Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : During the GWADASEIS cruise (Lesser Antilles volcanic arc, February-March 2009) a very high resolution (VHR) seismic-reflection survey was performed in order to constrain Late Quaternary to Present faulting. The profiles we obtained evidence frequent "ponding" of reworked sediments in the deepest areas, similar to the deposition of Mediterranean "homogenites". These bodies are acoustically transparent (few ms t.w.t. thick) and are often deposited on the hanging walls of dominantly normal faults, at the base of scarps. Their thickness appears sufficient to compensate (i.e. bury) co-seismic scarps between successive earthquakes, resulting in a flat and horizontal sea floor through time. In a selected area (offshore Montserrat and Nevis islands), piston coring (4 to 7m long) was dedicated to a sedimentological analysis of the most recent of these particular layers. It corresponds to non-stratified homogenous calcareous silty sand (reworked calcareous plankton and minor volcanoclastics). This layer can be up to 2 m thick, and overlies fine-grained hemipelagites. The upper centimeters of the latter represent the normal RedOx water/sediment interface. Pb-210 and Cs-137 activities lack in the massive sands, while a normal profile of unsupported Pb-210 decrease is observed in the hemipelagite below, together with a Cs-137 peak corresponding to the Atmospheric Nuclear Experiments (1962). The RedOx level was thus capped by a recent instantaneous major sedimentary event considered as post-1970 AD; candidate seismic events to explain this sedimentary deposits are either the 16 March 1985 earthquake or the 8 October 1974 one (M-w = 6.3 and M-w = 7.4, respectively). This leads to consider that the syntectonic sedimentation in this area is not continuous but results from accumulation of thick homogenites deposited after the earthquakes (as observed in the following weeks after Haiti January 2010 event, McHugh et al., 2011). The existence of such deposits suggests that, in the area of study, vertical throw likely results from cumulated effects of separated earthquakes rather than from aseismic creep. Examination of VHR profiles shows that all major co-seismic offsets are recorded in the fault growth sequence and that co-seismic offsets can be precisely estimated. By using a sedimentation rate deduced from Pb-210 decrease curve (0.5 mmyr(-1)) and taking into account minor reworking events detected in cores, we show that the Redonda system may have been responsible for five > M-6 events during the last 34 000 yr. The approach presented in this work differs from fault activity analyses using displaced sets of isochronous surfaces and postulating co-seismic offsets. Combining VHR seismic imagery and coring we can decipher co-seismic vs. slow continuous displacement, and thus actually estimate the amplitude and the time distribution of major co-seismic offsets.
Natural Hazards And Earth System Sciences (1561-8633) (Copernicus Gesellschaft Mbh), 2012 , Vol. 12 , N. 5 , P. 1755-1767

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00089/20040/21990.pdf
DOI:10.5194/nhess-12-1755-2012
http://archimer.ifremer.fr/doc/00089/20040/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This paper presents Digital Image Correlation (DIC) and Infrared Thermography (IRT) methods to investigate the thermomechanical behavior of an aluminum at the microstructural scale. Electron BackScattered Diffraction (EBSD) is used to characterize the microstructure of a 3 mm thick specimen with centimetric grain size. This study combines the following imaging techniques: DIC to obtain displacement and strain fields during the test, and IRT to estimate temperature and heat source fields induced by the mechanical loading. Ultimately, the aim of this methodology is to provide energy balance during mechanical test at the scale of the microstructure, in order to propose thermomechanical con-stitutive modelling of crystalline plasticity.
ISSN: 0143-8166

hal-01287711
https://hal.archives-ouvertes.fr/hal-01287711
https://hal.archives-ouvertes.fr/hal-01287711/document
https://hal.archives-ouvertes.fr/hal-01287711/file/Local_experimental_investigations_Li_al_2016.pdf
DOI : 10.1016/j.optlaseng.2016.01.001

