Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The actin cytoskeleton is a dynamic structure that provides an interactive platform for organelles and cellular components. It also serves as track for membranes and vesicles that move via myosin. The actin cytoskeleton of Symbiodinium is a well-organized reticular structure suggestive of multiple membrane interactions, very likely including those of the chloroplast. The Symbiodinium chloroplast membrane network is, in turn, a highly organized structure, suggestive of being under the control of an organizing network. We visualized the chloroplast membranes of cultured Symbiodinium sp. under various light conditions and observed changes dependent on illumination intensity. Since we suspected interaction between these two organelles, and we knew that the Symbiodinium actin cytoskeleton collapses upon treatment with either latrunculin B, an actin microfilament-disrupting agent, or butanedione monoxime, a myosin function inhibitor, we tested the Symbiodinium sp. oxygen evolution in their presence. Upon latrunculin B addition, the oxygen production decreased compared to non-treated cells; however, this was not observed after a 24 h latrunculin treatment. On the contrary, butanedione monoxime treatment caused a non-recoverable dysfunction of the chloroplast causing a severe loss in oxygen production even after long-term exposure. Using electron microscopy, we observed an alteration of the Symbiodinium sp. chloroplast distribution after latrunculin B treatment, with respect to untreated cells. Furthermore, a thorough disorganization of the chloroplast grana was observed after butanedione monoxime treatment. These data suggest that an actomyosin system would be important for chloroplast organization and distribution, and critical for normal photosynthetic function of Symbiodinium sp.
ISSN: 0166-8595

hal-01546164
https://hal.archives-ouvertes.fr/hal-01546164
DOI : 10.1007/s11120-015-0142-9

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
ISSN: 0027-8424

hal-01544803
https://hal.archives-ouvertes.fr/hal-01544803
DOI : 10.1073/pnas.1206541109

Résumé : Les graphes définis à partir de structures algébriques possèdent d’excellentes propriétés de symétries particulièrement intéressantes. L’exemple le plus flagrant est la notion de graphe de Cayley qui s’est révélée très riche non seulement du point de vue théorique mais aussi pratique par ses applications à de nombreux domaines incluant l’architecture des réseaux ou les machines parallèles. Néanmoins, la régularité des graphes de Cayley se révèle parfois être une limite étant donné qu’ils sont toujours sommet-transitifs et donc en particulier non pertinents pour générer des réseaux semiréguliers.Cette observation a motivé, en 2005, la définition d’une nouvelle classe de graphes définis à partir d’un groupe, appelés G-graphes. Ils possèdent aussi de nombreuses propriétés de régularité mais de manière moins restrictive.Cette thèse propose un nouveau regard sur cette classe de graphes par une approche plutôt orientée recherche opérationnelle alors que la grande majorité des études précédentes est dominée par des approches essentiellement algébriques. Nous-nous sommes alors intéressés à plusieurs questions :— La caractérisation des G-graphes : nous proposons des améliorations par rapport aux précédents résultats.— Identifier des classes de graphes comme des G-graphes grâce à des isomorphismes ou en utilisant le théorème de caractérisation.— Etudier la structure et les propriétés de ces graphes, en particulier pour de possibles applications aux réseaux : colorations semi-régulières, symétries et robustesse.— Une approche algorithmique pour la reconnaissance de cette classe avec notamment un premier exemple de cas polynomial lorsque le groupe est abélien.
Interactions between graph theory and group theory have already led to interesting results for both domains. Graphs defined from algebraic groups have highly symmetrical structure giving birth to interesting properties. The most famous example is Cayley graphs, which revealed to be particularly interesting both from a theoretical and a practical point of view due to their applications in several domains including network architecture or parallel machines. Nevertheless, the regularity of Cayley graphs is also a limit as they are always vertex-transitive and therefore not relevant to generate semi-regular networks. This observation motivated the definition, in 2005, of a new family of graphs defined from a group, called G-graphs. They also have many regular properties but are less restrictive. These graphs are in particular semi-regular k-partite, with a chromatic number k directly given in the group representation and they can be either transitive or not.This thesis proposes a new insight into this class of graphs using an approach based on operational research while most of previous studies have been so far dominated by algebraic approaches. Then, the thesis addresses different kind of questions:— Characterizing G-graphs: we propose improvements of previous results.— Identifying some classes of graphs as G-graphs through isomorphism or using the characterization theorem.— Studying the structure and properties of these graphs, in particular for possible applications to networks: semi-regular coloring, symmetries and robustness.— Algorithmic approach for recognizing this class with a first example of polynomial case when the group is abelian.

http://www.theses.fr/2014AGUY0787/document

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Traditional network generation models aim to replicate global structural properties observed on various real-world networks through synthetic link formation mechanisms such as triadic closure or preferential attachment. Nowadays, the large amount of data available allow to study more precisely the link formation processes and to compare models with real situations. In this work, we analyze the network formed by the communication activities of the users of a telephony operator for studying the link formation process. Our goal is to identify the underlying formation mechanisms and checking if they match those proposed in traditional models. Indeed, the communications emitted and received by users are strong indicators for understanding the underlying patterns of the link formation process and highlighting how some individual properties induce the formation process in such a network. In a first study conducted at a global level, we show that the traditional mechanisms commonly used in network generation models cannot reproduce alone the link formation in this network. In a second study, we adopt a new point of view and analyze locally the link formation process by searching for correlations between some user attributes and the formation of the new links. The results obtained show that a very strong percentage of new links are formed between individuals with strong similarity.
ISSN: 1869-5450

hal-01312310
https://hal.univ-antilles.fr/hal-01312310
DOI : 10.1007/s13278-015-0304-y

