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 CRC Press
Résumé : International audience
Biology of damselfishes

hal-01384262
https://hal-univ-perp.archives-ouvertes.fr/hal-01384262

Éditeur(s) : HAL CCSD Elsevier
Résumé : revue électronique. consulter : http://religec.org/pdf/article%20Macdissi%20et%20al%202.pdf
L'existence et la persistance de disparités régionales en matière de chômage sont des problèmes communs à de nombreux pays européens. Dans ce papier, nous analysons les disparités des mécanismes d'ajustement des taux de chômage régionaux de la France à la suite de chocs économiques purement locaux ou nationaux. Les résultats mettent en évidence des disparités significatives dans les caractéristiques des mécanismes d'ajustement dynamiques (vitesse d'ajustement, effet multiplicateur) des taux de chômage régionaux en cas de choc macroéconomique national.
Revue Libanaise de Gestion et d'Economie

halshs-00433078
https://halshs.archives-ouvertes.fr/halshs-00433078
DOI : 10.1016/S1999-7620(09)70009-6

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Cyanobacteria are ubiquitous microorganisms considered as important contributors to the formation of Earth's atmosphere and nitrogen fixation. However, they are also frequently associated with toxic blooms. Indeed, the wide range of hepatotoxins, neurotoxins and dermatotoxins synthesized by these bacteria is a growing environmental and public health concern. This paper provides a state of the art on the occurrence and management of harmful cyanobacterial blooms in surface and drinking water, including economic impacts and research needs. Cyanobacterial blooms usually occur according to a combination of environmental factors e.g., nutrient concentration, water temperature, light intensity, salinity, water movement, stagnation and residence time, as well as several other variables. These environmental variables, in turn, have promoted the evolution and biosynthesis of strain-specific, gene-controlled metabolites (cyanotoxins) that are often harmful to aquatic and terrestrial life, including humans. Cyanotoxins are primarily produced intracellularly during the exponential growth phase. Release of toxins into water can occur during cell death or senescence but can also be due to evolutionary-derived or environmentally-mediated circumstances such as allelopathy or relatively sudden nutrient limitation. Consequently, when cyanobacterial blooms occur in drinking water resources, treatment has to remove both cyanobacteria (avoiding cell lysis and subsequent toxin release) and aqueous cyanotoxins previously released. Cells are usually removed with limited lysis by physical processes such as clarification or membrane filtration. However, aqueous toxins are usually removed by both physical retention, through adsorption on activated carbon or reverse osmosis, and chemical oxidation, through ozonation or chlorination. While the efficient oxidation of the more common cyanotoxins (microcystin, cylindrospermopsin, anatoxin and saxitoxin) has been extensively reported, the chemical and toxicological characterization of their by-products requires further investigation. In addition, future research should also investigate the removal of poorly considered cyanotoxins (β-methylamino-alanine, lyngbyatoxin or aplysiatoxin) as well as the economic impact of blooms.
Environment International

hal-00875835
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00875835
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00875835/document
DOI : 10.1016/j.envint.2013.06.013
PUBMED : 23892224

Éditeur(s) : HAL CCSD
Résumé : International audience
Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, weconducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the totaltrait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.
Ecology Letters

hal-01237101
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01237101
DOI : 10.1111/ele.12508
PUBMED : 26415616

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Justafterthereefcolonization,fishspeciescouldusetheacousticcuetosettleondifferentsuitablehabitats.Inthepresent study, we used the auditory evoked potential (AEP) technique to measure and compare the detectionabilities in five coral reef fish species, with some of these species that are found in the same habitat. We also ex-aminedtheeffectoffishsizeonsensitivityatthespecieslevel.Allstudiedspeciesexceptoneshowedsize-relatedchangesinsensitivitycharacterizedbyeitheradecrease(i.e.higherAEPthresholds)oranincrease(i.e.lowerAEPthresholds) in detection abilities with increasing size. The interspecific comparison of audiograms revealed thatsome species are more sensitive than others in terms of sound pressure level and frequency detection.Overall,thisstudy indicatesthattheAEPthresholdandthefrequencybandwidthatearlylifestagesmay vary be-tween andwithin fish species.Thedetectionabilities aredifferent infish species thatarenotphylogeneticallyre-lated, which might suggest that the establishment of their capabilities is not necessarily related to the reefconquest.
ISSN: 0022-0981