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. The area is characterized by very localized NSextension at a rate of1.5cm/year, the occurrence of frequent and intensive microseismic crises and occasionalmoderate to large earthquakes like in 1995 (Mw=6.1).Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary naturalobservatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studieshave improved our view about fault geometry and mechanics within CRL, but there is still a critical need for a betterknowledge of the structure at depth both for the accuracy of earthquake locations and for mechanical interpretationof the seismicity.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by usingrecently developed methodologies of structural imaging, in order to determine at the same time and with highresolution, the local 3D structure and the earthquake locations.We perform an iterative joint determination of 3D velocity model and earthquake coordinates. In a first step, Pand S velocity models are determined using first arrival time tomography method proposed by Taillandier et al.(2009). It consists in the minimization of the cost function between observed and theoretical arrival times which isachieved by the steepest descent method (e.g. Tarantola 1987). This latter requires computing the gradient of thecost function by using the adjoint state method (Chavent 1974). In a second step, earthquakes are located in thenew velocity model with a non-linear inversion method based on a Bayesian formulation (Gesret et al. 2015). Step1 and 2 are repeated until the cost function no longer decreases.We present preliminary results consisting in: (1) the adjustement of a 1D velocity model that is used as initialmodel of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquakelocation.In addition to the tomographic imaging, we perform a preliminary receiver function analysis of teleseismic datarecorded by the broadband stations of the CRL network. The RF analysis should provide the interface depthsbeneath seismometers and increase the imaging resolution of the upper crustal structures provided by the 3Dtomography. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar aspossible to the observed RF for a subset of data. We compare the identified interfaces with structures imaged bythe tomography.
EGU general assembly 2016
Vienne, Austria

hal-01306224
https://hal-mines-paristech.archives-ouvertes.fr/hal-01306224

Éditeur(s) : HAL CCSD
Résumé : International audience
In this paper, we use a segmentation method applied to the plants images analysis. The segmentation gives groups of pixels, and we propose to use merging operators to address the most relevant groups in order to improve the recognitions systems performance. In particular, we use an operator called Pi fully reinforced. The experiments carried out show that the use of Pi improves outcomes for structuring groups of pixels.
Advanced Information Networking and Applications
Fukuoka, Japan

hal-00652125
https://hal.archives-ouvertes.fr/hal-00652125
DOI : 10.1109/WAINA.2012.40

Éditeur(s) : Public Library Science
Résumé : Observing spatial and temporal variations of marine biodiversity from non-destructive techniques is central for understanding ecosystem resilience, and for monitoring and assessing conservation strategies, e.g. Marine Protected Areas. Observations are generally obtained through Underwater Visual Censuses (UVC) conducted by divers. The problems inherent to the presence of divers have been discussed in several papers. Video techniques are increasingly used for observing underwater macrofauna and habitat. Most video techniques that do not need the presence of a diver use baited remote systems. In this paper, we present an original video technique which relies on a remote unbaited rotating remote system including a high definition camera. The system is set on the sea floor to record images. These are then analysed at the office to quantify biotic and abiotic sea bottom cover, and to identify and count fish species and other species like marine turtles. The technique was extensively tested in a highly diversified coral reef ecosystem in the South Lagoon of New Caledonia, based on a protocol covering both protected and unprotected areas in major lagoon habitats. The technique enabled to detect and identify a large number of species, and in particular fished species, which were not disturbed by the system. Habitat could easily be investigated through the images. A large number of observations could be carried out per day at sea. This study showed the strong potential of this non obtrusive technique for observing both macrofauna and habitat. It offers a unique spatial coverage and can be implemented at sea at a reasonable cost by non-expert staff. As such, this technique is particularly interesting for investigating and monitoring coastal biodiversity in the light of current conservation challenges and increasing monitoring needs.
Plos One (1932-6203) (Public Library Science), 2012-02 , Vol. 7 , N. 2 , P. -

Droits : 2012 Pelletier et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License
http://archimer.ifremer.fr/doc/00078/18879/16453.pdf
DOI:10.1371/journal.pone.0030536
http://archimer.ifremer.fr/doc/00078/18879/

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : La provincia de Limón, en la costa caribeña de Costa Rica, es conocida por su alto índice de pobreza, el alto desempleo y la violencia en comparación con el resto del país. Este artículo es una revisión de la historia de la región a través de las imágenes de la ciudad de Limón, entre el siglo XIX y el año 1967, fecha de la celebración de la apertura de Limón como puerto internacional. El objetivo es tratar de entender la situación actual a partir del análisis de las representaciones del pasado. Pero más específicamente, el trabajo pretende poner de relieve la diferencia étnica en la región como un importante obstáculo para su integración en el conjunto nacional.
La province de Limón dans le Caraïbe costaricien est connue pour sa condition de grande pauvreté, son taux de chômage élevé et sa violence par rapport au reste du pays. Cet article fait un bilan de l’histoire de la région à travers les images de la ville de Limón entre le xixe siècle et l’année 1967 ; date de la célébration de l’ouverture de Limón comme port international. Le but est d’essayer de mieux comprendre la situation actuelle à partir de l’analyse des représentations du passé. Mais, plus particulièrement, le travail cherche à mettre en relief la différence ethnique de la région comme un obstacle important à son intégration dans l’ensemble national.
The province of Limón in the Caribbean Coast of Costa Rica is known for its high rate of poverty, the high unemployment and violence compared to the rest of the country. This article is a review of the history of the region through the images of the city of Limón between the nineteenth century and the year 1967, date of the celebration of the opening of Limón as an international port. The goal is to try to understand the current situation from the analysis of representations of the past. But more specifically, the work seeks to highlight the ethnic difference in the region as a major obstacle to its integration into the national set.
Limón
Costa Rica