Éditeur(s) : Université de la Rochelle
Résumé : In order to better understand the functioning of the Brouage intertidal mudflat (Marennes- Oléron Basin, France), its carbon-based trophic web has been modelled and analyzed. The foodweb building is based on the 4 step method of Inverse Analysis: 1) conceive an a priori model as the graph of compartments (nodes) between which exist fluxes of material (vertices). These vertices are the unknowns for the problem; 2) gather all the existing knowledge about the ecosystem and translate it into linear equations and inequalities involving the fluxes; 3) complete this set of data by common knowledge on the behaviour of the compartments and translate it into inequalities, 4) solve the obtained linear system under the parsimony principle to find a unique solution vector. The food-web analysis is based on. The first purpose of this work was a methodological one: inverse analysis method has been adapted to consider the seasonal and spatial variability of the temperate ecosystem: two seasons have been coupled in the computation and the area has been divided into three geographical zones along a cross-shore gradient. Hence, two types of physical exchanges are involved: the benthicpelagic ones and the advection ones. Statistical results can also be obtained by coupling Monte Carlo methods to Inverse Analysis. To study the obtained networks, new indices based on Markov Chains take delay into account in describing integrative transfers of material between compartments. This lets emerge the systems' properties that are not obvious at first sight and emphasizes the role of peculiar components. The second purpose was to apply such methods to the Brouage mudflat ecosystem in order to better understand its functioning. As the knowledge and methods evolve, various food webs were computed and analyzed with the help such indices and existing ones. Sensitivity analyses allow to point at the most crucial lacks of knowledge, which can orientate future field research. New data would improve the quality of the model in two ways: one the one hand, they would validate or invalidate the outcomes and on the other hand, they would give useful information to better constrain some of the black boxes and most uncertain fluxes, especially the advection and vertical flows. The main results of the study show a strongly seasonal system in which benthic and pelagic components are linked with intensity. The system is driven by its high local benthic primary production, but also depends on imports from the basin. Each of the 3 geographic zones has a peculiar functioning. The central zone corresponds to the classical description of European intertidal mudflats: very productive, it can feed the other regions. It is a production zone. The upper part is less productive but is fed by the middle one via the water column and can be exploited by shorebirds. It is a degradation zone (material is transformed for less qualitative). The lower part strongly depends on the basin imports for its functioning, as the cultivated bivalves act as a pump for pelagic material of which a great part is deposited under the cultivation structures (oyster racks or mussels "bouchots"). It is a transformation zone.
Un double objectif (méthodologique et appliqué) a été visé par une modélisation du réseau trophique de la vasière de Brouage (Bassin de Marennes Oléron, France) à l'aide de l'analyse inverse, et son étude à l'aide de l'analyse des réseaux. L'Analyse Inverse permet en effet de reconstruire l'ensemble du réseau à partir de données éparses, le problème du manque de données étant récurrent en Ecologie. Au plan méthodologique, l'analyse inverse a été adaptée à la prise en compte des caractères saisonnier et spatialement hétérogène d'un écosystème tempéré de zone intertidale : deux saisons ont ainsi été couplées et la vasière a été considérée le long d'un transect perpendiculaire au rivage et divisé en trois zones spatiales. Deux types de flux physiques interviennent donc : les flux verticaux de dépôt et remise en suspension, et les flux d'advection via la colonne d'eau. Des pistes d'amélioration et de nouvelles méthodes sont proposées. Un résultat sous forme statistique peut être obtenu en couplant l'utilisation de méthodes de Monte Carlo à l'analyse inverse pour la construction des réseaux trophiques. Les moyens d'étude des modèles ont été enrichis par la mise au point d'indices issus de la construction de chaînes de Markov et prenant en compte le caractère temporel des transferts de matière entre compartiments. Enfin, la transformation mathématique du modèle statique pour une étude dynamique de la stabilité de l'équilibre décrit est abordée. Plusieurs modèles ont été construits au cours de l'évolution des méthodes et de l'acquisition de connaissances sur le site. Des méthodes d'analyses existantes et d'autres mises au point dans le cadre de cet ouvrage ont été appliquées aux réseaux obtenus afin de faire émerger les propriétés du fonctionnement de la vasière et de souligner le rôle de certains compartiments. Des analyses de sensibilité permettent d'évaluer la robustesse des résultats et d'orienter les recherches futures en mettant en évidence les manques les plus cruciaux. Des données supplémentaires, notamment concernant les foraminifères benthiques, le zooplancton ou les mouvements verticaux du microphytobenthos permettront de fournir de meilleures contraintes et de valider (ou non) les résultats obtenus. Les principaux résultats montrent un système au fort caractère saisonnier dont les compartiments benthiques et pélagiques sont très liés. La production primaire benthique locale est un moteur important, mais qui ne suffirait pas à suppléer l'indispensable importation de matériel détritique. Le découpage de la vasière en trois zones fait apparaître les particularités de chacune. La zone centrale correspond à la description classique des « vasières intertidales européennes » : très productive, elle peut alimenter les autres régions. C'est une zone de production et d'exportation. La partie supérieure est moins productive et reçoit de la matière de la zone de milieu d'estran via la colonne d'eau. Sa production secondaire peut alors être exploitée par les limicoles, nombreux en hiver. C'est une zone de dégradation et d'exportation. Le bas d'estran dépend fortement des importations extérieures, « pompées » par les bivalves cultivés qui sont ainsi directement responsables d'une forte sédimentation sous les structures mytilicoles et ostréicoles. C'est une zone de transformation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2005/these-2260.pdf
http://archimer.ifremer.fr/doc/00000/2260/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Structural controls are critical during magmatic-to-hydrothermal transition in the formation of intrusion-related gold deposits. They may explain why only some parts of intrusions are mineralized and why only very few intrusions host large deposits. Moreover, most of these gold deposits postdate peak regional metamorphism and were formed in zones of relatively low strain. Indeed, the efficiency of structural gold traps is highest along favourably oriented intrusion/host-rock contacts where mechanical instability maintains high permeability in the cracked thermal aureole. This may be reinforced by melt injections from an underlying root zone. We present a structural analysis of the deformation features of a granite-pluton roof; large-scale dykes and a network of gold veins are intensively developed in this roof, recording a succession of mechanical instabilities. Our gravity survey underlines the presence of a pluton feeder zone located just beneath the mineralized network. It is argued that interferences between regional stress and melt injection in the feeder zone favoured the development of the network by strain located close to the granite roof. This stresses the role of mechanical instabilities triggered by the combined effects of regional stress and melt dynamics in determining the location and size of this type of gold deposit.
ISSN: 0191-8141

