Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
From outcrops located in Provence (South-East France), we describe the distribution, the microstructures, and the petrophysical properties of deformation band networks related to both contractional and extensional tectonic events. In contraction, pervasively distributed networks of reverse-sense compactional shear bands are observed in all folded sand units of the foreland, whereas localized networks of clustered reverse-sense shear bands are only observed close to a large-scale thrust. In extensional setting, networks of clustered normal-sense shear bands are generally observed adjacent to map-scale faults (100 m–10 km scale), although some randomly distributed bands are also observed between these faults. Normal-sense cataclastic faults, i.e. zone of deformation bands containing a localized slip-surface, are also observed to be restricted to sand units, suggesting that faults initiated in the sands during extension, but not during contraction. Shear bands and faults show cataclastic microstructures with high-permeability reduction whereas compactional shear bands show crush microbreccia or protocataclastic microstructures with moderate permeability reduction. This basin-scale analysis underlines the major role of tectonic settings (thrust-fault versus normal-fault andersonian-stress regime) and the influence of inherited large-scale faults on the formation/localization of low-permeability shear bands. We also provide a geometrical analysis of the band network properties (spacing, thickness, shear/compaction ratio, degree of cataclasis, petrophysical properties) with respect to the median grain size, porosity and grain sorting of host sand. This analysis suggests that grain size, although less important than stress-state conditions and the presence of large-scale faults, has a non-negligible effect on band network geometry. No correlations are observed between the grain sorting, porosity and band network geometry.
ISSN: 0264-8172

hal-01116421
https://hal.archives-ouvertes.fr/hal-01116421
DOI : 10.1016/j.marpetgeo.2013.12.020

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The evaluation of geographical healthcare accessibility in residential areas provides crucial information to public policy. Traditional methods - such as Physician Population Ratios (PPR) or shortest travel time - offer only a one-dimensional view of accessibility. This paper developed an improved indicator: the Index of Spatial Accessibility (ISA) to measure geographical healthcare accessibility at the smallest available infra-urban level, that is, the Ilot Regroupe pour des Indicateurs Statistiques. Methods: This study was carried out in the department of Nord, France. Healthcare professionals are geolocalized using postal addresses available on the French state health insurance website. ISA is derived from an Enhanced Two-Step Floating Catchment Area (E2FCA). We have constructed a catchment for each healthcare provider, by taking into account residential building centroids, car travel time as calculated by Google Maps and the edge effect. Principal Component Analyses (PCA) were used to build a composite ISA to describe the global accessibility of different kinds of health professionals. Results: We applied our method to studying geographical healthcare accessibility for pregnant women, by selecting three types of healthcare provider: general practitioners, gynecologists and midwives. A total of 3587 healthcare providers are potentially able to provide care for inhabitants of the department of Nord. On average there are 92 general practitioners, 22 midwives and 21 gynecologists per 100,000 residents. The composite ISA for the three types of healthcare provider is 39 per 100,000 residents. A comparative analysis between ISA and physician-population ratios indicates that ISA represents a more even distribution whereas the physician-population ratios show an 'all-or-nothing' approach. Conclusion: ISA is a multidimensional and improved measure, which combines the volume of services relative to population size with the proximity of services relative to the population's location, available at the smallest feasible geographical scale. It could guide policy makers towards highlighting critical areas in need of more healthcare providers, and these areas should be earmarked for further knowledge-based policy making.
ISSN: 1475-9276

hal-01359567
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01359567
DOI : 10.1186/s12939-016-0411-z
PUBMED : 27485740

