Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD
Résumé : International audience
In the external Western Alps, the collision started with the shortening of the proximal European (Dauphinois) margin. One peculiar feature is the crustal thickening that finally led to the exhumation of the basement External Crystalline Massifs (ECM) during the Neogene. In these massifs, various age of shortening, structural style and sequence of deformation have been proposed leading to different kinematics along the Alpine arc that in turn do not imply the same crustal/lithospheric strength. In this contribution, we present new structural and microstructural data along with Ar/Ar ages from field studies in the Oisans-Grandes Rousses massifs, between Grenoble and Briançon). From balanced cross-sections, we show that about half of the external zone crustal shortening is accommodated within the ECM with similar Ar/Ar ages in all massifs. Furthermore, the shear zones present very large thicknesses (several hundred meters) and do not reactivated either the inherited Liassic normal faults or the Variscan foliation. Finally, the main shortening structures are localized beneath inherited Liassic syn-rift basins. These results suggest that the crust was weak during its shortening. Such behavior is most likely due to the combination of several factors: the crust burial (below the overthrusting internal units) down to about 10km, the presence of weak inherited syn-rift basins, and the strain softening in shear zones that evolve in mica-rich phyllonites. These results are consistent with the studies in the Aar massif and should most likely apply to the Mont Blanc massif, whose relationships with its cover are still debated.
EGU General Assembly
Vienne, Austria

insu-00839426
https://hal-insu.archives-ouvertes.fr/insu-00839426
BIBCODE : 2013EGUGA..15.8837B

Résumé : En 2003 des mesures au spectromètre IR à Transformée de Fourier (FTIR) ont permis d'identifier et de mesurer les COV émis par la décharge à ciel ouvert de la Gabarre, principale de l'île Guadeloupe, située entre une zone urbaine et une mangrove. Ces COV ont été retrouvés (2004) la nuit dans les cités, justifiant les plaintes des riverains. Dans le cadre de cette thèse, des mesures au spectromètre de masse portatif MS 200 ont validé ces résultats du FTIR. De nouvelles mesures au MS 200 ont été menées dans toute la zone de la décharge. Les cités concernées étant à l'opposé du flux synoptique d'Alizés-Est, les facteurs météorologiques permettant la dispersion et le transport des COV de la décharge vers la zone urbaine ont été recherchés. La diminution nocturne de l'intensité des Alizés au dessus de l'ile peut laisser place à des phénomènes locaux tels les brises. L'idée d'une brise terre-mer a été éliminée. Un maillage autou~ de la décharge (cités et mangrove) avec 8 thermomètres a révélé un îlot de chaleur urbain nocturnegénérant une brise thermique d'environ Ims- I (mesurée et calculée). Avec les radiosondages Météo France et un SODAR installé dans la décharge, une très forte stabilité dans les basses couches atmosphériques de la couche limite nocturne avec une inversion de surface d'environ 120mvv apparait. Ces facteurs expliquent la pollution des cités par les COV de la décharge, Un modèlevGaussien en tenant compte a été validé par les mesures de COV.vCette étude peut être étendue à d'autres décharges à ciel ouvert et à d'autres types de traitement de polluants de décharge.
In 2003, the VOC emissions coming from "La Gabarre", the main open landfill in Guadeloupe, located in-between an urban area and a mangrove, were identified and quantified with a portable FTIR spectrometer. In 2004, COVs found at nighttime in the urban area nearby confirmed why residents complain about. As part of this thesis, portable mass spectrometer MS 200 measurements validated these FTIR figures. New systematic SM measurements have been carried on around the landfill. Since the polluted urban area stands on the opposite way of the East Trade winds synoptic flux, aIl the weather factors likely to scatter and transport the dump COVs were scrutinized. At night, the strength of the Trade winds decreases over Guadeloupe, which may give way to local phenomena such as breezes. The occurrence of land/sea breeze was eliminated. A close surveying surrounding the landfill with 8 thermometers both in the projects and in the mangrove revealed an urban heat island causing thermal breezes of about lms-l (measured and calculated). Using soundings from Meteo France, and a SODAR inside the dump, we found a great stability of the night boundary layer with a surface inversion near 120m. Pollution of the nearby urban area with landfill COVs is elucidatcd by the above factors. A transport Gaussian model is in agreement with COV measurements. This study can be extended to different open landfills and different types of polluting matters processes in dumps

http://www.theses.fr/2013AGUY0700/document

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : National audience
The immune system contributes to maintaining the integrity of the organism. It can be the target of many xenobiotics, and immunotoxicology attempts to analyze the immunological alterations caused by exposure to these xenobiotics. Several environmental pollutants are strongly suspected of acting on the immune system to cause a decrease in the organism protective functions. Thus, polycyclic aromatic hydrocarbons, well known for their carcinogenic effects, have also been shown to induce immunosuppressive effects, pro-inflammatory actions and some hypersensitivity reactions, involved in the development of various pathologies. These different immunotoxic effects have mainly been identified by experimental studies on animals and our knowledge of the effects on humans remains incomplete. To better understand the immunotoxic effects of exposure to environmental pollutants and their consequences for human health, it is appropriate to strengthen immunotoxicology studies on humans.
Le système immunitaire contribue à la surveillance et au maintien de l’intégrité de l’organisme. Il peut être la cible de nombreux xénobiotiques, et l’immunotoxicologie s’attache à étudier les différentes atteintes immunologiques induites par l’exposition à ces xénobiotiques. De nombreux polluants environnementaux sont fortement suspectés d’agir sur le système immunitaire pour entraîner une diminution des fonctions de protection de l’organisme. Ainsi, les hydrocarbures aromatiques polycycliques, bien connus pour leurs effets cancérogènes, se sont révélés également capables d’induire des effets immunosuppresseurs, d’entraîner des actions pro-inflammatoires et de majorer certaines réactions d’hypersensibilité, impliqués dans le développement de diverses pathologies. Ces différents effets immunotoxiques ont surtout été identifiés par des études expérimentales chez l’animal et la transposition de ces effets à l’homme reste incomplète. Pour mieux appréhender les effets immunotoxiques de l’exposition aux polluants environnementaux et leurs conséquences sur la santé humaine, il convient donc de renforcer les études en immunotoxicologie chez l’homme.
ISSN: 1775-8785