insu-00914780
https://hal-insu.archives-ouvertes.fr/insu-00914780
https://hal-insu.archives-ouvertes.fr/insu-00914780/document
https://hal-insu.archives-ouvertes.fr/insu-00914780/file/manuscript.pdf
DOI : 10.1016/j.jsg.2013.11.006

Éditeur(s) : HAL CCSD American Association of Petroleum Geologists
Résumé : In reservoir engineering, hydrodynamic properties can be estimated from downhole electrical data using heuristic models (e.g., Archie and Kozeny-Carman's equations) relating electrical conductivity to porosity and permeability. Although proven to be predictive for many sandstone reservoirs, the models mostly fail when applied to carbonate reservoirs that generally display extremely complex pore network structures. In this article, we investigate the control of the three-dimensional (3-D) geometry and morphology of the pore network on the electrical and flow properties, comparing core-scale laboratory measurements and 3-D x-ray microtomography image analysis of samples from a Miocene reefal carbonate platform located in Mallorca (Spain). The results show that micrometer- to centimeter-scale heterogeneities strongly influence the measured macroscopic physical parameters that are then used to evaluate the hydrodynamic properties of the rock, and therefore, existing models might not provide accurate descriptions because these heterogeneities occur at scales smaller than those of the integration volume of the borehole geophysical methods. However, associated with specific data processing, 3-D imagery techniques are a useful and probably unique mean to characterize the rock heterogeneity and, thus, the properties variability.
ISSN: 0149-1423

hal-00950066
https://hal.archives-ouvertes.fr/hal-00950066
DOI : 10.1306/05221312134

Éditeur(s) : HAL CCSD Taylor & Francis (Routledge)
Résumé : International audience
The French Antilles (Martinique, Saint Martin and Guadeloupe) and French Guiana are the French territories most affected by the HIV epidemic. Some population groups such as men who have sex with men (MSM), especially those involved in transactional sex, are thought to be particularly vulnerable to HIV but few data exist to help characterize their health-related needs and thus implement relevant prevention interventions. To fill this knowledge gap, we used data collected from an HIV/AIDS Knowledge, Attitudes, Behaviours and Practices survey conducted in 2012 among MSM living in the French Antilles and French Guiana and recruited through snowball sampling. Our objectives were to compare social and demographic characteristics and sexual behaviours between MSM engaging in transactional sex and MSM not engaging in transactional sex and to identify factors associated with transactional sex involvement using a logistic regression model. A total of 733 MSM were interviewed, 21% of whom reported to undergo transactional sex. Their behaviour and social and demographic characteristics were different from other MSMs’ and they were more exposed to factors that are recognized to potentiate HIVvulnerability, at the individual, community, network and structural levels. The variables positively associated with sex trade involvement were having ever consumed drug (OR = 2.84 [1.23–6.52]; p = .002), having a greater number of sex partners than the median (OR = 8.31 [4.84–14.30]; p < .001), having experienced intimate partner violence (OR = 1.72 [0.99–3.00]; p = .053) and having undergone physical aggression because of sexual orientation (OR = 2.84 [1.23–6.52];p = .014). Variables negatively associated with sex trade involvement were being older (OR = 0.93 [0.90–0.97] per year; p = .001), having a stable administrative situation (OR = 0.10 [0.06–0.19]; p < .001), having a stable housing (OR = 0.29 [0.15–0.55]; p < .001) and being employed full-time (OR = 0.29 [1.23–6.52]; p = .002).
ISSN: 0954-0121

inserm-01407263
http://www.hal.inserm.fr/inserm-01407263
http://www.hal.inserm.fr/inserm-01407263/document
http://www.hal.inserm.fr/inserm-01407263/file/AIDS%20Care%20final%20version.pdf
DOI : 10.1080/09540121.2016.1234680

