intra-only video encoding scheme based on the H.264/AVC standard, that outputs two service differentiated macroblocks categories, namely the Region Of Interest and the Background. Empirical models describing the physical behavior of the measured energies and distortions, during the video encoding and transmission phases, are derived. These models enable the video source node to dynamically adapt its video encoder's configuration in order to meet the desired quality, while extending the network lifetime. An energy-efficient and reliable multipath multi-priority routing protocol is proposed to route the encoded streams to the sink, while considering the remaining energy, the congestion level as well as the packet loss rates of the intermediate nodes. Moreover, this protocol interacts with the application layer in order to bypass congestion situations and continuously feed it with current statistics. Through extensive numerical simulations, we demonstrate that the proposed framework does not only extend the video sensor lifetime by 54%, but it also performs significant end-to-end video quality enhancement of 35% in terms of Mean Squared Error (MSE) measurement.
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- 2017
31. Randomised, double-blind, placebo-controlled clinical trial for evaluating the efficacy of intracoronary injection of autologous bone marrow mononuclear cells in the improvement of the ventricular function in patients with idiopathic dilated myocardiopathy: a study protocol
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Miguel Romero, José Suárez-de-Lezo, Concha Herrera, Manuel Pan, José López-Aguilera, Flor Baeza-Garzón, Francisco Javier Hidalgo-Lesmes, Olga Fernández-López, Juliana Martínez-Atienza, Eva Cebrián, Vanesa Martín-Palanco, Rosario Jiménez-Moreno, Rosario Gutiérrez-Fernández, Sonia Nogueras, Maria Dolores Carmona, Soledad Ojeda, Natividad Cuende, Rosario Mata, [Romero,M, Suárez-de-Lezo, Pan,M, López-Aguilera,J, Suárez-de-Lezo Jr,J, Baeza-Garzón,F, Hidalgo-Lesmes,FJ, Cebrián,E, Ojeda,S] Cardiology Unit, Reina Sofía University Hospital, Córdoba, Spain. [Herrera,C, Martín-Palanco,V, Jiménez-Moreno,R, Gutiérrez-Fernández,R, Nogueras,S, Carmona,MD] Cell Production Unit, Reina Sofía University Hospital, Córdoba, Spain. [Fernández-López,O, Martínez-Atienza,J, Cuende,N, Mata,R] Andalusian Initiative for Advanced Therapies, Andalusian Public Foundation Progress and Health, Seville, Spain., and This paper presents an investigator-driven Clinical trial partially funded by research grant provided by the Regional Ministry of Health of Andalusia (Grant Reference Number salud-201600073587-tra).
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Male ,lcsh:Diseases of the circulatory (Cardiovascular) system ,Time Factors ,Ensayo clínico controlado aleatorio ,030204 cardiovascular system & hematology ,Cell therapy ,Ventricular Function, Left ,law.invention ,Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings] ,Study Protocol ,Cardiomiopatía dilatada ,0302 clinical medicine ,Randomized controlled trial ,law ,Dilated myocardiopathy ,Multicenter Studies as Topic ,030212 general & internal medicine ,Myocardial infarction ,Diseases::Cardiovascular Diseases::Heart Diseases::Cardiomyopathies::Cardiomyopathy, Dilated [Medical Subject Headings] ,Bone Marrow Transplantation ,Randomized Controlled Trials as Topic ,Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Evaluation Studies as Topic::Clinical Trials as Topic::Controlled Clinical Trials as Topic::Randomized Controlled Trials as Topic [Medical Subject Headings] ,Diseases::Cardiovascular Diseases::Vascular Diseases::Myocardial Ischemia::Myocardial Infarction [Medical Subject Headings] ,Ejection fraction ,Middle Aged ,Treatment Outcome ,Disciplines and Occupations::Natural Science Disciplines::Science::Research::Biomedical Research [Medical Subject Headings] ,Female ,Cardiology and Cardiovascular Medicine ,Adult ,Cardiomyopathy, Dilated ,medicine.medical_specialty ,Information Science::Information Science::Communications Media::Publications [Medical Subject Headings] ,Adolescent ,Cell- and tissue-based therapy ,Células de la médula ósea ,Bone Marrow Cells ,Placebo ,Transplantation, Autologous ,Young Adult ,03 medical and health sciences ,Clinical Trials, Phase II as Topic ,Double-Blind Method ,Tratamiento basado en trasplante de células y tejidos ,Internal medicine ,medicine ,Humans ,Analytical, Diagnostic and Therapeutic Techniques and Equipment::Therapeutics::Biological Therapy::Cell- and Tissue-Based Therapy [Medical Subject Headings] ,Aged ,Angiology ,Anatomy::Cells::Bone Marrow Cells [Medical Subject Headings] ,business.industry ,Consolidated Standards of Reporting Trials ,Recovery of Function ,medicine.disease ,Interim analysis ,Clinical trial ,lcsh:RC666-701 ,Spain ,Bone marrow mononuclear cells ,business - Abstract