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The minerals constituting the Earth's upper mantle are nominally anhydrous silicates (NAMs). However they do contain hydrogen as a trace element, decorating point defects in their crystalline structure. Experimental petrology and mineralogy have quantified the maximum concentration under several compositional and thermodynamic conditions, but systematic studies on the hydrogen concentration in minerals from mantle-derived rocks have only recently been carried out. Here, we have compiled the distribution of hydrogen in upper mantle peridotite xenoliths, from which several conclusions can be drawn. NAMs from peridotite xenoliths contain a few ppm wt. H2O in their structure. From the current database, the hydrogen concentrations in olivine regularly increase with increasing depth. The amount of hydrogen in NAMs from peridotite xenoliths from subduction contexts is not higher than in other geological context for similar temperature and pressure conditions. The highest hydrogen concentrations is found in peridotitic olivines from cratonic mantle, and are likely due to the depth of origin. The increasing hydrogen concentration in olivine with increasing depth is likely controlled by the increase of H partitioning into olivine at the expense of orthopyroxene as imposed by a decrease in Al content in opx with depth. However, the sparse data could also indicate that the bulk hydrogen concentration slightly increases with depth > 150 km. In this case, it would suggest, locally (Udachnaya for example), a possible increase in water fugacity due to fluid saturation. Even if the most abundant mineral in mantle rocks is olivine, the bulk hydrogen concentration in peridotites is controlled by the amount of hydrogen stored in pyroxenes. However, hydrogen concentration in olivine remains crucial for consequences on physical properties such as rheology and electrical conductivity. Kinetics of hydrogen transport is reviewed and hydrous melt/fluid percolation appears necessary to homogenize the hydrogen distribution at km-scale. Sampling of natural rock specimens is currently biased (e.g., in favor of optically attractive samples) and needs improvement, which will be achieved by increasing sample diversity (all type of grain sizes, lithologies, geological settings) and size of rock samples, as well as advances in analytical techniques. Acquisition of high quality data will be achieved by studying the co-existing minerals in mantle specimens, exploring each sample by linear and mapping measurements, and using appropriate FTIR calibrations for polarized and unpolarized radiation.
ISSN: 0024-4937

hal-01306676
https://hal.archives-ouvertes.fr/hal-01306676
DOI : 10.1016/j.lithos.2015.11.012

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In order to better constrain the relationship between tectonics and sedimentation of the Eastern Sardinian Margin, from the Messinian to the present day (METYSS project), a lithostratigraphic study was carried out on the Late Neogene deposits along the Cedrino Valley (eastern Sardinia). The late Neogene evolution is documented from sedimentological and tectonic analysis, biostratigraphic dating, and by mapping and logging stratigraphic sections. Previous authors have differentiated an early Pliocene marine formation from an older continental formation, possibly Miocene, the entire system being covered by late Pliocene to Quaternary lava flows. Preliminary biostratigraphic data suggest the absence of the lowermost Pliocene, based on the absence of Globorotalia margaritae and the presence of Globorotalia puncticulata, implying a sediment age between 3.81 and 2.41 Ma. At the foot of the Fiuli cliff, some mud clasts include a coccolith microflora, Tortonian in age, suggesting reworking. The Pliocene marine deposits consist of a single filling sequence instead of a succession of superimposed sequences as we would expect during this period of time; the occurrences of terms rarely respect the usual transgressive-regressive succession. Contrasting bathymetric environments (fore-shore, pro-delta, shelf or upper slope) can be abruptly superimposed on top of the other, along few meter thick intervals. A rapidly flooded term is observed in several sites and indicates a spatial variability over only a few kilometers distance. Some deep water deposits are in the middle of the infilling Pliocene sequence, whereas shallower water deposits can be repeated along a vertical section, or even interrupted by emersion. These marked differences can express syn-, or possibly post-sedimentation tectonic uplifts. The 10–25° bed dips originated through local tectonic uplift. At Fiuli, the geometry of the bedding planes is indicative of tilting toward the west, in a direction opposite to the one observed at Onifai. These Pliocene series form a wide syncline with an approximately NNE–SSW axis. This morpho-structural behavior appears to be largely atypical of this East-Sardinian coastal area.
ISSN: 1040-6182

hal-01134707
https://hal.archives-ouvertes.fr/hal-01134707
DOI : 10.1016/j.quaint.2014.11.022