Éditeur(s) : HAL CCSD
Résumé : International audience
More and more animal species are endangered. In order to study and protect them, several measures have been taken, which now seem to show their limit. This work focuses on the counting process, a key issue for any project that aims to protect animals. Indeed, this paper proposes an algorithm for automatic counting of singing birds in their habitat by using wireless sensors fitted with microphone. Sensors are used to record audio samples of bird songs. These samples are used to extract some kinds of song fingerprint that are thereafter used to recognize the bird species, through a classification process. Afterwards, by analyzing data which have been collected by a central base, the network structure derived from detection fields of sensors, allows our algorithm to propose an estimate of singing birds in the habitat. This paper details the counting algorithm which uses graph theory and audio inputs comparison. Finally, we demonstrate our scheme efficiency through experimentations.
Local Computer Networks (LCN)
Clearwater, United States

hal-00786165
https://hal.archives-ouvertes.fr/hal-00786165
DOI : 10.1109/LCNW.2012.6424060

Éditeur(s) : ICES 2008 Annual Science Conference, 22-26 september 2008, HALIFAX, CANADA
Résumé : The development on the ecosystem-based approach to fisheries implies to improve integrated analysis of fisheries by considering the biological as well as the socio-economic dimensions of the exploitation and thus, an improvement in the knowledge of fleets structure, evolution and activity. Since 2000, Ifremer has been implemented a Fisheries Information System (FIS), a multidisciplinary monitoring network allowing an integrated and comprehensive view of fishery systems including biological, technical, environmental and economical components. The FIS covers all the French fisheries, including the so-often neglected small-scale fisheries. One of the originalities of the FIS lies in the fleet monitoring procedure: a comprehensive collection of annual activity calendars aiming at characterizing the inactivity or activity of the vessels each month of the year and, in the latter case, the métiers practised (use of a gear to target one or several species) and the main fishing areas. This survey covers all the French fishing fleets and provides minimum but exhaustive information on the vessels. It is particularly instructive for the small-scale fisheries, where catches and effort data are often incomplete. Furthermore, this exhaustive data allows stratifying the fleet in fleets (typologies) and thus provides the basis (i) for the implementation of sampling schemes to estimate catches, landings, discards or economic performance of the different fleets and (ii) for the development of a fleet-métier matrix giving the possibility of identifying at the time, the structure of the whole fleet in fleets, the métier polyvalence of the vessels and the allocation of fishing effort on the different exploited fishing resources.

Droits : 2008 ICES
http://archimer.ifremer.fr/doc/00059/16996/14498.pdf
http://archimer.ifremer.fr/doc/00059/16996/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Approximately 4 yr of campaign and continuous Global Positioning System (GPS) measurements across the Dead Sea fault system (DSFS) in Lebanon provide direct measurements of interseismic strain accumulation along a 200-km-long restraining bend in this continental transform fault. Late Cenozoic transpression within this restraining bend has maintained more than 3000 m of topography in the Mount Lebanon and Anti-Lebanon ranges. The GPS velocity field indicates 4-5 mm yr(-1) of relative plate motion is transferred through the restraining bend to the northern continuation of the DSFS in northwestern Syria. Near-field GPS velocities are generally parallel to the major, left-lateral strike-slip faults, suggesting that much of the expected convergence across the restraining bend is likely accommodated by different structures beyond the aperture of the GPS network (e.g. offshore Lebanon and, possibly, the Palmyride fold belt in SW Syria). Hence, these geodetic results suggest a partitioning of crustal deformation involving strike-slip displacements in the interior of the restraining bend, and crustal shortening in the outer part of the restraining bend. Within the uncertainties, the GPS-based rates of fault slip compare well with Holocene-averaged estimates of slip along the two principal strike-slip faults: the Yammouneh and Serghaya faults. Of these two faults, more slip occurs on the Yammouneh fault, which constitutes the primary plate boundary structure between the Arabia and Sinai plates. Hence, the Yammouneh fault is the structural linkage that transfers slip to the northern part of the transform in northwestern Syria. From the perspective of the regional earthquake hazard, the Yammouneh fault is presently locked and accumulating interseismic strain.
ISSN: 0956-540X

hal-00406620
https://hal.archives-ouvertes.fr/hal-00406620
DOI : 10.1111/j.1365-246X.2006.03328.x

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Total mercury (HgT) and monomethylmercury (MMHg) were investigated in a tropical head watershed (1 km(2)) of French Guiana. The watershed includes a pristine area on the hill slopes and a former gold mined flat in the bottomland. Concentrations of dissolved and particulate HgT and MMHg were measured in rain, throughfall, soil water and at three points along the stream. Samples were taken in-between and during 14 storm events at the beginning and middle of the 2005 and 2006 rainy seasons. Dissolved and particulate HgT concentrations in the stream slightly increased downstream, while dissolved and particulate MMHg concentrations were low at the pristine sub-watershed outlet (median = 0.006 ng L-1 and 1.84 ng g(-1), respectively) and sharply increased at the gold mined flat outlet (median = 0.056 ng L-1 and 6.80 ng g(-1), respectively). Oxisols, which are dominant in the pristine area act as a sink of HgT and MMHg from rain and throughfall inputs. Hydromorphic soils in the flat are strongly contaminated with Hg (including Hg droplets) and their structure has been disturbed by former gold-mining processes, leading to multiple stagnant water areas where biogeochemical conditions are favorable for methylation. In the former gold mined flat high dissolved MMHg concentrations (up to 0.8 ng L-1) were measured in puddles or suboxic soil pore waters, whereas high dissolved HgT concentrations were found in lower Eh conditions. Iron-reducing bacteria were suggested as the main methylators since highest concentrations for dissolved MMHg were associated with high dissolved ferrous iron concentrations. The connection between saturated areas and stagnant waters with the hydrographic network during rain events leads to the export of dissolved MMHg and HgT in stream waters, especially at the beginning of the rainy season. As both legal and illegal gold-mining continues to expand in French Guiana, an increase in dissolved and particulate MMHg emissions in the hydrographic network is expected. This will enhance MMHg bio-amplification and present a threat to local populations, whose diet relies mainly on fish.
Water Research (0043-1354) (Pergamon-elsevier Science Ltd), 2011-04 , Vol. 45 , N. 8 , P. 2659-2669