Cellular therapies have been increasingly applied to diverse human diseases. Intracoronary infusion of bone marrow-derived mononuclear cells (BMMNC) has demonstrated to improve ventricular function after acute myocardial infarction. However, less information is available about the role of BMMNC therapy for the treatment of dilated myocardiopathies (DCs) of non-ischemic origin. This article presents the methodological description of a study aimed at investigating the efficacy of intracoronary injection of autologous BMMNCs in the improvement of the ventricular function of patients with DC. This randomised, placebo-controlled, double-blinded phase IIb clinical trial compares the improvement on ventricular function (measured by the changes on the ejection fraction) of patients receiving the conventional treatment for DC in combination with a single dose of an intracoronary infusion of BMMNCs, with the functional recovery of patients receiving placebo plus conventional treatment. Patients assigned to both treatment groups are monitored for 24 months. This clinical trial is powered enough to detect a change in Left Ventricular Ejection Fraction (LVEF) equal to or greater than 9%, although an interim analysis is planned to re-calculate sample size. The study protocol was approved by the Andalusian Coordinating Ethics Committee for Biomedical Research (Comite Coordinador de Etica en Investigacion Biomedica de Andalucia), the Spanish Medicines and Medical Devices Agency (Agencia Espanola de Medicamentos y Productos Sanitarios), and is registered at the EU Clinical Trials Register (EudraCT: 2013–002015-98). The publication of the trial results in scientific journals will be performed in accordance with the applicable regulations and guidelines to clinical trials. ClinicalTrials.gov Identifier NCT02033278 (First Posted January 10, 2014): https://clinicaltrials.gov/ct2/show/NCT02033278 ; EudraCT number: 2013–002015-98, EU CT Register: https://www.clinicaltrialsregister.eu/ctr-search/search?query=2013-002015-98 . Trial results will also be published according to the CONSORT statement at conferences and reported peer-reviewed journals.
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- 2019
32. Films based on crosslinked TEMPO-oxidized cellulose and predictive analysis via machine learning
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Jouni Paltakari, Merve Özkan, Alp Karakoç, Orlando J. Rojas, Maryam Borghei, Paper Converting and Packaging, Department of Bioproducts and Biosystems, Aalto-yliopisto, and Aalto University
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Materials science ,Oxidized cellulose ,lcsh:Medicine ,02 engineering and technology ,010402 general chemistry ,Machine learning ,computer.software_genre ,01 natural sciences ,Polyvinyl alcohol ,Article ,chemistry.chemical_compound ,Transmittance ,Surface roughness ,Cellulose ,lcsh:Science ,Multidisciplinary ,business.industry ,lcsh:R ,021001 nanoscience & nanotechnology ,Flexible electronics ,0104 chemical sciences ,chemistry ,Nanofiber ,lcsh:Q ,Wetting ,Artificial intelligence ,0210 nano-technology ,business ,computer - Abstract
We systematically investigated the effect of film-forming polyvinyl alcohol and crosslinkers, glyoxal and ammonium zirconium carbonate, on the optical and surface properties of films produced from TEMPO-oxidized cellulose nanofibers (TOCNFs). In this regard, UV-light transmittance, surface roughness and wetting behavior of the films were assessed. Optimization was carried out as a function of film composition following the “random forest” machine learning algorithm for regression analysis. As a result, the design of tailor-made TOCNF-based films can be achieved with reduced experimental expenditure. We envision this approach to be useful in facilitating adoption of TOCNF for the design of emerging flexible electronics, and related platforms.