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.5715
http://journals.openedition.org/etudescaribeennes/5715

Résumé : After a period of rapid development of the sites (an increase in both reared surface area and production), tropical shrimp aquaculture is currently being faced with critical problems due to economical and ecological constraints. In many countries with favourable conditions for shrimp aquaculture such as indonesia or Vietnam, sites are often badly selected and/or over-exploited. This conducts to sorne extent to decreases or collapses in the production due to the difficulty in predicting the maximum production capacity of the sites. Furthermore, it appears that production sustainability depends on many factors among which socio-economy and ecolo gy are of prime importance. The STD3 project titled « Assessment of tropical shrimp aquaculture impact on the environment in tropical countries using hydrobiology, ecology and remote sensing as helping tools for diagnosis )) was initiated in 1994, with the aim to study the sustainability of marine shrimp aquaculture in tropical areas, main! y Indonesia and Vietnam, through the following tasks: (i) improve site selection and study the impact of aquaculture on marine environments presenting a variable sensitivity to organic sewage, (ii) analyse the socio-economical aspects and profitability of the aquaculture industry and of common resources (iii) use remote sensing and geographical data bases for diagnosis and monitoring of site degradation (iv) reinforce the capacity of Asian scientists through training. Severa! aquaculture sites have been investigated in the Lampung region (South Sumatra, Indonesia), the Mekong delta (Vietnam) and on the West coast of New-Caledonia, providing a large range of typical ecosystems encountered in Asia and in the Pacifie, from coralline sites to coastal plains with mangrove and deltaic areas. The study concerned the spatial structure and seasonal influence of these ecosystems, the temporal variation during the course of the project (3 years) and the relation between the ecological structure and farm productions. Remote sensing provides a synoptic vision over large land expanses. Severa! scenes were processed for landuse mapping using conventional classification techniques. Concerning water quality assessment, a general relation for the Java sea was found between image and field data in terms of total suspended matter. Applying this relation to a new site in Sumatra has provided an initial approach to water type and, together with land use mapping, a preliminary assessment of the suitability of the area to shrimp aquaculture development. Socio-economic research has been focused on the identification ofneeds for collective action, including public policy, in the perspective of shrimp farming sustainability. The main concern is in the regulation of shrimp farming intensification and extensification at the scale of coastal ecosystemic entities in a common property resource management perspective. The common considered here is coastal water quality. Comparing the local development profiles and the institutional grounds for the design and implementation of collective management rules shows that variables such as land tenure system, farm owner socio-economic profile, social homogeneity or heterogeneity of the farmers are key factors to analyse the potential for sustainability. The defmition of water quality and the possible means to ensure its collective management are discussed. The main conclusion is that the economie incentives to farming development are strong but there is no significant difference among traditional, semi-intensive and intensive systems in terms of economie efficiency or wealth distribution. The description of the functioning of the different kinds of ecosystems make it possible to give an advice concerning the positioning of the activity inside the ecosystem, and furthermore to have a reference state in order to determine the impact of the activity on the coastal environnement. This impact can be summarized as an increase in the concentration of total suspended matt€?r, of particulate organic matter and of sulfate reducing bacterias. This organic ma~.er is either issued from rearing activities or from telluric origine, due to mangrove eradication when building the ponds. An evaluation of the relationship existing between productivity and characteristics of each ecosystem bas been conducted by correlating ecological indicators data (concentration of total suspended matter, particulate organic matter, chlorophyll, percentage of pheopigments in total pigments and cyanobacteria and sulfatereducing bacteria in water and sediments) with the average production of the farms. This comparison lead to the compilation of a scale of observed production integrating the range of these environmental parameters with shrimp production levels, bound to facilitate the positioning of shrimp farming in relation with the confmement leve! of each ecosystem. Lastly, ali geographie data originated from the various compartments of the study have been geo-referenced and loaded into a geographical information system. This allows to display any query made on spatial variables and their related statistical data, including the ir variations over the last few years and to reveal patterns and phenomena otherwise not obvious.
Le programme mis en oeuvre par la DRV (Paris, CREMA-L'Houmeau, DELIAO Brest, COP Tahiti, GIE/RA Nouvelle Calédonie), dans le cadre d'un projet européen STD3 «(Sciences et Technique au Service du Développement», en collaboration avec l'Université de Montpellier II, l'Ecole Nationale d'Agronomie de Rennes, l'ITC (Hollande), l'Institut Océanographique de Nha Trang (Vietnam), le BADC de Jepara et le BPPT de Jakarta (Indonésie), avait pour but la mise au point de méthodes permettant d'améliorer la sélection des sites ainsi que le suivi du développement et de l'impact de l'aquaculture des crevettes Péneides en milieu tropical pour éviter la surexploitation. Quatre axes de recherche ont été défmis : a) identifier la nature et quantifier les rejets de déchets issus de ce type d'aquaculture, b) définir les caractéristiques écologiques des écosystèmes susceptibles d'accueillir l'activité aquacole et suivre leur évolution sous l'influence des rejets, c) déterminer l'influence de la gestion des fermes et des ressources (aspects économiques) sur les performances de productivité, d) déterminer la capacité de la télédétection comme outil de diagnostic d'impact à l'échelle de la région, e) mener un programme de formation d'étudiants et jeunes chercheurs Vietnamiens et Indonésiens.