hal-01467562
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467562
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467562/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467562/file/Effets%20immunotoxiques%20des%20polluants%20environnementaux_accepted.pdf
DOI : 10.1016/j.admp.2016.09.003

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Fractures or discontinuities perpendicular to the least stress σ3 were generated in a synthetic rock analogue (granular, frictional, cohesive, and dilatant) material in axisymmetric extension tests. These fractures are of two types defined by the mean stress σ. When σ is very small, the fractures form through the mode I cracking at tensile σ3 equal to the material tensile strength. The fracture walls have smooth surfaces. At higher σ, these surfaces become rougher, with the topography features forming faint or delicate plumose patterns. The amplitude of the plumose topography increases with σ. The axial stress σ3 at fracturing reduces in magnitude and changes in sign with the σ increase. Thus σ3 orthogonal discontinuities can form at compressive σ3. SEM observations show that these discontinuities are deformation localization bands where the material is characterized by the heterogeneous decohesion and volume and porosity increase due to dilatancy. The band thickness is several grain sizes. At formation, the bands are not opened, so they are not mode I fractures. They become fractures with plumose fractography after the separation of the sample parts along the band. The formation mechanism of these discontinuities or fractures is not completely clear, but it is suggested that it represents a running constitutive instability in the form of dilatancy banding (with further σ increase the bands become inclined to σ1, i.e., shear). The similarity between the experimentally generated plumose surface fractures and natural joints is discussed, and it is suggested that they can be formed as propagating constitutive instabilities.
ISSN: 0148-0227

hal-00585846
https://hal.archives-ouvertes.fr/hal-00585846
DOI : 10.1029/2010JB008104

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Pyrethroids are insecticides frequently used in agriculture and in the home; exposure occurs through dietary and non-dietary pathways, including indoor and outdoor environmental contamination. Our objective was to study the potential determinants of pyrethroid metabolite concentrations measured in children's urine samples and in the dust of their homes. Specifically, we measured urinary metabolites from morning spot samples of 245 six-year- old children living in Brittany (France) in 2009-2012 and from dust vacuumed from the floor of their homes. Mothers reported home insecticide use, dietary habits, sociodemographic data; residential and school proximity to agricultural crops was assessed with spatialized data. The metabolites cis-DBCA, trans-DCCA, cisDCCA, 3-PBA, and F-PBA were detected in 84, 95, 64, 63, and 16% of the urine samples, respectively. Permethrin, cypermethrin, cyfluthrin, deltamethrin, and tetramethrin pyrethroids were detected in 100, 56, 9, 15, and 26% of the dust samples, respectively. Multiple regression analysis suggested diet plays a role in children's exposure, in particular, the food groups "pasta, rice or semolina" (for cis-DCCA and F-PBA), fruit (3-PBA), "breakfast cereals and whole grain bread" (cis-DBCA), and the global proportion of organic food in diet (for cis-DBCA, trans-DCCA). Children with a parent occupationally exposed to pesticides were about 3-times more likely to have higher urinary concentrations of 3-PBA (OR = 2.8, 95% CI [1.2; 6.5]). Dust content was correlated mainly with household insecticide use: higher mean concentrations of permethrin (beta = 0.8 [0.3; 1.3], in mu g/g) and an increased risk of a detectable level of cyfluthrin (OR = 4.7 [1.7; 12.9]) were observed in home dust, for indoor use of at least twice a year. Outdoor insecticide use at least once a year was associated with detection in dust of cypermethrin (OR = 3.0 [1.3; 6.7]) and tetramethrin (OR = 3.7 [1.6; 8.3]). Three positive and one negative correlations (out of 11) between urinary metabolite concentrations and home dust contents of their possible corresponding parent compounds were observed. The strength of this study lies in its concurrent use of biomarkers, environmental measurements, and potential sources of exposure. Its limitations include the use of a single urine sample and imprecise data about pyrethroid use in local agriculture.
ISSN: 0160-4120

hal-01560147
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560147
DOI : 10.1016/j.envint.2017.04.007
PUBMED : 28453973