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- 2018
33. Forests and global change: what can genetics contribute to the major forest management and policy challenges of the twenty-first century?
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Arantxa Prada, Joan Cottrell, Santiago C. González-Martínez, Bart Muys, Lennart Ackzell, Ricardo Alía, Bruno Fady, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forest Research, Northern Research Station, The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Federation of Swedish Family Forest Owners, Partenaires INRAE, Centro de Investigacion Forestal (INIA-CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), European Forest Institute (EFI), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), General Directorate for Environment, Centro de Tecnologías Físicas [Universitat Politècnica de València], Universitat Politècnica de València (UPV), This paper stems from the work of the stakeholder panel of the EU supported EraNet BiodivERsA project 'Linking genetic variability with ecological responses to environmental changes: forest trees as model systems (LinkTree)' whose financial help is acknowledged. BF wishes to thank the French 'Commission des ressources genetiques forestieres (http://agriculture.gouv.fr/conservation-des-ressources)' (CRGF) and EUFORGEN (http://www.euforgen.org/) for insightful discussions. SCG-M acknowledges receipt of a Senior Marie Curie Intra European Fellowship within the 7th European Community Framework Programme (PIEF-GA-2012-328146) at the Department of Ecology and Evolution, University of Lausanne, Switzerland, European Project: 328146,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IEF,SEX-NGS(2013), Institut National de la Recherche Agronomique (INRA), Forest Research, Northern Research Station, European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI), and Université Catholique de Louvain = Catholic University of Louvain (UCL)
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0106 biological sciences ,Environmental change ,[SDE.MCG]Environmental Sciences/Global Changes ,media_common.quotation_subject ,Forest management ,Climate change ,Context (language use) ,adaptation ,010603 evolutionary biology ,01 natural sciences ,Adaptability ,Ecosystem services ,assisted migration ,Resilience (network) ,media_common ,2. Zero hunger ,Genetics ,Global and Planetary Change ,business.industry ,Environmental resource management ,genetic diversity ,15. Life on land ,[SDE.ES]Environmental Sciences/Environmental and Society ,sustainable forestry ,climate change ,gene conservation ,13. Climate action ,Sustainability ,Business ,010606 plant biology & botany - Abstract
International audience; The conservation and sustainable use of forests in the twenty-first century pose huge challenges for forest management and policy. Society demands that forests provide a wide range of ecosystem services, from timber products, raw materials and renewable energy to sociocultural amenities and habitats for nature conservation. Innovative management and policy approaches need to be developed to meet these often-conflicting demands in a context of environmental change of uncertain magnitude and scale. Genetic diversity is a key component of resilience and adaptability. Overall, forest tree populations are genetically very diverse, conferring them an enormous potential for genetic adaptation via the processes of gene flow and natural selection. Here, we review the main challenges facing our forests in the coming century and focus on how recent progress in genetics can contribute to the development of appropriate practical actions that forest managers and policy makers can adopt to promote forest resilience to climate change. Emerging knowledge will inform and clarify current controversies relating to the choice of appropriate genetic resources for planting, the effect of silvicultural systems and stand tending on adaptive potential and the best ways to harness genetic diversity in breeding and conservation programs. Gaps in our knowledge remain, and we identify where additional information is needed (e.g., the adaptive value of peripheral populations or the genetic determinism of key adaptive traits) and the types of studies that are required to provide this key understanding.