Droits : 1998 Ifremer
http://archimer.ifremer.fr/doc/00132/24357/22357.pdf
http://archimer.ifremer.fr/doc/00132/24357/

Éditeur(s) : HAL CCSD Springer Verlag (Germany) Springer Verlag
Résumé : Direct numerical simulations of flow through two millimeter-scale rock samples of limestone and sandstone are performed using three diverse fluid dynamic simulators. The resulting steady-state velocity fields are compared in terms of the associated empirical probability density functions (PDFs) and key statistics of the velocity fields. The pore space geometry of each sample is imaged at 5.06−μm voxel size resolution using X-ray microtomography. The samples offer contrasting characteristics in terms of total connected porosity (about 0.31 for the limestone and 0.07 for the sandstone) and are typical of several applications in hydrogeology and petroleum engineering. The three-dimensional fluid velocity fields within the explicit pore spaces are simulated using ANSYS® FLUENT® ANSYS Inc. (2009), EULAG Prusa et al. (Comput. Fluids 37, 1193–1207 2008), and SSTOKES Sarkar et al. (2002). These computational approaches are highly disperse in terms of algorithmic complexity, differ in terms of their governing equations, the adopted numerical methodologies, the enforcement of internal no-slip boundary conditions at the fluid-solid interface, and the computational mesh structure. As metrics of comparison to probe in a statistical sense the internal similarities/differences across sample populations of velocities obtained through the computational systems, we consider (i) integral quantities, such as the Darcy flux and (ii) main statistical moments of local velocity distributions including local correlations between velocity fields. Comparison of simulation results indicates that mutually consistent estimates of the state of flow are obtained in the analyzed samples of natural pore spaces despite the considerable differences associated with the three computational approaches. We note that in the higher porosity limestone sample, the structures of the velocity fields obtained using ANSYS FLUENT and EULAG are more alike than either compared against the results obtained using SSTOKES. In the low-porosity sample, the structures of the velocity fields obtained by EULAG and SSTOKES are more similar than either is to the fields obtained using ANSYS FLUENT. With respect to macroscopic quantities, ANSYS FLUENT and SSTOKES provide similar results in terms of the average vertical velocity for both of the complex microscale geometries considered, while EULAG tends to render the largest velocity values. The influence of the pore space structure on fluid velocity field characteristics is also discussed.
ISSN: 1420-0597

hal-01174152
https://hal.archives-ouvertes.fr/hal-01174152
DOI : 10.1007/s10596-015-9486-7