Droits : 2011 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/00035/14628/12134.pdf
DOI:10.1016/j.watres.2011.02.022
http://archimer.ifremer.fr/doc/00035/14628/

Éditeur(s) : HAL CCSD
Résumé : The present PhD thesis is devoted to the numerical simulation and analysis of shear on cohesive granular materials. In the framework of the Contact Dynamics method, we developed a model of cohesive bonding, which mimics cohesion by cementation. This model involves three contact strength parameters (a tensile strength, a coefficient of sliding friction, and a coefficient of rolling friction) as well as a local criterion, which controls the creation and the breaking of cohesive bonds. All contacts are cohesive at the beginning of the numerical simulations, and contact rupture leads to an irreversible loss of tensile strength (debonding). We varied systematically the three contact strength parameters and studied their influence on the shear strength, the dilatancy, and the microstructure of the granular media. Our results show that internal friction and macroscopic tensile strength have different origins at the contact scale. We also find that the microstructure of the granular media, when sheared at the steady state (also known as the `critical state"), is strongly affected by the local coefficients of sliding and rolling friction. In particular, the mechanical role of the weak network changes with these two contact parameters, which results from the formation of a new structure of force transmission. On the other hand, we also applied the same numerical simulation method to the simulation of landslides. We developed a methodology, which takes into account the initial morphology of the hillslope, the strength of geomaterials, and a triggering factor, integrating in the same model the initiation and propagation phases of the landslide. To illustrate this methodology, we applied it to the simulation of a hypothetical example of avalanche triggered by the progressive rise of a water table.
Ce travail de thèse porte sur la modélisation numérique et l'analyse du cisaillement dans les milieux granulaires cohésifs. Dans le cadre de la méthode de la Dynamique des Contacts, nous avons développé un modèle de cohésion qui cherche à imiter la cohésion par cimentation. Ce modèle fait intervenir trois paramètres de résistance au niveau des contacts (une résistance à la traction, un coefficient de frottement de glissement, et un coefficient de frottement de roulement) ainsi qu'un critère de création et de rupture des liens cohésifs. Les contacts sont cohésifs au début des simulations et leur rupture entraîne la perte irréversible de la résistance à la traction. Nous avons fait varier les trois paramètres microscopiques et nous avons étudié leur influence dans la résistance au cisaillement, la dilatance, et la microstructure du milieu. Nos résultats montrent que le frottement interne et l'adhésion macroscopiques ont des origines microscopiques différentes. Nous observons aussi que la microstructure du milieu cisaillé à l'état stationnaire (aussi connu comme ``l'état critique") est fortement affectée par l'angle de frottement et la résistance au roulement au niveau des contacts. En particulier, le rôle mécanique du réseau faible change avec ces deux paramètres microscopiques, ce qui résulte de la formation d'une nouvelle structure de transmission de forces. D'autre part, nous avons appliqué cette méthode de simulation numérique à l'étude d'un processus naturel : les glissements de terrain. Nous avons développé une méthodologie qui tient compte de la morphologie initiale du système, de la résistance des géomatériaux, et d'un mécanisme de déclanchement, ce qui permet d'intégrer dans le même modèle les phases d'initiation et de propagation du glissement. Pour illustrer cette méthodologie, nous l'avons appliquée à la modélisation d'un exemple hypothétique d'avalanche déclenchée par la montée progressive du niveau d'une nappe d'eau.
https://tel.archives-ouvertes.fr/tel-00311303

tel-00311303
https://tel.archives-ouvertes.fr/tel-00311303
https://tel.archives-ouvertes.fr/tel-00311303/document
https://tel.archives-ouvertes.fr/tel-00311303/file/these_estrada.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Our knowledge and understanding of the 3-D lithospheric structure of the Himalayas and the Tibetan Plateau is still challenging although numerous geophysical studies have been performed in the region. The GOCE satellite mission has the ambitious goal of mapping Earth's gravity field with unprecedented precision (i.e. an accuracy of 1-2 mGal for a spatial resolution of 100 km) to observe the lithosphere and upper-mantle structure. Consequently, it gives new insights in the lithospheric structure beneath the Himalayas and the Tibetan Plateau. Indeed, the GOCE gravity data now allow us to develop a new strategy for joint gravimetry-seismology inversion. Combined with teleseismic data over a large region in a joint inversion scheme, they will lead to lithospheric velocity-density models constrained in two complementary ways. We apply this joint inversion scheme to the Hi-CLIMB (Himalayan-Tibetan Continental Lithosphere during Mountain Building) seismological network which was deployed in South Tibet and the Himalayas for a 3-yr period. The large size of the network, the high quality of the seismological data and the new GOCE gravity data set allow us to image the entire lithosphere of this active area in an innovative way. We image 3-D low velocity and density structures in the middle crust that fit the location of discontinuous low S-velocity zones revealed by receiver functions in previous geophysical studies. In the deeper parts of our velocity model we image a positive anomaly interpreted to be the heterogenous Indian lithosphere vertically descending beneath the centre of the Tibetan Plateau.
ISSN: 0956-540X

hal-00858024
https://hal.archives-ouvertes.fr/hal-00858024
DOI : 10.1093/gji/ggs110