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- 2015
34. Natural Scales in Geographical Patterns
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Telmo Menezes, Camille Roth, Centre Marc Bloch (CMB), Ministère de l'Europe et des Affaires étrangères (MEAE)-Bundesministerium für Bildung und Forschung-Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)-Centre National de la Recherche Scientifique (CNRS), Médialab (Sciences Po) (Médialab), Sciences Po (Sciences Po), Centre National de la Recherche Scientifique (CNRS), This paper has been partially supported by grants 'Phantomgrenzen' and 'Algodiv' (ANR-15-CE38-0001), funded respectively by the BMBF (German Federal Ministry for Education and Research) and by the ANR (French National Agency of Research)., and ANR-15-CE38-0001,ALGODIV,Algodiv: Recommandation algorithmique et diversité des informations du web(2015)
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FOS: Computer and information sciences ,0301 basic medicine ,Physics - Physics and Society ,FOS: Physical sciences ,Distribution (economics) ,computer science ,Network science ,Physics and Society (physics.soc-ph) ,Space (commercial competition) ,human movement ,Article ,[INFO.INFO-SI]Computer Science [cs]/Social and Information Networks [cs.SI] ,Natural (archaeology) ,geographical networks ,03 medical and health sciences ,network science ,community detection ,applied mathematics ,91D20 ,91D30 ,Social and Information Networks (cs.SI) ,[SHS.STAT]Humanities and Social Sciences/Methods and statistics ,Multidisciplinary ,business.industry ,Orders of magnitude (acceleration) ,Computer Science - Social and Information Networks ,[SHS.GEO]Humanities and Social Sciences/Geography ,Partition (database) ,Discontinuity (linguistics) ,030104 developmental biology ,Geography ,business ,Scale (map) ,Cartography - Abstract
Human mobility is known to be distributed across several orders of magnitude of physical distances, which makes it generally difficult to endogenously find or define typical and meaningful scales. Relevant analyses, from movements to geographical partitions, seem to be relative to some ad-hoc scale, or no scale at all. Relying on geotagged data collected from photo-sharing social media, we apply community detection to movement networks constrained by increasing percentiles of the distance distribution. Using a simple parameter-free discontinuity detection algorithm, we discover clear phase transitions in the community partition space. The detection of these phases constitutes the first objective method of characterising endogenous, natural scales of human movement. Our study covers nine regions, ranging from cities to countries of various sizes and a transnational area. For all regions, the number of natural scales is remarkably low (2 or 3). Further, our results hint at scale-related behaviours rather than scale-related users. The partitions of the natural scales allow us to draw discrete multi-scale geographical boundaries, potentially capable of providing key insights in fields such as epidemiology or cultural contagion where the introduction of spatial boundaries is pivotal.
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- 2017
35. Derandomizing random walks in undirected graphs using locally fair exploration strategies
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Ralf Klasing, Adrian Kosowski, Colin Cooper, David Ilcinkas, Department of Computer Science (DCS), King‘s College London, Algorithmics for computationally intensive applications over wide scale distributed platforms (CEPAGE), Université Sciences et Technologies - Bordeaux 1-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Algorithmique, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), See paper for details., ANR-07-BLAN-0322,ALADDIN,Algorithm Design and Analysis for Implicitly and Incompletely Defined Interaction Networks(2007), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Department of Algorithms and Systems Modelling [ETI GUT] (Gdansk University of Technology), Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] (ETI), Gdańsk University of Technology (GUT)-Gdańsk University of Technology (GUT), ANR-05-MMSA-0006,ALPAGE,ALgorithmique des Plates-formes A Grande Echelle(2005), Université Sciences et Technologies - Bordeaux 1 (UB)-Inria Bordeaux - Sud-Ouest, 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), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
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Mathematical optimization ,Computer Networks and Communications ,Computer science ,[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS] ,Comparability graph ,Random walk ,0102 computer and information sciences ,02 engineering and technology ,01 natural sciences ,law.invention ,Theoretical Computer Science ,Combinatorics ,Indifference graph ,Graph exploration ,law ,Graph power ,Line graph ,Random regular graph ,0202 electrical engineering, electronic engineering, information engineering ,Pancyclic graph ,Mathematics ,Discrete mathematics ,Block graph ,graph exploration : Propp machine ,Directed graph ,Feedback arc set ,Computational Theory and Mathematics ,010201 computation theory & mathematics ,Hardware and Architecture ,Robbins' theorem ,Graph (abstract data type) ,020201 artificial intelligence & image processing ,[INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC] ,MathematicsofComputing_DISCRETEMATHEMATICS - Abstract
International audience; We consider the problem of exploring an anonymous undirected graph using an oblivious robot. The studied exploration strategies are designed so that the next edge in the robot's walk is chosen using only local information, and so that some local equity (fairness) criterion is satisfied for the adjacent undirected edges. Such strategies can be seen as an attempt to derandomize random walks, and are natural counterparts for undirected graphs of the rotor-router model for symmetric directed graphs. The first of the studied strategies, known as Oldest-First (OF), always chooses the neighboring edge for which the most time has elapsed since its last traversal. Unlike in the case of symmetric directed graphs, we show that such a strategy in some cases leads to exponential cover time. We then consider another strategy called Least-Used-First (LUF) which always uses adjacent edges which have been traversed the smallest number of times. We show that any Least-Used-First exploration covers a graph G=(V,E) of diameter diam within time O(diam|E|), and in the long run traverses all edges of G with the same frequency.