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
We present Contact Dynamics discrete element simulations of the earthquake-triggered Jiufengershan avalanche, which mobilized a 60 m thick, 1.5 km long sedimentary layer, dipping similar to 22 degrees SE toward a valley. The dynamic behavior of the avalanche is simulated under different assumptions about rock behavior, water table height, and boundary shear strength. Additionally, seismic shaking is introduced using strong motion records from nearby stations. We assume that seismic shaking generates shearing and frictional heating along the surface of rupture, which, in turn, may induce dynamic weakening and avalanche triggering; a simple "slip-weakening'' criterion was adopted to simulate shear strength drop along the rupture surface. We investigate the mechanical processes occurring during triggering and propagation of an avalanche mobilizing shallowly dipping layers. Incipient deformation forms a pop-up structure at the toe of the dip slope. As the avalanche propagates, the pop-up deforms into an overturned fold, which overrides the surface of separation along a decollement. Simultaneously, uphill layers slide at high velocity (125 km/h) and are folded and disrupted as they reach the toe of the dip slope. The avalanche foot forms a wedge that is pushed forward as deformed rocks accrete at its rear. We simulated five cross sections across the Jiufengershan avalanche, which differ in the geometry of the surface of separation. Topographic and simulated surface profiles are similar. The friction coefficient at the surface of separation determined from back analysis is abnormally low (mu(SS) = 0.2), possibly due to lubrication by liquefied soils. The granular deposits of simulated earthquake- and rain-triggered avalanches are similar.
ISSN: 0148-0227

hal-00420882
https://hal.archives-ouvertes.fr/hal-00420882
DOI : 10.1029/2008JF001075

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : International audience
Mount Pinatubo volcano erupted in June 1991 in the main island of Luzon belonging to the Philippines archipelago. Huge economic losses and population exodus have followed. This major crisis has been relayed with other crises due to rainfed lahars which have been supplied with eruption deposits. These lahars have occurred every year since 1991 during the rainy season. They will probably last until 2005. After a brief presentation of the Philippine official response system to disasters, this paper draws up a critical analysis of the different kinds of institutional and social responses deployed to manage the different crisis and post-crisis phases of this event. Based on three viewpoints: from population, media and other actors, this analysis attempts to point out the strengths and weaknesses of the official management system, especially by studying the efficiency and the range of the solutions taken. So, it appears that the management of the June 1991 main crisis (eruption) was a success. On the other hand, difficulties have occurred with lahars risk management. Indeed, these lahars have obliged the authorities to protect and relocate thousands of people. In spite of persistent problems, the management system (monitoring/warning/evacuation) of lahar crises improves year after year. Failures appear especially within the rehabilitation program (protection/rehousing). Many direct (lack of means, preparedness, coordination, dialog,
etc.) and indirect (politico-administrative, socio-economic, cultural contexts) factors come together to lock the wheels of
the institutional response system. They defer the socio-economic start of this vital northern Philippines area.
GeoJournal

halshs-00119436
https://halshs.archives-ouvertes.fr/halshs-00119436
https://halshs.archives-ouvertes.fr/halshs-00119436/document

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Microsatellites (SSRs) are highly susceptible to expansions and contractions. When located in a coding sequence, the insertion or the deletion of a single unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR creates a frameshift. As a consequence, one would expect to find only very few of these SSRs in coding sequences because of their strong deleterious potential. Unexpectedly, genomes contain many coding SSRs of all types. Here, we report on a study of their evolution in a phylogenetic context using the genomes of four primates: human, chimpanzee, orangutan, and macaque. In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions. We show that the rate of substitution in all types of coding SSRs is typically two times higher than in the rest of coding sequences. Additionally, we observe that although numerous coding SSRs are created and lost by substitutions in the lineages, their numbers remain constant. This last observation suggests that the coding SSRs have reached equilibrium. We hypothesize that this equilibrium involves a combination of mutation, drift, and selection. We thus estimated the fitness cost of mono-SSRs and show that it increases with the number of units. We finally show that the cost of coding mono-SSRs greatly varies from function to function, suggesting that the strength of the selection that acts against them can be correlated to gene functions.
ISSN: 1759-6653

hal-01544762
https://hal.archives-ouvertes.fr/hal-01544762
DOI : 10.1093/gbe/evt003

Éditeur(s) : HAL CCSD American Public Health Association
Résumé : International audience
BACKGROUND: It is well established that high adherence to HIV-infected patients on highly active antiretroviral treatment (HAART) is a major determinant of virological and immunologic success. Furthermore, psychosocial research has identified a wide range of adherence factors including patients' subjective beliefs about the effectiveness of HAART. Current statistical approaches, mainly based on the separate identification either of factors associated with treatment effectiveness or of those associated with adherence, fail to properly explore the true relationship between adherence and treatment effectiveness. Adherence behavior may be influenced not only by perceived benefits-which are usually the focus of related studies-but also by objective treatment benefits reflected in biological outcomes. METHODS: Our objective was to assess the bidirectional relationship between adherence and response to treatment among patients enrolled in the ANRS CO8 APROCO-COPILOTE study. We compared a conventional statistical approach based on the separate estimations of an adherence and an effectiveness equation to an econometric approach using a 2-equation simultaneous system based on the same 2 equations. RESULTS: Our results highlight a reciprocal relationship between adherence and treatment effectiveness. After controlling for endogeneity, adherence was positively associated with treatment effectiveness. Furthermore, CD4 count gain after baseline was found to have a positive significant effect on adherence at each observation period. This immunologic parameter was not significant when the adherence equation was estimated separately. In the 2-equation model, the covariances between disturbances of both equations were found to be significant, thus confirming the statistical appropriacy of studying adherence and treatment effectiveness jointly. CONCLUSIONS: Our results, which suggest that positive biological results arising as a result of high adherence levels, in turn reinforce continued adherence and strengthen the argument that patients who do not experience rapid improvement in their immunologic and clinical statuses after HAART initiation should be prioritized when developing adherence support interventions. Furthermore, they invalidate the hypothesis that HAART leads to "false reassurance" among HIV-infected patients.
ISSN: 0025-7079

hal-00875196
https://hal.archives-ouvertes.fr/hal-00875196
DOI : 10.1097/MLR.0b013e3182422f61
PUBMED : 22362167