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and disadvantages of mixed species plantations. The network currently consists of 18 experiments, distributed over 36 sites and five ecoregions. With plantations 1-15 years old, TreeDivNet can already provide relevant data for forest policy and management. In this paper, we highlight some early results on the carbon sequestration and pest resistance potential of more diverse plantations. Finally, suggestions are made for new, innovative experiments in understudied regions to complement the existing network.
ISSN: 0044-7447

hal-01204232
https://hal.archives-ouvertes.fr/hal-01204232
DOI : 10.1007/s13280-015-0685-1
PRODINRA : 324368
PUBMED : 26264716

Éditeur(s) : HAL CCSD
Résumé : The recent accumulation of genomic sequence data has shown that gene evolution is not strictly tree-Like. Many evolutionary processes, like exon shuffling, gene fusion or nonhomologous recombination remodel genes by creating composite structures that are made from parts with different evolutionary histories. The development of sequence similarity networks provides an analytical framework to study the impact of these processes on molecular evolution, by structuring the resemblance relationships between sequences and by formalizing, in terms of graph theory, the detection of composite genes (intransitive triplets) and gene families (clique minimal separators). The size of current data sets, typically several million sequences, has also required the development of new tools and methods: sequence comparison parallelization, large networks visualization with Louvain communities and large cycles identification. When applied to eukaryotic and viral genome data sets, these methods have shown that composite genes are found throughout cellular organisms and mobile genetic elements. Proportionally, composite genes are more numerous in eukaryotic genomes; in absolute number, they are more numerous in viruses. In the latter, composite genes functional distribution is biased (enrichment of genes families that are essential for the perpetuation of the viral cycle), and the various parts of composite genes sometimes even originate from the genetic material of different viral classes. More generally, the extent of combinatorial processes, by unravelling other evolutionary bonds than homology bonds in the strictest sense, legitimates a pluralistic study of similarity relationships between sequences.
L’accumulation récente de données de séquences génomiques a montré que l’évolution des gènes n’est pas strictement arborescente. De nombreux processus évolutifs, comme l’exon shuffling, la fusion de gènes ou la recombinaison illégitime remodèlent les gènes, créant des structures composites, formées de parties dont les histoires évolutives sont différentes. Le développement de réseaux de similarité de séquences fournit un cadre analytique permettant d’étudier l’impact de ces processus sur l’évolution moléculaire, en structurant les relations de ressemblance entre séquences et en formalisant en termes de graphes la détection de gènes (triplets intransitifs) et de familles de gènes (cliques minimales séparatrices) composites. La taille des jeux de données actuels, de l’ordre de plusieurs millions de séquences, a également requis le développement de nouveaux outils et méthodes : parallélisation des comparaisons de séquences, visualisation de très grands réseaux par simplification en communautés de Louvain et identification de grands cycles. Appliquées à des jeux de données de génomes eucaryotes et viraux, ces méthodes ont démontré la présence de gènes composites dans tout le vivant et les éléments génétiques mobiles. En proportion, les gènes composites sont plus nombreux dans les génomes eucaryotes ; en nombre absolu, ils sont plus nombreux à être portés par des virus. Chez ces derniers, la distribution fonctionnelle des gènes composites est biaisée (enrichissement dans les familles essentielles pour la perpétuation du cycle viral), et les éléments des gènes composites trouvent même parfois leurs origines dans le matériel génétique de classes virales différentes. Plus généralement, l’étendue des processus combinatoires, en révélant des liens évolutionnaires autres que les liens d’homologie au sens fort, justifie une étude pluraliste des relations de similarité entre séquences.
https://tel.archives-ouvertes.fr/tel-01127379

NNT : 2014PA066358
tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379/document
https://tel.archives-ouvertes.fr/tel-01127379/file/2014PA066358.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper proposes a new knowledge discovery method called FLMin to discover frequent patterns in a social network. The algorithm works without previous knowledge on the network and exploits both the structure and the attributes of nodes to extract regularities called Frequent Links. Unlike traditional works in this area that solely exploit structural regularities of the network, the originality of FLMin is its ability to gather these two kinds of information in the search for patterns. In this paper, we detail the method proposed for extracting frequent links and discuss its complexity and its flexibility. The efficiency of our solution is evaluated by conducting qualitative and quantitative studies for understanding how behaves FLMin according to different parameters.
Networked Digital Technologies
Dubai, United Arab Emirates

hal-00768431
https://hal.archives-ouvertes.fr/hal-00768431
DOI : 10.1007/978-3-642-30567-2_38