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- 2011
36. SSR-based analysis of clonality, spatial genetic structure and introgression from the Lombardy poplar into a natural population of Populus nigra L. along the Loire River
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Marc Villar, Catherine Bastien, Romain Valade, Sophie Arnaud-Haond, José-Luis Almeida, Nicolas Chenault, Arnaud Dowkiw, Mary Juteau, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique et Biomasse Forestières Orléans (GBFOR), The authors thank Catherine Pasquier from INRA Orleans, UR 0272 USS, for crucial field and laboratory assistance with the geographic information systems, Vanina Guerin and Veronique Jorge from INRA Orleans, UR 0588 UAGPF, for their help and advice on SSR genotyping, Patrick Poursat and the INRA Orleans UE 0995 GBFOR for assistance with fieldwork, and special thanks to Frederic Millier for the increment core sample collection and preparation, Francoise Laurans and Alain Moreau from INRA Orleans, UR 0588 UAGPF, for their meticulous help with the core analysis, Jean Dufour from INRA Orleans, UR 0588 UAGPF, and Michel Chantereau, Administrator of the Saint-Mesmin French Natural Reserve, for floristic inventories, and and two anonymous reviewers who made very useful comments about this work and the resulting paper. Nicolas Chenault was supported by a PhD grant co-financed by INRA and Conseil Regional de la Region Centre, France. This study was carried out with financial support from INRA (programme ECOGER, projet INTERPOPGER).
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genetics and heredity ,0106 biological sciences ,Introgression ,Vegetative reproduction ,clonality ,Spatial genetic structure ,Horticulture ,Biology ,Spatial distribution ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Clonal growth form ,Botany ,Genetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Molecular Biology ,030304 developmental biology ,Hybrid ,Lombardy poplar ,0303 health sciences ,Forestry ,15. Life on land ,biology.organism_classification ,Natural population growth ,Seedling ,Genetic structure ,Species richness ,Populus nigra ,Clonality - Abstract
International audience; A scarcity of favourable habitats and introgression from exotic cultivars are two major threats to black poplars (Populus nigra L.) in Europe. Natural vegetative propagation contributes to maintenance of the species in areas where seedling recruitment is limited. Exhaustive sampling of all mature trees in a natural P. nigra stand (413 individuals at recorded positions), genotyping at 11 SSR loci, and a standardized analysis framework resulted in a precise description of clonality in terms of (a) frequency, (b) spatial growth form, and (c) impacts on the overall spatial genetic structure (SGS). The high proportion of replicated genotypes detected resulted in a genotypic richness (R) of 0.47. Up to 18 ramets were found per multilocus lineage (MLL), but 95% of MLLs contained fewer than five ramets (Pareto index β = 1.07). No significant difference in vegetative propagation potential was found between genders. Uneven spatial distribution of ramets, with clustering of clonal ramets (aggregation index A c = 0.62) and near-zero intermingling between MLLs (clonal dominance index D c = 0.99), resulted in a ‘phalanx’ clonal growth form, explaining most of the SGS observed over short distances (0–20 m, Sp = 0.0324). Although they did not exhibit the typical columnar shape of the Lombardy poplar (P. nigra var. italica), five trees were found to be probable F1 hybrids of this old and widely distributed cultivar.