Résumé : La tuberculose (TB), maladie infectieuse contagieuse, est causée par une mycobactérie appartenant au complexe Mycobacterium tuberculosis (MTBC). Malgré de nombreuses campagnes de vaccination par le BCG (Bacilles de Calmette et Guérin) et les traitements antituberculeux, on observe une réémergence de la maladie depuis les années 80. Ce bouleversement s’explique par la coïnfection avec le virus du VIH/SIDA, la désorganisation des systèmes de santé et par l’apparition des bactéries résistantes aux principaux antibiotiques antituberculeux. Dans ce contexte une meilleure connaissance des mouvements et de l’évolution des clones circulants du bacille tuberculeux permettrait de détecter plus rapidement et de façon plus pertinente l’émergence d’épidémies. Le contrôle et la surveillance de la maladie représentent des moyens essentiels pour lutter contre l’expansion mondiale de la tuberculose. C’est ainsi que l’unité de la Tuberculose et des Mycobactéries de l’Institut Pasteur de la Guadeloupe (IPG) a mis en place une base de données de profils génotypiques pour l’étude de l’épidémiologie globale de la tuberculose. Dans le cadre de cette thèse, nous décrirons les méthodes de bioinformatique qui ont été utilisées pour la gestion et l’exploitation de la 6ème version (SITVIT2) de cette base de données des génotypes pour mieux comprendre l’évolution et la dissémination mondiale du bacille tuberculeux. Cette base intègre aussi plusieurs marqueurs moléculaires tels que les MIRU-VNTRs (« mycobacterial interspersed repetitive units-variable number of tandem repeats ») et le Spoligotype43 servant à mieux décrire et identifier les familles de profils génotypiques du MTBC. La banque de données SITVIT2 ne cesse d’évoluer, et elle contient actuellement des informations épidémiologiques sur 111 635 isolats cliniques. Cette base de données est consultable en ligne à l’adresse suivante : http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. Nous avons également réalisé une base de données nommée SITVITBovis qui est dédiée à la tuberculose bovine. Cette base de données sera accessible à l’adresse : http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/. Parallèlement au développement et à la gestion des bases de données, ce travail de thèse s’est appuyé sur plusieurs études épidémiologiques et phylogéographiques mettant en corrélation les données disponibles sur la résistance aux médicaments ou les caractéristiques démographiques (dont le sexe, l’âge, le statut VIH, et l’origine du patient). Notre initiative de recherche permet ainsi d’améliorer la caractérisation phylogénétique détaillée des lignées du MTBC, ainsi que l’épidémiologie des clones en circulation, afin d’élaborer une cartographie géographique des isolats cliniques prédominants pour les bacilles tuberculeux principalement impliqués dans la maladie, à l’échelle nationale, régionale et mondiale. La superposition ultérieure de ces cartes avec des données sociopolitiques, économiques et démographiques obtenues auprès de Systèmes d’information géographique (SIG) ont permis de dresser un portrait précis des disparités actuelles par pays ou sous-région. Cette thèse représente une importante collaboration avec plusieurs équipes de chercheurs travaillant également dans le domaine de l’épidémiologie moléculaire de la tuberculose. L’objectif à long terme de ce travail, est d’optimiser la structure de la base, et de pérenniser l’enrichissement de celle-ci (notamment par l’automatisation et la facilité de la saisie de données). Une représentation optimale et une meilleure accessibilité des données de la base conforteraient les efforts faits pour le contrôle et la surveillance de la TB dans monde.
Tuberculosis (TB) is a contagious infectious disease caused by mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Despite numerous campaigns of vaccination by the BCG (Bacillus Calmette-Guérin) vaccine, and TB treatments, there was a resurgence of the disease since the 80s. This disruption is due to coinfection with HIV/AIDS, disorganization of health systems and the emergence of bacteria resistant to anti-TB drugs. In this context, a better understanding of the movements and changes of circulating clones of tubercle bacilli would detect faster and more relevant emerging epidemics. The control and monitoring of the disease are essential means to fight against the worldwide spread of tuberculosis. Thus the TB and Mycobacteria unit of the Pasteur Institute of Guadeloupe (IPG) has developed a database of genotypic profiles for the study of global epidemiology of tuberculosis.In this thesis, we discuss the Bioinformatical methods that have been used for the management and development of the 6th version (SITVIT2) of this database of genotypes to better understand the evolution and global dissemination of the tubercle bacillus. The database also includes several molecular markers such as MIRU-VNTRs (mycobacterial interspersed repetitive units- variable number of tandem repeats) and Spoligotype43 allowing a better description and identification of the families of genotypic profiles of Mycobacterium tuberculosis complex. SITVIT2 database is constantly evolving, and it currently contains epidemiological information on 111,635 clinical isolates. This database is available online at the following address: http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. We also developed a database named "SITVITBovis", which is dedicated to bovine tuberculosis. This database will be accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/.Alongside the development and management of databases, this work was based on several epidemiological and phylogeographic studies correlating data on drug resistance or demographic characteristics (including sex, age, HIV status, and the origin of the patient). Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages, as well as the epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superposition of these maps with socio-political, economical and demographical available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities at the level of country or sub-region. This thesis represents an important collaboration with several researchers teams also working in the field of molecular epidemiology of tuberculosis.The long-term goal of this work is to further optimize the database structure, and sustain enriching it (including automation and ease of data entry). Optimum performance and accessibility of data in the database would reinforce efforts to control and surveillance of TB in the world.