Résumé : En 2013, Le Groupe d'experts Intergouvernemental sur l'Evolution du Climat (GIEC) publie son cinquième rapport concernant les changements climatiques. Il y est souligné que le réchauffement climatique est sans équivoque, et que de nouvelles émissions de gaz à effet de serre impliqueront une poursuite du réchauffement et des changements affectant toutes les composantes du système climatique. En région tropicale, une hausse de la température, ainsi qu'une intensification des événements de sécheresse et de pluviométrie extrêmes sont à prévoir. C'est dans ce contexte que s'inscrit ce travail, dont le but est d'étudier la réponse de la forêt tropicale à ces changements climatiques prédits en Guyane Française. Pour ce faire, j'ai utilisé les données du dispositif de suivi forestier de Paracou pour construire un modèle de dynamique individuel basé sur les traits fonctionnels des arbres. Un modèle de mortalité a d'abord été réalisé puis couplé à un modèle de croissance.Le modèle couplé ainsi construit permet de modéliser la croissance et la mortalité des arbres sur un pas de temps de 2 ans tout en tenant compte de leur ontogénie et de leurs traits fonctionnels. Ce modèle a d'abord été appliqué aux essences commerciales de Guyane Française en forêt naturelle et exploitée en y ajoutant un indice de stress hydrique. Ceci permet de montrer que le stress hydrique fait baisser la croissance et augmenter la mortalité, tandis que l'exploitation a l'effet inverse. Malgré le signal commun, différentes réponses sont observées selon les espèces. Le modèle a ensuite été appliqué à la communauté en forêt naturelle pour identifier les drivers climatiques et les processus impactés. Il ressort que la croissance est impactée par le stress hydrique et la température, et que la mortalité est impactée par le stress hydrique et la pluviométrie totale.Ces résultats ont enfin permis de construire un modèle complet de dynamique forestière climat dépendant, et de simuler l'évolution d'une communauté pendant un siècle selon différents scénarios correspondant aux prédictions du GIEC. Les simulations mettent en évidence une très forte diminution de la croissance, ainsi qu'une plus faible diminution de la mortalité. Ceci entraine une diminution notable de la surface terrière, du diamètre quadratique et de la biomasse fraiche. Une analyse de sensibilité montre que ces changements sont principalement dus à l'augmentation sévère des températures prédites pour le siècle à venir. Des pistes de réflexion sur les enjeux de modélisation et les échelles considérées sont proposées en discussion de ce travail.
In 2013 the intergovernmental panel on climate change (ipcc) publishes its fifth report. This report underlines that an increase of temperature and a strengthening of drought and extreme rainfall are expected in tropical regions. This work was made in this context of climate changes, and aimed to study the response of the rainforest to predicted climate changes. To do this, i used the data from the study site of Paracou French Guiana to build an individual based dynamics model based on the functional traits of trees. This model was first applied to species with a commercial interest in French Guiana, in natural and logged forest and adding a water stress index as predictor. Water stress decreases growth and increases mortality, while logging had the opposite effect. The model was then applied to the community in natural forest for identifying potential climate drivers and impacted processes. Growth is impacted by the water stress and temperature and mortality is imp acted by the water stress and the total rainfall. These results allowed us to build a climate dependent model of forest dynamics and to run simulations of the evolution of a community under different scenarios for the next century. Simulations showed a decrease of growth and a small decrease of mortality. This resulted in a substantial decrease of basal area, squared diameter and fresh biomass.

http://www.theses.fr/2014AGUY0802/document

Éditeur(s) : HAL CCSD Geological Society of America
Résumé : International audience
In this study, a novel application of a statistical approach is utilized for analysis of downhole logging data from Miocene-aged siliciclastic shelf sediments on the New Jersey Margin (eastern USA). A multivariate iterative nonhierarchical cluster analysis (INCA) of spectral gamma-ray logs from Integrated Ocean Drilling Program (IODP) Expedition 313 enables lithology within this siliciclastic succession to be inferred and, through comparison with the 1311 m of recovered core, a continuous assessment of depositional sequences is constructed. Signifi cant changes in INCA clusters corroborate most key stratigraphic surfaces interpreted from the core, and this result has particular value for surface recognition in intervals of poor core recovery. This analysis contributes to the evaluation of sequence stratigraphic models of large-scale clinoform complexes that predict depositional environments, sediment composition, and stratal geometries in response to sea-level changes. The novel approach of combining statistical analysis with detailed lithostratigraphic and seismic refl ection data sets will be of interest to any scientists working with downhole logs, especially spectral gamma-ray data, and also provides a reference for the strengths and weaknesses of multi component analysis applied to continental margin lithofacies. The method presented here is appropriate for evaluating successions elsewhere and also has value for hydrocarbon exploration where sequence stratigraphy is a fundamental tool.
EISSN: 1553-040X

insu-00858238
https://hal-insu.archives-ouvertes.fr/insu-00858238
DOI : 10.1130/GES00913.1