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- 2011
37. Consistency of the French white certificates evaluation system with the framework proposed for the European energy services
- Author
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Luc Bodineau, Jérôme Adnot, Bernard Bourges, Jean-Sébastien Broc, Dominique Osso, Paul Baudry, Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Mines Nantes (Mines Nantes)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS), Mines Nantes (Mines Nantes), EDF R&D (EDF R&D), EDF (EDF), CEP/Paris, Centre Énergétique et Procédés (CEP), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), This paper was built on the work carried out under the EMEEES project. Financial support from Intelligent Energy Europe (EIE) program of the European Community is gratefully acknowledged., European Project, Université de Nantes (UN)-Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS), Mines Paris - PSL (École nationale supérieure des mines de Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Mines Paris - PSL (École nationale supérieure des mines de Paris)
- Subjects
Engineering ,Building retrofitting ,020209 energy ,media_common.quotation_subject ,02 engineering and technology ,010501 environmental sciences ,7. Clean energy ,01 natural sciences ,Unit (housing) ,Consistency (database systems) ,Energy services directive ,[SPI.ENERG]Engineering Sciences [physics]/domain_spi.energ ,0202 electrical engineering, electronic engineering, information engineering ,Operations management ,Quality (business) ,National energy efficiency action plans ,0105 earth and related environmental sciences ,media_common ,Sustainable development ,Energy savings (or White) certificates ,business.industry ,Bottom-up evaluation ,Environmental economics ,Directive ,Energy conservation ,General Energy ,13. Climate action ,business ,White certificates ,Efficient energy use - Abstract
International audience; According to the directive on energy end-use efficiency and energy services (ESD), the European Member States shall adopt a national indicative energy savings target of 9% (or beyond) in 2016. The issue of the energy savings evaluation is crucial for its implementation. The French White Certificates (FWC) scheme is one of the important measures for France to fulfill its ESD target. However, the accountings of energy savings in the FWC scheme and in the ESD are different. Therefore, an analysis of the consistency of the two systems is needed. A concrete example of actions on residential buildings is used to illustrate the challenges for policy marker and stakeholders to set harmonized evaluation rules. The FWC and ESD calculations appear to be consistent from a physics point of view, as long as calculations are well-documented. But due to differences in the policy objectives, calculation routines may be necessary to convert national energy savings unit (e.g., kWh cumac) into supranational energy savings unit (e.g., ESD kWh). Finally, the work done to establish a transparent evaluation system brings additional benefits (e.g., increased visibility and quality of the actions), which will improve the results of the energy efficiency policies on long term.
- Published
- 2010
38. Comparative analysis of thermally modified and native spruce loaded perpendicular to the grain
- Author
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Beate Buchelt, Alexander Pfriem, Mario Zauer, André Wagenführ, Institute of Wood and Paper Technology, and Technische Universität Dresden = Dresden University of Technology (TU Dresden)
- Subjects
040101 forestry ,0106 biological sciences ,Materials science ,Scanning electron microscope ,Forestry ,04 agricultural and veterinary sciences ,Bending ,Thermal treatment ,01 natural sciences ,Radial direction ,Brittleness ,Flexural strength ,010608 biotechnology ,Physical Sciences ,Perpendicular ,Fracture (geology) ,0401 agriculture, forestry, and fisheries ,General Materials Science ,Composite material - Abstract
International audience; The aim of this work was to analyse the material behaviour of thermally modified and native spruce by load applied perpendicularly to the grain. Therefore, thermally modified and native samples were prepared for bending tests with the load in tangential direction. The bending strength in radial direction decreases significantly with the thermal treatment. The fracture surfaces in the tangential section of the bending samples after testing were analysed with a scanning electron microscope. For native samples, the typical failure was found in the intercellular area. For thermally modified samples, failure of the entire cell wall was observed. The material behaviour is more brittle, as demonstrated by the load-deflection curves, but also by anatomical studies of the fracture surfaces.