Éditeur(s) : HAL CCSD
Résumé : International audience
Le nombre de satellites et de capteurs pour la télédétection dédiés à l'observation de la Terre ne cesse d'augmenter, permettant ainsi d'avoir une masse de données importante en particulier en matière d'images. Parallèlement, un effort permanent vise, d'une part, à améliorer l'accès à ces données et, d'autre part, à développer d'avantages d'outils pour les manipuler. De tels efforts sont particulièrement utiles dans des contextes socio-environnementaux très dynamiques spatialement et temporellement, pour lesquels il est nécessaire de suivre et de prédire les événements environnementaux et sociétaux. En revanche, en présence d'un tel flux de données, nous avons besoin de méthodes automatiques d'interprétation d'images. Une solution envisageable pour répondre à ce besoin est de bénéficier des atouts de l'intelligence artificielle pour l'obtention de cartes d'occupation du sol issues d'une classification des régions des images. Afin de contribuer à l'automatisation de la classification, nous proposons une méthode d'induction de règles interprétables par des non-experts et mettant en évidence, explicitement, des connaissances structurelles. Cette méthode s'appuie sur la programmation logique inductive (PLI) et en particulier sur le système inductif ”Aleph”. L'application de la méthode de classification Multi-class Rule Set Intersection (MRSI) permet ensuite de classifier tout nouvel objet au regard des ses caractéristiques intrinsèques et de celles des objets environnants. Nous avons appliqué notre méthodologie à l'étude de la dynamique du littoral de la Guyane Française. Suite à ce travail, nous avons induit 136 règles de classification pour 38 classes d'occupation du sol. Ces règles sont intelligibles et simples à interpréter de par l'utilisation de la logique du premier ordre. Les performances du système ont été évaluées par la validation croisée. En moyenne, la précision, la spécificité et la sensibilité sont, respectivement, égales à 84,62%, 99,57% et 77,22%. Ces résultats quantitatifs montrent une bonne performance de la méthodologie pour la mise à jour automatique de cartes d'occupation du sol et/ou l'assistance aux opérateurs utilisant l'analyse d'image orientée-objet.
11èmes Rencontres des Jeunes Chercheurs en Intelligence Artificielle
Lille, France

hal-01376400
https://hal.archives-ouvertes.fr/hal-01376400
https://hal.archives-ouvertes.fr/hal-01376400/document
https://hal.archives-ouvertes.fr/hal-01376400/file/Bayoudh_RJCIA2013.pdf

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Both flow field heterogeneity and mass transfer between mobile and immobile domains have been studied separately for explaining observed anomalous transport. Here we investigate non-Fickian transport using high-resolution 3-D X-ray microtomographic images of Berea sandstone containing microporous cement with pore size below the setup resolution. Transport is computed for a set of representative elementary volumes and results from advection and diffusion in the resolved macroporosity (mobile domain) and diffusion in the microporous phase (immobile domain) where the effective diffusion coefficient is calculated from the measured local porosity using a phenomenological model that includes a porosity threshold ( inline image) below which diffusion is null and the exponent n that characterizes tortuosity-porosity power-law relationship. We show that both flow field heterogeneity and microporosity trigger anomalous transport. Breakthrough curve (BTC) tailing is positively correlated to microporosity volume and mobile-immobile interface area. The sensitivity analysis showed that the BTC tailing increases with the value of inline image, due to the increase of the diffusion path tortuosity until the volume of the microporosity becomes negligible. Furthermore, increasing the value of n leads to an increase in the standard deviation of the distribution of effective diffusion coefficients, which in turn results in an increase of the BTC tailing. Finally, we propose a continuous time random walk upscaled model where the transition time is the sum of independently distributed random variables characterized by specific distributions. It allows modeling a 1-D equivalent macroscopic transport honoring both the control of the flow field heterogeneity and the multirate mass transfer between mobile and immobile domains.
ISSN: 0043-1397

hal-01278285
https://hal.archives-ouvertes.fr/hal-01278285
DOI : 10.1002/2015WR017645

Éditeur(s) : HAL CCSD Montpellier : CIRAD
Résumé :  
Cette étude s'inscrit dans le cadre du suivi de l'exploitation forestière à faible impact en forêt tropicale humide. L'importance des dégâts liés à l'exploitation forestière conditionne fortement la durabilité de cette activité et un contrôle efficace de la qualité des travaux forestiers s'impose donc au gestionnaire. Dans cette étude, l'imagerie satellitaire aide à suivre la progression des chantiers d'exploitation et à estimer les dégâts, par l'acquisition d'images en cours et en fin d'exploitation des parcelles. L'analyse d'images à haute résolution (10 m) permet de bien identifier les trouées d'abattage et certaines pistes de débusquage. Ainsi, on a une évaluation de l'ouverture de la canopée. Plusieurs parcelles ont été étudiées en Guyane française. Pour chacune d'entre elles, un diagnostic simple a été mis en place pour évaluer l'intensité d'exploitation, relever les pistes créées et les pertes de bois. L'outil satellite permet alors de mieux considérer la qualité de l'exploitation et d'en tirer les conséquences vis-à-vis de l'exploitant. Cette étude a permis de démontrer l'utilité de la télédétection pour identifier les concentrations de dégâts après exploitation forestière. Une validation de l'outil a été menée grâce à une base de données de suivi d'exploitation et par des missions de terrain. Cet outil de contrôle postexploitation peut désormais s'automatiser de façon à le rendre totalement opérationnel pour le gestionnaire forestier.
ISSN: 0006-579X