hal-01391589
https://hal-univ-perp.archives-ouvertes.fr/hal-01391589

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
ISSN: 0722-4028

hal-00655363
https://hal.archives-ouvertes.fr/hal-00655363

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Purpose: Marine mangrove sediments in the Manche-à-Eau lagoon (Guadeloupe, Caribbean Sea) harbor locally extensive, white microbial mats. These mats cover the surface of reduced sediments near the roots of red mangrove trees, Rhizophora mangle, and are mainly composed of sulfur-oxidizing bacteria belonging to the Beggiatoaceae family, with some filamentous cyanobacteria. The goal of this study was to investigatethe possible influence of sediment characteristics on the presence of these microbial mats. Materials and methods: Four push cores were collected in April 2013, two from zones with microbial mats and two from zones without mats. Sediment characteristics (grain-size distribution, mineralogy, total organic carbon (TOC) and total nitrogen (TN) contents, atomic TOC/TN ratios, and organic matter (OM) δ13C values) were compared for all four cores.Results and discussion: Significant differences were observed between sediments below microbial mats and those without mats. Sediments with microbial mats contained greater amounts of clay, and higher TOC, TN, and TOC/TN ratios, with lower total carbonate content andδ13C values. The higher clay content most likely results from lower fluid flow velocity near to mangrove roots, while higher TOC/TN ratiosand lower δ13C values indicate higher inputs of OM from mangrove trees. These results are consistent with the fact that microbial mats were observed near the roots of mangrove trees, which trap OM from terrestrial vegetation and fine sediments.Conclusions: The grain-size distribution of sediment particles, the total carbonate content, and the δ13C values are the main parameters discriminating between zones with microbial mats and those without mats. Variations in total carbonate content, which is mainly of biogenic origin, result from conditions that are more favorable for benthic organisms in zones without microbial mats. Variations of the TOC/TN ratios are controlled by the presence of a non-negligible amount of inorganic nitrogen bound to surface clay mineral particles and/or by microbial processes.
ISSN: 1439-0108

hal-01682110
https://hal.univ-antilles.fr/hal-01682110
DOI : 10.1007/s11368-016-1555-6

Éditeur(s) : HAL CCSD Cambridge University Press
Résumé : International audience
The reproduction of Rhinecanthus aculeatus (Linnaeus,1758), a tropical Indo-Pacific reef fish, occurs aroundthe full and new moon (Kuwamura 1997). Spawningbegins 16 to 45 min before the sunrise. The courtshipsbegin 7 to 27 min before the spawning. A specific behaviourof the courtships is when the male places itsrostrum against the caudal peduncle of the female(Kuwamura 1997).Observations have been recorded in the lagoon ofTiahura [shallow sandy area (0.5 - 2 m deep) withalgae Hypnea spinella (C.Agardh) Kützing, 1847 -Moorea, French Polynesia; 17°29′27′ S, 149°53′32″O]in March and April 2015. Fifteen R. aculeatus (fivemales and ten females) lived in this area where themales have territories, which included the subterritoriesof the females. During video-recorded courtships,in addition to the behaviour described byKuwamura (the nuzzling), two new behaviours havebeen observed: circling and touching. During the circling,the male and the female swim to the surface inprogressively larger circles (Fig. 1). The circling behaviourhas been observed in other Balistidae such asPseudobalistes flavimarginatus (Rüppell, 1829) andBalistapus undulatus (Park, 1797) (Lobel andJohannes 1980). During the touching, the abdomensof the male and the female’s touch each other withoutgametes emission (Fig. 2). The touching has been reportedfor Xanthichthys mento (Jordan and Gilbert1882) (Kawase 2003).Although Balistidae present different reproductivestrategies, they have common reproduction features,such as the time and the day of hatching andspawning (Kawase 2003). Our observations are innovativebecause the courtship of R. aculeatus is morecomplicated than previously described. This resultsuggests, thus, that Balistidae have also some commoncourtship behaviour features. These behaviours mayfacilitate the release of gametes, as with the nuzzling(Kuwamura 1997) or can convince the partner to mate.We do not know if these patterns are phylogeneticallyrelated. But as the egg care strategy of Balistidae (biparentalvs maternal) appears to be related to the distributionof food and breeding sites, more than by thephylogeny (Kuwamura 1997), more studies on thistopic will be useful to better understand the establishement of these behaviours.
EISSN: 1755-2672

hal-01562097
https://hal-univ-perp.archives-ouvertes.fr/hal-01562097
DOI : 10.1007/s12526-016-0464-7

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Plasma membrane is an early target of polycyclic aromatic hydrocarbons (PAH). We previously showed that the PAH prototype, benzo[a]pyrene (B[a]P), triggers apoptosis via DNA damage-induced p53 activation (genotoxic pathway) and via remodeling of the membrane cholesterol-rich microdomains called lipid rafts, leading to changes in pH homeostasis (non-genotoxic pathway). As omega-3 (n-3) fatty acids can affect membrane composition and function or hamper in vivo PAH genotoxicity, we hypothesized that addition of physiologically relevant levels of polyunsaturated n-3 fatty acids (PUFAs) might interfere with B[a]P-induced toxicity. The effects of two major PUFAs, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), were tested on B[a]P cytotoxicity in the liver epithelial cell line F258. Both PUFAs reduced B[a]P-induced apoptosis. Surprisingly, pre-treatment with DHA increased the formation of reactive B[a]P metabolites, resulting in higher levels of B[a]P-DNA adducts. EPA had no apparent effect on B[a]P metabolism or related DNA damage. EPA and DHA prevented B[a]P-induced apoptotic alkalinization by affecting Na(+)/H(+) exchanger 1 activity. Thus, the inhibitory effects of omega-3 fatty acids on B[a]P-induced apoptosis involve a non-genotoxic pathway associated with plasma membrane remodeling. Our results suggest that dietary omega-3 fatty acids may have marked effects on the biological consequences of PAH exposure.
ISSN: 0009-2797

hal-00950341
https://hal.archives-ouvertes.fr/hal-00950341
https://hal.archives-ouvertes.fr/hal-00950341/document
https://hal.archives-ouvertes.fr/hal-00950341/file/DENDELE_et_al_2013-unmarked.pdf
PUBMED : 24246761