- Published
- 2010
39. The cost of monotonicity in distributed graph searching
- Author
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Nicolas Nisse, David Soguet, David Ilcinkas, Département d'Informatique et d'Ingénierie (DII), Université du Québec en Outaouais (UQO), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Additional supports from the project 'Fragile' of the ACI Sécurité Informatique, and from the project 'Grand Large' of INRIA., Eduardo Tovar, Philippas Tsigas, Hacène Fouchal, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Algorithmics for computationally intensive applications over wide scale distributed platforms (CEPAGE), Université Sciences et Technologies - Bordeaux 1-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Algorithms, simulation, combinatorics and optimization for telecommunications (MASCOTTE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-COMmunications, Réseaux, systèmes Embarqués et Distribués (Laboratoire I3S - COMRED), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), See paper for details., ANR-07-BLAN-0322,ALADDIN,Algorithm Design and Analysis for Implicitly and Incompletely Defined Interaction Networks(2007), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1 (UB)-Inria Bordeaux - Sud-Ouest, 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)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
- Subjects
Monotonicity ,Mathematical optimization ,Theoretical computer science ,Computer Networks and Communications ,Computer science ,[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS] ,050801 communication & media studies ,0102 computer and information sciences ,02 engineering and technology ,Strength of a graph ,Biconnected graph ,01 natural sciences ,Theoretical Computer Science ,law.invention ,0508 media and communications ,Graph power ,law ,Line graph ,0202 electrical engineering, electronic engineering, information engineering ,Graph property ,Complement graph ,Graph searching ,Distance-hereditary graph ,Mobile agent ,Discrete mathematics ,020203 distributed computing ,05 social sciences ,Voltage graph ,Directed graph ,Butterfly graph ,Competitive ratio ,Graph bandwidth ,Computational Theory and Mathematics ,010201 computation theory & mathematics ,Hardware and Architecture ,[INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC] ,Null graph ,Graph factorization ,MathematicsofComputing_DISCRETEMATHEMATICS - Abstract
International audience; Blin {\it et al.} (2006) proposed a distributed protocol that enables the smallest number of searchers to clear any unknown asynchronous graph in a decentralized manner. {\it Unknown} means that the searchers are provided no {\it a priori} information about the graph. However, the strategy that is actually performed lacks of an important property, namely the monotonicity. That is, the clear part of the graph may decrease at some steps of the execution of the protocol. Actually, the protocol of Blin {\it et al.} is executed in exponential time. Nisse and Soguet (2007) proved that, in order to ensure the smallest number of searchers to clear any $n$-node graph in a monotone way, it is necessary and sufficient to provide $\Theta(n \log n)$ bits of information to the searchers by putting short labels on the nodes of the graph. This paper deals with the smallest number of searchers that are necessary and sufficient to monotoneously clear any graph in a decentralized manner, when the searchers have no a priori information about the graph. The distributed graph searching problem considers a team of searchers that is aiming at clearing any connected contaminated graph. The clearing of the graph is required to be {\it connected}, i.e., the clear part of the graph must remain permanently connected, and {\it monotone}, i.e., the clear part of the graph only grows. The {\it search number} $\mcs(G)$ of a graph $G$ is the smallest number of searchers necessary to clear $G$ in a monotone connected way in centralized settings. We prove that any distributed protocol aiming at clearing any unknown n-node graph in a monotone connected way, in decentralized settings, has {\it competitive ratio} $\Theta(\frac{n}{\log n})$. That is, we prove that, for any distributed protocol $\cal P$, there exists a constant $c$ such that for any sufficiently large $n$, there exists a $n$-node graph $G$ such that $\cal P$ requires at least $c\frac{n}{\log n}\, \mcs(G)$ searchers to clear $G$. Moreover, we propose a distributed protocol that allows $O(\frac{n}{\log n})\, \mcs(G)$ searchers to clear any unknown asynchronous $n$-node graph $G$ in a monotone connected way.
- Published
- 2009
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