http://www.theses.fr/2014AGUY0791/document

Éditeur(s) : HAL CCSD Ethnobotany Research and Applications
Résumé : We examined the limitations of parataxonomic inventories for developing management plans for woody plant resources in tropical rain forests of southwestern Amazonia. Using compilations of herbarium labels, forest personnel interviews and published species descriptions, we assessed the accuracy of common names as parataxonomic units (PUs). We identified 384 common names for 310 harvested woody plant species in the Brazilian state of Acre, of which only 50% were unique to a single taxonomic species. About 10% of common names referred to more than one species, more than half of which included multiple genera. For the 106 species from the Acre sample common to the MAP region including Madre de Dios, Peru and Pando, Bolivia, we identified 198 common names. Splitting was much more frequent in this sample, with more than 80% of species having more than one common name. When the Acre sample was expanded to 131 species from the Brazilian Amazon region, including the states of Amazonas and Para, we identified 740 common names, with nearly 90% of species being represented by more than one common name. Errors and inaccuracy of parataxonomy may contribute to market instability if product orders can not be homogenized within regional markets, and to unsustainable harvests if species are mistakenly lumped into single parataxonomic units. We discuss several programs currently being implemented by our collaborative team in the region to address this issue, including field guides based on digital photography, field courses, and workshops featuring discussions between regional inventory personnel and botanists.
ISSN: 1547-3465

hal-01032404
https://hal.archives-ouvertes.fr/hal-01032404

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
UNLABELLED: ABSTRACT: BACKGROUND: Malaria remains a major health problem in French Guiana, with a mean of 3800 cases each year. A previous study in Camopi, an Amerindian village on the Oyapock River, highlighted the major contribution of environmental features to the incidence of malaria attacks. We propose a method for the objective selection of the best multivariate peridomestic landscape characterisation that maximises the chances of identifying relationships between environmental features and malaria incidence, statistically significant and meaningful from an epidemiological point of view. METHODS: A land-cover map, the hydrological network and the geolocalised inhabited houses were used to characterise the peridomestic landscape in eleven discoid buffers with radii of 50, 100, 200, 300, 400, 500, 600, 700, 800, 900 and 1000 metres. Buffer-based landscape characterisations were first compared in terms of their capacity to discriminate between sites within the geographic space and of their effective multidimensionality in variable space. The Akaike information criterion (AIC) was then used to select the landscape model best explaining the incidences of P. vivax and P. falciparum malaria. Finally, we calculated Pearson correlation coefficients for the relationships between environmental variables and malaria incidence, by species, for the more relevant buffers. RESULTS: The optimal buffers for environmental characterisation had radii of 100 m around houses for P. vivax and 400 m around houses for P. falciparum. The incidence of P. falciparum malaria seemed to be more strongly linked to environmental features than that of P. vivax malaria, within these buffers. The incidence of P. falciparum malaria in children was strongly correlated with proportions of bare soil (r = -0.69), land under high vegetation (r = 0.68) and primary forest (r = 0.54), landscape division (r = 0.48) and the number of inhabited houses (r = -0.60). The incidence of P. vivax malaria was associated only with landscape division (r = 0.49). CONCLUSIONS: The proposed methodology provides a simple and general framework for objective characterisation of the landscape to account for field observations. The use of this method enabled us to identify different optimal observation horizons around houses, depending on the Plasmodium species considered, and to demonstrate significant correlations between environmental features and the incidence of malaria.
ISSN: 1476-072X