Éditeur(s) : HAL CCSD
Résumé : A section of ancient fast-spreading ocean crust was sampled at Wadi Gideah, located in the Wadi Tayin Massif of the Oman ophiolite. This sample suite was used for generating a coherent data set combining various petro-geochemical and structural investigations, with the aim of building a reference section for advancing our understanding of crustal accretion processes at fast-spreading mid-ocean ridges. Additionally, this study focuses on one outcrop that represents part of the fossil axial melt lens (AML).Major and trace element analyses reveal a trend of chemical evolution up section in the lower crust, with a marked difference between the layered gabbros and the foliated gabbros above. Petrological modeling shows that the chemical evolution up section can be produced by hydrous fractionation crystallization, with melt H2O contents of ~0.8 wt% and 0.8 to 1.2 wt% for the lower and upper crust, respectively. Together with the observed very steep bulk Zr/Hf vs. Zr gradient, high F and Cl content of magmatic amphibole, general Nb-Ta depletion of melts compared with NMORB, and high Sr87/Sr86 ratio compared with modern fast-spread crust, this suggests that Wadi Gideah layered gabbros were accreted by crystallization of ascending melts in sills, in a context of subduction initiation. The distinct changes in chemical trends and average grain size at the layered to foliated gabbro transition are tentatively explained by enhanced hydrothermal cooling deeper than the AML. The gabbro/dike transition displays complex structural and lithological relationships that, together with fractional crystallization modeling, point to episodic vertical movements of the AML. Plagioclase crystallographic preferred orientations (CPO) measured over the whole gabbro section are always consistent with magmatic flow. The CPO strength generally increases downward, with more scattering in the layered gabbro section. From the top to the bottom of the layered gabbros, CPO become progressively more prolate, possibly reflecting increasing shear induced by active mantle flow underneath.Wadi Gideah lower crust recorded a formation history consistent with a hybrid accretion model, combing several processes such as downward magmatic flow and/or upward melt migration in the upper foliated gabbros, sill intrusions in the layered gabbros, and deep hydrothermal circulation. The latter was presumably focused in channels, preserved today as several, up to 100 m wide zones of extensively altered former layered gabbro, cross-cutting the magmatic layering. These metagabbros display significantly higher Sr87/Sr86 ratio, late stage magmatic phases, and evidence for high temperature partial melting.
Une coupe d'ancienne croute océanique rapide a été échantillonnée dans le Wadi Gideah, situé dans le Massif de Wadi Tayin de l'Ophiolite d'Oman. Cette série d'échantillons a permis de générer un jeu de données cohérent, combinant des études pétro-géochimiques et structurales, dans le but de construire une coupe de référence pour mieux contraindre notre compréhension des processus d'accrétion crustale aux dorsales océaniques rapides. Ce travail intègre aussi l'étude détaillée d'un affleurement représentant en partie la lentille magmatique axiale (LMA) fossile.Les analyses d'éléments majeurs et traces révèlent une évolution chimique dans la croûte inférieure, avec une nette différence entre les gabbros lités et les gabbros foliés sus-jacents. La modélisation pétrologique montre que l'évolution chimique vers le haut peut être produite par cristallisation fractionnée hydratée, avec des teneurs en H2O des magmas de ~0.8 wt% dans la croute inférieure et 0.8 to 1.2 wt% dans la croute supérieure. Combiné aux forts gradients de Zr/Hf vs. Zr, aux teneurs élevées de F et Cl dans les amphiboles magmatiques, à l'appauvrissement général en Nb-Ta des magmas comparé aux NMORB, et aux rapports Sr87/Sr86 élevés comparés à la croûte rapide moderne, ceci suggère que les gabbros lités du Wadi Gideah ont été formés par la cristallisation des magmas ascendants dans des sills, dans un contexte d'initiation de subduction. Les changements de signature géochimique et de taille de grain à la transition entre gabbros lités et gabbros foliés témoignent possiblement d'un fort refroidissement hydrothermal plus profond que la LMA. La transition complexe filonien/gabbro montre des relations structurale et lithologiques complexes, qui, combinées o la modélisation de la cristallisation fractionnée, traduisent les mouvements verticaux épisodiques de la LMA. Les orientations préférentielles cristallographiques (OPC) des plagioclases mesurées sur l'ensemble de la coupe dans les gabbros témoignent toujours d'une déformation magmatique. L'intensité des OPC a tendance à augmenter vers le bas, avec une plus forte variabilité dans les gabbros lités. Dans les gabbros lités, les OPC sont de plus en plus linéaires vers le bas, résultant possiblement d'un cisaillement plus fort induit par l'écoulement actif du manteau sous-jacent.La croûte inférieure dans le Wadi Gideah a enregistré une histoire compatible avec un modèle d'accrétion hydride, combinant plusieurs processus tels que l'écoulement magmatique vers le bas et/ou la migration de liquides magmatiques vers le haut dans les gabbros foliés supérieurs, l'intrusion de sills dans les gabbros lités, et une circulation hydrothermale profonde. Cette dernière était probablement concentrée dans des chenaux, préservés aujourd'hui sous la forme de plusieurs zones, dont l'épaisseur atteint 100 m, de gabbros lités fortement altérés, recoupant le litage magmatique. Ces métagabbros ont des rapports Sr87/Sr86 élevés, comportent des phases magmatiques tardives et montrent des évidences de fusion partielle.
https://hal.archives-ouvertes.fr/tel-01302675