Résumé : Le concept de réseau offre un modèle de représentation pour une grande variété d'objets et de systèmes, aussi bien naturels que sociaux, dans lesquels un ensemble d'entités homogènes ou hétérogènes interagissent entre elles. Il est aujourd'hui employé couramment pour désigner divers types de structures relationnelles. Pourtant, si chacun a une idée plus ou moins précise de ce qu'est un réseau, nous ignorons encore souvent les implications qu'ont ces structures dans de nombreux phénomènes du monde qui nous entoure. C'est par exemple le cas de processus tels que la diffusion d'une rumeur, la transmission d'une maladie, ou même l'émergence de sujets d'intérêt commun à un groupe d'individus, dans lesquels les relations que maintiennent les individus entre eux et leur nature s'avèrent souvent être les principaux facteurs déterminants l'évolution du phénomène. C'est ainsi que l'étude des réseaux est devenue l'un des domaines émergents du 21e siècle appelé la "Science des réseaux". Dans ce mémoire, nous abordons trois problèmes de la science des réseaux: le problème de la diffusion dans les réseaux sociaux, où nous nous sommes intéressés plus particulièrement à l'impact de la dynamique du réseau sur le processus de diffusion, le problème de l'analyse des réseaux sociaux, dans lequel nous avons proposé une solution pour tirer parti de l'ensemble des informations disponibles en combinant les informations sur la structure du réseau et les attributs des noeuds et le problème central de la collecte de données sociales, où nous nous sommes intéressés au cas particulier de la collecte de données en milieux sauvages
The concept of network provides a model for representing a wide variety of objects and systems, both natural and social, in which a set of homogeneous or heterogeneous entities interact. It is now widely used to describe various kinds of relational structures. However, if everyone has an idea of the concept of network, we often ignore the implications that these structures have in real world phenomena. This is for example the case of processes such as the spread of a rumor, the disease transmission, or even the emergence of subjects of common interest for a group of individuals, in which the relations maintained between individuals, and their nature, often prove to be the main factors determining the evolution of the phenomenon. This is the reason why the study of networks has become one of the emerging areas in the 21st century called the "Science of networks." ln this thesis, we address three issues of the domain of the science of networks: the problem of diffusion in social networks, where we have addressed more particularly the impact of the network dynamics on the diffusion process, the problem of the analysis of social networks, in which we have proposed a solution to take full advantage of all information available on the network by combining information on both structure and node attributes and the central problem of the social data collection, for which we have focused on the particular case of the data collection in a wild environment.

http://www.theses.fr/2012AGUY0569/document

Éditeur(s) : HAL CCSD
Résumé : The Franceville Basin (2.1 Ga) in southeastern Gabon, hosts a black shale series well preserved (FB Formation) which represents an exceptional example of unmetamorphised Paleoproterozoic sediment strata. This basin includes the protore of one of the largest Mn-oxide laterite ore worldwide, mined by Eramet-Comilog. The aim of this this work is to determine formation conditions of this protore and to characterize the global sedimentary evolution of the FB Formation which include the protore. This 75 m thick protore is constituted of Mn carbonate-rich black shales which represent a potential ore deposit for the future. It was drilled, on the Bangombé plateau, during a recent campaign of 24 boreholes with an average depth of 125 m.Through multidisciplinary study on these cores and key outcrops of the basin, this work focuses on : i) the depositional environment of the Mn-protore and FB Formation ; ii) the processes of formation of the Mn-carbonates at 2.1 Ga and iii) the architecture and distribution of Mn-rich levels of the protore on the Bangombé Plateau.A detailed sedimentological and petrological study allowed us to redefine the division of the FB into nine units, named U1 to U9 from the base to the top. These units show a fine upward cycle up to U5 and a reverse coarse loop until U9. This division leads to a new interpretation to propose an evolution from a shoreface depositional environment controlled by deltaic currents (U1) to an offshore depositional environment with anoxic conditions (U2). In this basin, a system of submarine fan is developed, feeding a network of sand injections (injectites) covering the Bangombé plateau (70 km²) and with a thickness of 150 m affecting U4 to U7, including the Mn-protore. The protore depositional environment formed below the wave base limit (U4, U5 and U6) in a starved basin, controlled by biochemical sedimentation allowed the formation of Mn-carbonates. The end of starved basin, would allow the re-opening of the detrital input into the offshore basin (U7). This basin is then filled by storm bar deposits intersected by deltaic sub-aquatic channels (U8). The U9 unit corresponds to a quiet lagoon environment, allowing the multicellular organism development for the first time on the planet.A geochemical study allowed the characterization of the depositional environment of Mn-carbonates as an anoxic to sub-oxic and alkaline environment. For the first time, we showed that the manganese carbonates, present as bacteriomorph forms, are precipitated from the seawater by the mediated photosynthetic cyanobacterial activity, which allows CO2 / HCO3 depression of the environment and a local increase of pH. The cyanobacterial activity is controlled by the absence of bottom currents, which increase the detrital input. This would stop the activity of the cyanobacteria and thus would lead to the decrease of the Mn-concentration along the protore.Finally, well-log and a sequential correlation analyses allowed us to detail spatial and timing repartition of FB Formation deposit, controlled by a tectono-sedimentary model. We propose two- tectono-sedimentary phases. A first syn-tectonic phase (U1 to U3) controls the depocentres and sedimentation gaps. Turbidite coarse deposits are located in the most subsident part, clay deposits rather on the slope and carbonates on shoals. A second post-tectonic phase (U4 to U7) allows isopach deposits. The Mn-protore formed during the post-tectonic phase. However, it shows a variable thickness due to subsidence to the north of the Bangombé plateau. So, on the Bangombé plateau, Mn-contents increase towards the south, whereas the protore thickness increases towards the NNE. Moreover sand injectites decrease Mn-content in the eastern part of the Bangombé plateau and impact on the economic evaluation of the Mn-carbonates. Currently, the protore is structured by post-sedimentary faults, which lead to a non-continuity of the high Mn levels on the Bangombé plateau.
Le Bassin de Franceville situé au SE du Gabon présente une série de black shales (Formation FB) d'âge Paléoprotérozoïque (2,1 Ga) surmontant les grès de la Formation FA. Ce bassin peu déformé et non métamorphique représente une archive exceptionnelle des processus de dépôt de cette période de l’histoire de la Terre où la vie commence à se développer. En particulier, la Formation FB contient le protore d'un gisement mondial d'oxydes de manganèse exploité par la société Eramet-Comilog. L’objectif de ce travail est de préciser les conditions de formation de ce protore et de le replacer dans l’histoire du remplissage du bassin. Ce protore d'une épaisseur moyenne de 75 m est constitué de carbonates de manganèse ; il a fait l'objet d'une récente campagne de 24 forages carottés d'une profondeur moyenne de 125 m sur le plateau de Bangombé.A travers une approche pluridisciplinaire comprenant l'étude de ces forages et des affleurements clefs du bassin, ce travail porte sur la caractérisation i) de l'environnement de dépôt du protore et des séries qui l'encadrent (du toit du FA au toit du FB) ; ii) du mode de formation des carbonates de Mn à 2,1 Ga et iii) de l'architecture et de la répartition des hautes teneurs en Mn du protore qui représente un gisement potentiel du futur.L’étude pétro-sédimentaire détaillée a permis de distinguer neuf unités (U1 à U9) au sein de la Formation FB organisées suivant un cycle rétrogradant jusqu’à U5 puis progradant jusqu’à U9. Ce découpage montre une évolution du milieu de dépôt depuis un domaine de shoreface contrôlé par des courants deltaïques (U1) évoluant vers des dépôts d’offshore restreint (U2). Ce bassin enregistre ensuite un système de chenaux-levées turbiditiques (U3) qui alimentent un réseau d'injectites reconnu sur l’ensemble du Pl. de Bangombé et qui traverse 150 m de série (U4 à U7) en affectant le protore et ainsi les teneurs en Mn. L'environnement de dépôt du protore (U5 et U6) marque l’isolement du bassin qui devient affamé et contrôlé par une sédimentation biochimique à l’origine du dépôt des carbonates de Mn. L'Unité 7 correspond à la réouverture des apports détritiques en domaine d'offshore supérieur puis en domaine de shoreface dominé par des dépôts de tempêtes et de chenaux sous-aquatiques deltaïques (U8), et enfin lagunaire (U9) dans lequel apparaissent les premiers métazoaires de l’histoire de la planète, suivant une séquence régressive.Une étude géochimique a permis de préciser les conditions de dépôt du protore qui se forme en milieu alcalin anoxique à sub-oxique. Dans ce milieu, nous montrons pour la première fois une précipitation directe des carbonates de Mn sous forme bactériomorphe induite par l'activité photosynthétique des cyanobactéries qui consomment le CO2/HCO3 et conduisent à une augmentation du pH favorable à la formation des carbonates de Mn. L'activité cyanobactérienne est conditionnée par l’absence de courants de fond qui augmentent la turbidité du milieu et stoppent cette dernière.Les corrélations diagraphiques et séquentielles permettent de préciser la répartition spatiale et temporelle du FB permettant ainsi de replacer le protore dans l’histoire tectono-sédimentaire du bassin. Une première phase syn-tectonique (U1 à U3) contrôle l’épaisseur et la mise en place de dépôts turbiditiques dans les parties subsidentes, de dépôts argileux sur les pentes et de dépôt de carbonates sur les hauts-fonds. La seconde phase post tectonique (U4 à U7) permet la mise en place de dépôts relativement isopaques, bien que le protore enregistre une subsidence plus importante au nord du Pl. de Bangombé. On observe ainsi, sur le Plateau de Bangombé, des teneurs en Mn qui augmentent vers le sud alors que l’épaisseur du protore augmente vers le NNE. Postérieurement au dépôt du FB, le protore est structuré par des failles qui le compartimentent en touches de piano limitant ainsi sa continuité sur le Plateau de Bangombé.
https://hal.archives-ouvertes.fr/tel-01621460