inserm-00674075
http://www.hal.inserm.fr/inserm-00674075
http://www.hal.inserm.fr/inserm-00674075/document
http://www.hal.inserm.fr/inserm-00674075/file/1476-072X-10-65.pdf
DOI : 10.1186/1476-072X-10-65

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
ISSN: 2041-1723

hal-01545322
https://hal.archives-ouvertes.fr/hal-01545322
DOI : 10.1038/ncomms3091

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : International audience
In this paper, we provide the first structural map of Les Saintes archipelago (Guadeloupe, Lesser Antilles). The finite strain pattern displays four families of fault systems characterized by their statistical structural orientations: N000-N020, N050-N070, N090-N110 and N130-N140 trending fault systems. Our onshore results thus underline a fault network much more complex than the one depicted by the previous offshore geophysical investigations around Les Saintes archipelago, which show only N120-N150 trending system. According to the available K-Ar dating of the volcanic rocks and the relative chronology of the faults defined in the field, we determine the deformation history in Les Saintes islands since the last 3 Ma. The four highlighted trending fault systems are already active since the Pliocene and are consistent with the present-day extensional tectonics in the Guadeloupe archipelago compatible with the reactiva-tion of inherited structures at the active arc scale. We interpret the tectonic evolution of Les Saintes islands as the result of interplay between subduction of aseismic ridges (Tiburon and Barracuda ridges) and oblique convergence. Furthermore , we recognized an exhumed geothermal paleo-system in Terre-de-Haut island which is a good analogue of the present-day active Bouillante geothermal system. Its duration is estimated at 400 k.y. during the Pliocene.
EISSN: 1777-5817

hal-01625778
https://hal.univ-antilles.fr/hal-01625778
https://hal.univ-antilles.fr/hal-01625778/document
https://hal.univ-antilles.fr/hal-01625778/file/VeratIEtAl_Final.pdf
DOI : 10.2113/gssgfbull.187.1.3

Éditeur(s) : HAL CCSD Wiley
Résumé : Outcrossing rates, pollen dispersal and male mating success were assessed in Dicorynia guianensis Amshoff, a neotropical tree endemic to the Guiana shield. All adult trees within a continuous area of 40 ha (n = 157) were mapped, and were genotyped with six microsatellite loci. In addition, progenies were genotyped from 22 mature trees. At the population level, the species was mostly outcrossing (tm = 0.89) but there was marked variation among individuals. One tree exhibited mixed mating, confirming earlier results obtained with isozymes that D. guianensis can tolerate selfing. A Bayesian extension of the fractional paternity method was used for paternity analysis, and was compared with the neighbourhood method used widely for forest trees. Both methods indicated that pollen dispersal was only weakly related to distance between trees within the study area, and that the majority (62%) of pollen came from outside the study stand. Using maximum likelihood, male potential population size was estimated to be 1119, corresponding to a neighbourhood size of 560 hectares. Male mating success was, however, related to the diameter of the stem and to flowering intensity assessed visually. The mating behaviour of D. guianensis is a combination of long-distance pollen flow and occasional selfing. The species can still reproduce when it is extremely rare, either by selfing or by dispersing pollen at long distances. These results, together with the observation that male mating success was correlated with the size of the trees, could be implemented in management procedures aiming at regenerating the species
ISSN: 0962-1083

hal-01032227
https://hal.archives-ouvertes.fr/hal-01032227
DOI : 10.1111/j.1365-294X.2004.02127.x