tel-01302675
https://hal.archives-ouvertes.fr/tel-01302675
https://hal.archives-ouvertes.fr/tel-01302675/document
https://hal.archives-ouvertes.fr/tel-01302675/file/Th%C3%A8se_Tim-Mueller_2015.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We have inferred the deformation mechanisms of antigorite by high-resolution EBSD mapping of samples from Cerro del Almirez ultramafic massif (Betic Cordillera, SE Spain). Textural relations and phase diagram calculations constrain the foliation development conditions to the subduction prograde path at up to 600-630 °C and 1.6-1.9 GPa. Deformation was followed by static annealing of antigorite at ca. 680 °C. The Crystal Preferred Orientation (CPO) of antigorite is characterised by a strong alignment of (001) poles normal to the foliation plane and a weaker, but clear, parallelism between [100] axes and the macroscopic lineation defined by the elongation of magnetite aggregates. Analysis of misorientations across subgrains shows predominance of [010] rotation axis, consistent with activation of the [100](001) slip system. However, tilt subgrain boundaries subparallel to (100), probably formed by edge dislocations of this system, are subsidiary. Most subgrain boundaries are subparallel to (001) planes. They are interpreted as (001) twins wherein continuing viscoplastic deformation resulted in a slight increase of the misorientation between the twins. Modelling of the evolution of the antigorite CPO using a lower bound approach and considering different deformation regimes and sets of basal and non-basal slip systems has shown that intensities of [100] and [010] maxima reflect the relative strength of the antigorite [100](001) and [010](001) systems. Activation of other basal or non-basal slip systems does not change significantly the CPO patterns, but results in less concentrated CPO. 3D transpression models better reproduce the CPO of natural antigorite serpentinites. We propose that the widespread occurrence of strong CPO in high-pressure antigorite serpentinite is consistent with deformation by dislocation creep with dominant glide on [hk0](001), together with the activation of twinning, implying that a power law rheology would better account for the mechanical behaviour of antigorite serpentinite deep in the subduction channel and mantle wedge.
ISSN: 0012-821X

hal-00795511
https://hal.archives-ouvertes.fr/hal-00795511
DOI : 10.1016/j.epsl.2012.06.049