hal-01032146
https://hal.archives-ouvertes.fr/hal-01032146

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD
Résumé : Afin de prévoir l'évolution des phénomènes naturels, sans discontinuité, des milliers d'images satellites alimentent les stations météorologiques. Ce flot permanent d'informations nécessite rapidité et rigueur d'analyse. Il est donc indispensable de mettre en place des systèmes capables de travailler nuit et jour afin de dresser des bilans exploitables par les chercheurs. Nous proposons dans cet article une méthode, basée sur des techniques d'investigation en reconnaissance des formes, telles que la segmentation et la classification. Ces techniques seront utilisées pour localiser et discriminer les masses nuageuses issues d'images captées par le satellite géostationnaire GOES. Le traitement des formes nuageuses trouvées se fait en utilisant des opérations, telles que la morphologie mathématique afin d'extraire des caractéristiques discriminantes. Pour l'interprétation des caractéristiques obtenues et pour effectuer la classification des nuages, nous utilisons des systèmes de classeurs.
Journées d'Études et de Recherche des Antilles et de la Guyane
Pointe-à-Pitre, Guadeloupe

hal-00637787
https://hal.archives-ouvertes.fr/hal-00637787

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
Nowadays, technological advances in satellite imagery measurements as well as the development of dense geodetic and seismologic networks allow for a detailed analysis of surface deformation associated with active fault seismic cycle. However, the study of earthquake dynamics faces several limiting factors related to the difficulty to access the deep source of earthquake and to integrate the characteristic time scales of deformation processes that extend from seconds to thousands of years. To overcome part of these limitations and better constrain the role and couplings between kinematic and mechanical parameters, we have developed a new experimental approach allowing for the simulation of strike-slip fault earthquakes and analyze in detail hundreds of successive seismic cycle. Model rheology is made of multilayered visco-elasto-plastic analog materials to account for the mechanical behavior of the upper and lower crust and to allow simulating brittle/ductile coupling, postseismic deformation phase and far-field stress transfers. The kinematic evolution of the model surface is monitored using an optical system, based on subpixel spectral correlation of high-resolution digital images. First, results show that the model succeed in reproducing the deformation mechanisms and surface kinematics associated to the main phases of the seismic cycle indicating that model scaling is satisfactory. These results are comforted by using numerical algorithms to study the strain and stress distribution at the surface and at depth, along the fault plane. Our analog modeling approach appears, then, as an efficient complementary approach to investigate earthquake dynamics.
ISSN: 0278-7407

hal-01174176
https://hal.archives-ouvertes.fr/hal-01174176
DOI : 10.1002/2014TC003701

Éditeur(s) : HAL CCSD
Résumé : Satellite and in situ chlorophyll concentration data collected as part of VALidation HYperspectral of a BIOgeochemical model (ValHyBio), a PNTS-sponsored project dedicated to satellite ocean-colour imaging of the Southwest Pacific, are analyzed to describe chlorophyll variability in the Coral Sea, a vast oligotrophic region characterized by a deep chlorophyll maximum and blue waters of high transparency. Average chlorophyll concentrations estimated from MODIS-Aqua are very low (<0.2 mg m-3) except in the vicinity of main islands and coral reefs, where enrichment may occur due to upwelling or internal waves that bring nutrients to the euphotic zone from the deep part of the water column. During the summer season, blooms of cyanobacteria (Trichodesmium) develop in the surface waters and may form large slicks. The nitrogen fixed by these slicks is a potential source of new nitrogen later assimilated by picoplankton and the marine food chain. Coastal areas exhibit higher chlorophyll concentrations because of nutrient input from the land, as observed in 2008 around New Caledonia. In lagoon areas, the sea colour is influenced by turbidity and bathymetry, and the MODIS OC3 algorithm is inadequate, with a systematic overestimation of chlorophyll concentration in the New Caledonia lagoon. Improved bio-optical algorithms are needed for those turbid and shallow waters, to allow not only a better description of chlorophyll variability, but also evaluation of chlorophyll simulations by recently developed biogeochemical models.
of the 12th International Coral Reef Symposium, 18E
CAIRNS, Australia

hal-00746470
https://hal.archives-ouvertes.fr/hal-00746470
https://hal.archives-ouvertes.fr/hal-00746470/document