tel-01621460
https://hal.archives-ouvertes.fr/tel-01621460
https://hal.archives-ouvertes.fr/tel-01621460/document
https://hal.archives-ouvertes.fr/tel-01621460/file/these_Dubois2017-MnGabon.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Intraguild predation (IGP) is a type of biological interaction involving the killing and consuming of competing species that exploit similar and often limited resources. This phenomenon is widespread among a great variety of taxonomic groups and has already been reported for mosquito (Diptera: Culicidae) larvae. Moreover, the larvae of certain mosquito species of the tribe Sabethini have evolved modified mouthparts ending in rigid apical structures signaling their capacity to be effective intraguild predators. We assumed that IGP confers a selective advantage under severe competitive conditions by both providing an immediate energetic gain and reducing potential competition. Because potential competition is likely to increase with decreasing habitat size, we hypothesized that the proportion of species with modified mouthparts would increase in smaller aquatic habitats. We tested this hypothesis by examining the mosquito species naturally associated with phytotelmata of decreasing sizes in French Guiana. We show that the degree of specialization in mosquito-phytotelm associations is high, suggesting a long coevolutive process. Indeed, short-term interaction experiments confirmed that species with modified mouthparts are able to prey upon similarly-sized intraguild prey and are, thus, effective intraguild predators. In addition, these species are larger and associated with smaller phytotelmata than those with typical mouthparts. Moreover, below a certain threshold of phytotelm size, only species with modified mouthparts were present. These results show that IGP confers a selective advantage under severe competitive conditions and results from the coadaptation of mosquito species to their specific phytotelm habitat. The presence of functionally analogous structures in different mosquito genera also implies that IGP has emerged from convergent evolution in small phytotelmata.
ISSN: 0269-7653

hal-01603304
https://hal.archives-ouvertes.fr/hal-01603304
DOI : 10.1007/s10682-016-9862-3
PRODINRA : 405771