Éditeur(s) : HAL CCSD
Résumé : The Earth's magnetic field shows a large range of temporal variations from the year to several million years. I studied during my PhD thesis several aspects of these fluctuations, from recent secular variations to reversals. The first part of my manuscript deals with archeomagnetism, a discipline that allows to track the temporal variations of the Earth's magnetic field through millennia, mainly from archeological materials. I studied two sets of samples , one from Greece (Neolithic period 6800-3200 B.C.) and the other from Mexico (Palenque, Maya Classic period 320-840 A.D.), to acquire new archeointensity data in order to better constrain the secular variation of the geomagnetic field. By comparing my data with those available in the literature and with the various global and regional models, I showed that the secular variations during the Neolithic in Greece and during the first millennium in Central America are poorly defined. My data suggest that local components, not described by global models, may exist in these regions. They reinforce the importance of developing specific regional models. As a consequence, the acquisition of new high quality data is of main importance. The second part presents the description of a geomagnetic field reversal. This work was based on two points : first by studying transitional directions to provide new constraints on the possible preferred longitudinal paths of virtual geomagnetic poles (VGPs) and second by checking transitional paleointensities obtained on a volcanic sequence in Akaroa volcano (New Zealand). Indeed the transitional field intensity is significantly higher than the field intensity before and after the reversal. We re-sampled this sequence, and the directional results show a complex sequence of N-T-R-T-N-T-R polarity. The transitional VGPs obtained are clustered in two longitudinal bands through Australia and America. This observation seems to reinforce the assumption of a core-mantle interaction over several million years. Following a rock magnetic study, I selected samples that could provide a value for the Thellier and multispecimen paleointensity methods. The obtained paleointensity are relatively low (about 20 μT) during the polarity change and strong at the end of the sequence. Based both on the field strength values and on the radiochronological ages, showing that the sequence was erupted in a very short time, I suggest that only the C4AR.1n-C4Ar.1r reversal was recorded in this sequence. In this assumption, the reversal shows a complex path comparable to other reversals recorded in the northern hemisphere (for example the Steens Mountain ), including a rebound before stabilizing. Finally the last part is devoted to the development of a new methodology and a new apparatus to determine absolute paleointensity. Following the low success rate of paleointensity experiments from the previous study, I decided to test the multispecimen protocol, which can be applied to samples yielding a predominant multidomaine behavior. The main technical drawback of this method lies in the application of the laboratory field along the natural remanent magnetization, a difficult task to perform accurately in standard paleointensity ovens. Thus, we decided to adapt sample holders from our standard oven in order to allow the sample orientation in space and to develop an ultra-fast heating oven prototype particularly well-suited for this method, allowing to apply the laboratory field in the 3 dimensions. I checked the different multispecimen protocols on historical lavas from Reunion and Etna volcano, yielding very different magnetic mineralogies. For all flows, I obtained paleointensities very close from the expected values, regardless from the magnetic mineralogy, revealing the feasibility of our apparatus and the promising interest of the method. The application of various corrections on the statistical estimation of the intensity value or on the cooling rate had no significant impact on my results.
La première partie de ma thèse porte sur l'archéomagnétisme, discipline qui permet de retracer l'évolution temporelle du champ magnétique terrestre au travers des derniers millénaires, principalement à partir des matériaux archéologiques. J'ai étudié deux jeux d'échantillons provenant pour l'un de la Grèce (période néolithique, 6800-3200 avant J.C.) et pour l'autre du Mexique (Palenque, période Maya Classique 320-840 après J.C.), dans le but d'acquérir de nouvelles données d'archéointensité et de mieux contraindre la variation séculaire du champ magnétique terrestre. La comparaison de mes données avec celles disponibles dans la bibliographie et avec les différents modèles globaux et régionaux a mis en évidence que les variations séculaires au Néolithique en Grèce et au cours du premier millénaire en Amérique Centrale sont très mal définies. Mes données suggèrent que des composantes locales, non prisent en compte dans les modèles globaux peuvent exister au niveau de ces régions. Elles renforcent l'intérêt de développer des modèles régionaux précis. Pour ce faire, l'acquisition de nouvelles données de haute qualitéest un élément majeur. La deuxième partie traite de la description d'un renversement du champ magnétique terrestre. Cette étude a été basée sur deux points précis : étudier les directions transitionnelles afin d'apporter de nouvelles contraintes sur le possible confinement longitudinal des pôles géomagnétiques virtuels (PGV) d'une part, et d'autre part vérifier des paléointensités transitionnelles obtenues sur la séquence volcanique d'Akaroa (Nouvelle Zélande), dont l'intensité est significativement supérieure à celles des intensités avant et après le renversement. Nous avons ré-échantillonné cette séquence, et l'évolution directionnelle obtenue pour ce renversement est une succession complexe de polarités N-T-R-T-N-T-R. Les PGV obtenus semblent se regrouper sous deux bandes longitudinales sous l'Australie et l'Amérique, ce qui renforce l'hypothèse d'une interaction entre le manteau et le noyau sur plusieurs millions d'années. Suite à une étude de minéralogie magnétique, j'ai sélectionné les échantillons susceptibles de fournir une valeur de paléointensité par les méthodes de Thellier et du multispecimen. Les paléointensités obtenues sont relativement faibles (environ 20 μT) au cours du changement de polarité et forte à la fin de la séquence. Mon interprétation, basée à la fois sur les valeurs de l'intensité du champ et sur les données radiochronologiques montrant que la séquence s'est mise en place très rapidement, est de considérer que seul le renversement C4Ar.1n-C4Ar.1r a été enregistré dans cette séquence. Dans cette hypothèse, le renversement montre un cheminement complexe comparable à d'autres renversements enregistrés dans l'hémisphère nord (comme celui de la Steens Mountain par exemple), incluant un phénomène de rebond avant de se stabiliser. La troisième partie de ma thèse est consacrée au développement d'une nouvelle méthodologie et d'un nouvel appareillage pour déterminer des paléointensités. Le faible taux de réussite des expériences de paléointensité de l'étude précédente m'a poussé à m'intéresser au protocole multispecimen, qui peut s'appliquer aux échantillons possédant un comportement polydomaine. L'inconvénient technique majeur de cette méthode réside dans l'application du champ le long de l'aimantation naturelle, difficile à réaliser avec précision dans les fours standards. Pour ce faire, nous avons décidé de développer des porte-échantillons permettant d'orienter les échantillons dans l'espace pour le four standard et un prototype de four à chauffage ultra-rapide particulièrement bien adapté avec la possibilité d'orienter le champ appliqué dans les 3 dimensions. J'ai testé les différents protocoles de la méthode sur des laves historiques de la Réunion et de l'Etna, possédant des minéralogies très différentes. Pour l'ensemble des coulées étudiées, j'ai obtenu des paléointensités très proches des valeurs attendues, et ce indépendamment de la minéralogie, révélant ainsi le faisabilité de notre appareillage et le côté prometteur de la méthode. L'application de diverses corrections sur la statistique d'estimation de la valeur de l'intensité ou sur le taux de refroidissement n'ont eu aucun impact notable sur mes résultats.
https://tel.archives-ouvertes.fr/tel-00719380

tel-00719380
https://tel.archives-ouvertes.fr/tel-00719380
https://tel.archives-ouvertes.fr/tel-00719380/document
https://tel.archives-ouvertes.fr/tel-00719380/file/thesefanjat2012.pdf

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
We show that MLCK (myosin light chain kinase) plays a key role in cell cycle progression of hepatocytes: either chemical inhibitor ML7 or RNA interference led to blockade of cyclin D1 expression and DNA replication, providing evidence that MLCK regulated S phase entry. Conversely, inhibition of RhoK by specific inhibitor Y27632 or RhoK dominant-negative vector did not influence progression in late G1 and S phase entry. Inhibition of either MLCK or RhoK did not block ERK1/2 phosphorylation, whereas MLCK regulated ERK2-dependent p70S6K activation. In addition, DNA synthesis was reduced in hepatocytes treated with p70S6K siRNA, demonstrating the key role played by the kinase in S phase entry. Interestingly, after the G1/S transition, DNA replication in S phase was no longer dependent on MLCK activity. We strengthened this result by ex vivo experiments and evidenced an MLCK-dependent window in late G1 phase of regenerating liver after two-thirds partial hepatectomy. In conclusion, our results underline an MLCK-dependent restriction point in G1/S transition, occurring downstream of ERK2 through the regulation of p70S6K activation, and highlighting a new signaling pathway critical for hepatocyte proliferation.
ISSN: 0270-9139

hal-00702089
https://hal.archives-ouvertes.fr/hal-00702089
DOI : 10.1002/hep.21222
PUBMED : 16799973