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Introduction: Drug transporters are now recognized as major players involved in pharmacokinetics and toxicology. Methods for assessing their activity are important to consider, particularly owing to regulatory requirements with respect to inhibition of drug transporter activity and prediction of drug–drug interactions. In this context, the use of fluorescent-dye-based transport assays is likely to deserve attention.Areas covered: This review provides an overview of the nature of fluorescent dye substrates for ATP-binding cassette and solute carrier drug transporters. Their use for investigating drug transporter activity in cultured cells and clinical hematological samples, drug transporter inhibition, drug transporter imaging and drug transport at the organ level are summarized.Expert opinion: A wide range of fluorescent dyes is now available for use in various aspects of drug transporter studies. The use of these dyes for transporter analyses may, however, be hampered by classic pitfalls of fluorescence technology, such as quenching. Transporter-independent processes such as passive diffusion of dyes through plasma membrane or dye sequestration into subcellular compartments must also be considered, as well as the redundant handling by various distinct transporters of some fluorescent probes. Finally, standardization of dye-based transport assays remains an important on-going issue
ISSN: 1742-5255

hal-01162381
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01162381
DOI : 10.1517/17425255.2015.1053462
PUBMED : 26050735

Éditeur(s) : HAL CCSD European Geosciences Union (EGU)
Résumé : International audience
Storms and tsunamis, which may seriously endanger human society, are amongst the most devastating marine catastrophes that can occur in coastal areas. Many such events are known and have been reported for the Mediterranean, a region where high-frequency occurrences of these extreme events coincides with some of the most densely populated coastal areas in the world. In a sediment core from the Mar Menor (SE Spain), we discovered eight coarse-grained layers which document marine incursions during periods of intense storm activity or tsunami events. Based on radiocarbon dating, these extreme events occurred around 5250, 4000, 3600, 3010, 2300, 1350, 650, and 80 years cal BP. No comparable events have been observed during the 20th and 21st centuries. The results indicate little likelihood of a tsunami origin for these coarse-grained layers, although historical tsunami events are recorded in this region. These periods of surge events seem to coincide with the coldest periods in Europe during the late Holocene, suggesting a control by a climatic mechanism for periods of increased storm activity. Spectral analyses performed on the sand percentage revealed four major periodicities of 1228 ± 327, 732 ± 80, 562 ± 58, and 319 ± 16 years. Amongst the well-known proxies that have revealed a millennial-scale climate variability during the Holocene, the ice-rafted debris (IRD) indices in the North Atlantic developed by Bond et al. (1997, 2001) present a cyclicity of 1470 ± 500 years, which matches the 1228 ± 327-year periodicity evidenced in the Mar Menor, considering the respective uncertainties in the periodicities. Thus, an in-phase storm activity in the western Mediterranean is found with the coldest periods in Europe and with the North Atlantic thermohaline circulation. However, further investigations, such as additional coring and high-resolution coastal imagery, are needed to better constrain the main cause of these multiple events.
ISSN: 1814-9324

hal-01357199
https://hal.archives-ouvertes.fr/hal-01357199
https://hal.archives-ouvertes.fr/hal-01357199v2/document
https://hal.archives-ouvertes.fr/hal-01357199/file/cp-12-1389-2016.pdf
DOI : 10.5194/cp-12-1389-2016

Éditeur(s) : Amer Geophysical Union
Résumé : The origin of the Algerian margin remains one of the key questions still discussed in the Western Mediterranean sea, due to the imprecise nature and kinematics of the associated basin during the Neogene. For the first time, the deep structure of the Maghrebian margin was explored during the SPIRAL seismic survey. In this work, we present a N-S transect off Tipaza (west of Algiers), a place where the margin broadens due to a topographic high (Khayr-al-Din Bank). New deep penetration seismic profiles allow us to image the sedimentary sequence in the Algerian basin and the crustal structure at the continent-ocean boundary. Modeling of the wide-angle data shows thinning of the basement, from more than 15km in the continental upper margin to only 5–6km of oceanic-type basement in the Algerian basin, and reveals a very narrow or absent transitional zone. Analysis of the deep structure of the margin indicates features inherited from its complex evolution: (1) an oceanic-type crust in the deep basin, (2) similarities with margins formed in a transform-type setting, (3) a progressive deepening of the whole sedimentary cover, and the thickening of the Plio-Quaternary sediments at the margin foot, coeval with (4) a downward flexure of the basement in the basin. These features argue for a multiphased evolution of the margin, including (1) an early stage of rifting and/or spreading, (2) a late transcurrent episode related to the westward migration of the Alboran domain, and (3) a diffuse Plio-Quaternary compressional reactivation of the margin.
Journal Of Geophysical Research-solid Earth (0148-0027) (Amer Geophysical Union), 2013-08 , Vol. 118 , N. 8 , P. 3899-3916