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : During the Neoproterozoic orogeny, the middle crust of the Araçuaí belt underwent widespread partial melting. At the regional scale, this anatectic domain is characterized by a progressive rotation of the flow direction from south to north, suggesting a 3-D deformation of the anatectic middle crust. To better determine whether melt volumes present in the anatectic middle crust of the Araçuaí orogen were large enough to allow a combination of gravity-driven and convergence-driven deformation, we used the titanium-in-quartz (TitaniQ) geothermometer to estimate the crystallization temperatures of quartz grains in the anatectic rocks. When possible, we compared these estimates with thermobarometric estimates from traditional exchange geothermobarometers applied to neighboring migmatitic kinzigites. TitaniQ temperatures range from 750 to 900 °C, suggesting that quartz starts crystallizing at minimum temperatures of ≥ 800 °C. These results, combined with the bulk-rock chemical composition of diatexites, allows the estimation of a minimum of ~ 30% melt and a corresponding viscosity of ~ 109–1010 Pa s. Such a minimum melt content and low viscosity are in agreement with interconnected melt networks observed in the field. Considering that these characteristics are homogeneous over a wide area, this supports the finding that the strength of the middle crust was severely weakened by extensive partial melting, making it prone to gravity-driven flow and lateral extrusion.
ISSN: 1869-9510

hal-01116434
https://hal.archives-ouvertes.fr/hal-01116434
DOI : 10.5194/se-5-1223-2014

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
The outstanding exposure of deformation bands in a multilayer sequence of the Orange quarry, Provence, France, motivates a study investigating the development and controls of deformation band geometries by field mapping combined with finite element modeling. Field mapping yields new insights into angular relations between, and evolution of, the deformation bands as well as provides input parameters for the setup and boundary conditions of the numerical simulations using ADELI 2D. In particular, reverse-sense deformation bands are found to have developed within three of the four exposed layers of the multilayer stack with similar orientations to bedding, indicating layer-parallel contraction. Numerical simulations, carried out as a parametric study to investigate the influence on deformation band development and geometry, successfully reproduce the sequential development of deformation bands in the three layers as seen in the field as well as recreate the observed angular geometries of similar to 39 degrees to the maximum compression. This angular relationship is put into context with observations from other field studies and theoretical values to explore controls of deformation band orientations. Furthermore, band localization is impeded in the model by increased layer cohesive strength, demonstrating the importance of host-rock property variations on where localization of bands within the multilayer sequence. Results from both field investigation and numerical simulations are consistent with regional tectonics, where the strata underwent gentle folding due to thrust faulting at depth, and bring further insight into the development and geometry of deformation bands in both extensional and contractional tectonic regimes.
ISSN: 0148-0227

hal-00639452
https://hal.archives-ouvertes.fr/hal-00639452
DOI : 10.1029/2011JB008365

Éditeur(s) : HAL CCSD Elsevier
Résumé : The slow advance of a crack in soda-silicate glasses was studied at nanometer scale by in-situ and real-time atomic force microscopy (AFM) in a well-controlled atmosphere. An enhanced diffusion of sodium ions in the stress-gradient field at the sub-micrometric vicinity of the crack tip was revealed through several effects: growth of nodules in AFM height images, changes in the AFM tip–sample energy dissipation. The nodules patterns revealed a dewetting phenomenon evidenced by ‘breath figures'. Complementary chemical micro-analyses were done. These experimental results were explained by a two-step process: (i) a fast migration (typical time: few milliseconds) of sodium ions towards the fracture surfaces as proposed by Langford et al. [J. Mat. Res. 6 (1991) 1358], (ii) a slow backwards diffusion of the cations as evidenced in these AFM experiments (typical time: few minutes). Measurements of the diffusion coefficient of that relaxing process were done at room temperature. Our results strengthen the theoretical concept of a near-surface structural relaxation due to the stress-gradient at the vicinity of the crack tip. The inhomogeneous migration of sodium ions might be a direct experimental evidence of the presence of sodium-rich channels in the silicate structure [A. Meyer et al., Phys. Rev. Let. 93 (2004) 027801].
ISSN: 0022-3093

hal-00407634
https://hal.archives-ouvertes.fr/hal-00407634
DOI : 10.1016/j.jnoncrysol.2006.09.034

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : International audience
The interplay between tectonics and erosion has a predominant control on the evolution of the morphology of mountain belts. Here we investigate the modalities of deformation in Central Nepal on a c. 100 ka time scale in response to tectonic and external forcings, through the use of a finite-element thermomechanical model coupled with an integrative denudation formulation that accounts for fluvial incision and hillslope landsliding. We study the complex coupling existing between tectonics and erosion, with special emphasis on the influences of rock strength and rainfall distributions. Our results underline the key role played by lithologic variations in the elevation of both rivers and mean topography. We show that the location of the Main Frontal Thrust is mainly controlled by the low erodability of the unconsolidated sandstone in the Siwaliks Hills. As previously suspected (Burbank et al. 2003), our simulations demonstrate that the pattern of uplift in Nepal is mainly dependent on both erodability and fault geometry, rather than on rainfall distribution.
ISSN: 2041-4927

hal-01543331
https://hal-amu.archives-ouvertes.fr/hal-01543331
DOI : 10.1144/GSL.SP.2006.253.01.18