Droits : 2013. American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00152/26333/24412.pdf
DOI:10.1002/jgrb.50318
http://archimer.ifremer.fr/doc/00152/26333/

Éditeur(s) : Elsevier
Résumé : We investigated the influence of bioturbation by macrofauna on the vertical distribution of living (stained) benthic foraminifera in marine intertidal sediments. We investigated the links between macrofaunal bioturbation and foraminiferal distribution, by sampling from stations situated on a gradient of perturbation by oyster-farming, which has a major effect on benthic faunal assemblages. Sediment cores were collected on the French Atlantic coast, from three intertidal stations: an oyster farm, an area without oysters but affected by oyster biodeposits, and a control station. Axial tomodensitometry (CT-scan) was used for three-dimensional visualization and two-dimensional analysis of the cores. Biogenic structure volumes were quantified and compared between cores. We collected the macrofauna, living foraminifera, shells and gravel from the cores after scanning, to validate image analysis. We did not investigate differences in the biogenic structure volume between cores. However, biogenic structure volume is not necessarily proportional to the extent of bioturbation in a core, given that many biodiffusive activities cannot be detected on CT-scans. Biodiffusors and larger gallery-diffusors were abundant in macrofaunal assemblage at the control station. By contrast, macrofaunal assemblages consisted principally of downward-conveyors at the two stations affected by oyster farming. At the control station, the vertical distribution of biogenic structures mainly built by the biodiffusor Scorbicularia plana and the large gallery-diffusor Hediste diversicolor was significantly correlated with the vertical profiles of living foraminifera in the sediment, whereas vertical distributions of foraminifera and downward-conveyors were not correlated at the station affected by oyster farming. This relationship was probably responsible for the collection of foraminifera in deep sediment layers (> 6 cm below the sediment surface) at the control station. As previously suggested for other species, oxygen diffusion may occur via the burrows built by S. plana and H. diversicolor, potentially increasing oxygen penetration and providing a favorable microhabitat for foraminifera in terms of oxygen levels. By contrast, the absence of living foraminifera below 6 cm at the stations affected by oyster farming was probably associated with a lack of biodiffusor and large gallery-diffusor bioturbation. Our findings suggest that the effect of macrofaunal bioturbation on the vertical distribution of foraminiferal assemblages in sediments depends on the effects of the macrofauna on bioirrigation and sediment oxidation, as deduced by Eh values, rather than on the biogenic structure volume produced by macrofauna. The loss of bioturbator functional diversity due to oyster farming may thus indirectly affect infaunal communities by suppressing favorable microhabitats produced by bioturbation.
Journal of Experimental Marine Biology and Ecology (0022-0981) (Elsevier), 2009-03 , Vol. 371 , N. 1 , P. 20-33

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6146.pdf
DOI:10.1016/j.jembe.2008.12.012
http://archimer.ifremer.fr/doc/00000/6146/

Éditeur(s) : HAL CCSD Optical Society of America
Résumé : International audience
A linear least square (LLS) method is proposed to process polarization dependent SHG intensity analysis at pixel-resolution level in order to provide an analytic solution of nonlinear susceptibility χ(2) coefficients and of fibril orientation. This model is applicable to fibrils with identical orientation in the excitation volume. It has been validated on type I collagen fibrils from cell-free gel, tendon and extracellular matrix of F1 biliary epithelial cells. LLS is fast (a few hundred milliseconds for a 512 × 512 pixel image) and very easy to perform for non-expert in numerical signal processing. Theoretical simulation highlights the importance of signal to noise ratio for accurate determination of nonlinear susceptibility χ(2) coefficients. The results also suggest that, in addition to the peptide group, a second molecular nonlinear optical hyperpolarizability β contributes to the SHG signal. Finally from fibril orientation analysis, results show that F1 cells remodel extracellular matrix collagen fibrils by changing fibril orientation, which might have important physiological function in cell migration and communication.
ISSN: 1094-4087

hal-01139871
https://hal.archives-ouvertes.fr/hal-01139871
DOI : 10.1364/OE.23.013309
PUBMED : 26074581