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Seabirds concentrate nutrients from large marine areas on their nesting islands playing an important ecological role in nutrient transfer between marine and terrestrial ecosystems. Here we investigate the role of guano on corals reefs across scales by analyzing the stable nitrogen isotopic (delta N-15) values of the scleractinian coral Pocillopora damicornis on fringing reefs around two Pacific remote islets with large seabird colonies. Marine stations closest to the seabird colonies had higher nitrate + nitrite concentrations compared to more distant stations. Coral and zooxanthellae delta N-15 values were also higher at these sites, suggesting that guano-derived nitrogen is assimilated into corals and contributes to their nitrogen requirements. The spatial extent of guano influence was however restricted to a local scale. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystem, but also affect components of the adjacent marine ecosystem. Further studies are now needed to assess if this nutrient input has a positive or negative effect for corals. Such studies on remote islets also open fresh perspectives to understand how nutrients affect coral reefs isolated from other anthropogenic stressors.
ISSN: 2045-2322

hal-01681575
https://hal.archives-ouvertes.fr/hal-01681575
DOI : 10.1038/s41598-017-03781-y

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Because earthworms sustain soil functioning and fertility, there is a need to advance the knowledge of their adaptation potential to chemicals in anthropogenic landscapes. Our hypothesis is that there is acclimation to organic chemicals (pesticides) in earthworms that durably persist under conventional farming in anthropogenic landscapes. The adaptation capability of two populations of earthworms (Aporectodea caliginosa) having a different chemical exposure history, - one originating from 20 years of organic farming (naïve population) and another from 20 years of conventional farming (pre-exposed population) - to cope with soil organic pollutant (Opus®, epoxiconazole a worldwide used fungicide) were investigated. Several complementary metabolic and energetic endpoints were followed, and cast production was assessed as a behavioural biomarker related to earthworms ecological role for the soil. Basal metabolism reflected by respiration rate was increased in both fungicide-exposed worms compared to controls. Glycogen resources were decreased in the same proportion in the two populations but more rapidly for the naïve (7 days) than for the pre-exposed population (28 days). Soluble protein and most amino-acids contents increased in the pre-exposed population only, suggesting a detoxification mechanism. Metabolomic profiles showed a cut-off between fungicide-exposed and control groups in the pre-exposed earthworms only, with an increase in most of the metabolites. Exposure to a low dose of epoxiconazole increased cast production of pre-exposed earthworms, and this resulted in an increase in pesticide disappearance. As far as we know, this is the first study which evidenced there is an acclimation to an agricultural chemical in earthworms derived from conventional farming that also relates to a change in their burrowing behaviour, and for which larger consequences for the soil ecosystem need to be addressed. This original finding is of major interest in the frame of ecosystem resilience to global changes. Whether this physiological adaptation is a general pattern of response against fungicides or other pesticides would need to be confirmed with other molecules and agricultural contexts.
Soil Biology and Biochemistry

hal-01005821
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01005821
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01005821/document
DOI : 10.1016/j.soilbio.2014.01.032

Éditeur(s) : HAL CCSD
Résumé : International audience
With the health of the world’s oceans threatened as never before, it is becoming increasingly apparent that Marine Protected Areas (MPAs) play a vitally important role in protecting marine and coastal habitats. Management of Marine Protected Areas: A Network Perspective draws on the results of a major EU-sponsored research project related to the establishment of networks of MPAs in the Mediterranean and Black Seas that transpired from February 2011 to January 2016. Featuring contributions by leading university- and national research institute-based scientists, chapters utilize the latest research data and developments in marine conservation policy to explore issues related to ways in which networks of MPAs may amplify the effectiveness and conservation benefits of individual areas within them. Topics addressed include the broader socio-economic impacts of MPAs in the Mediterranean and Black Seas; the use of Marine Spatial Planning (MSP) to resolve conflicts between marine resource use and protection; special protection measures under the EU’s Marine Strategy Framework Directive (MSFD); ecological value assessments in the Black Sea; the Ecosystem Approach (EA) for managing marine ecosystems; MPAs along Turkey’s Black Sea coast; MPAs and offshore wind farms; and managing and monitoring MPA networks within and between the Black and Mediterranean Seas.Timely and important, Management of Marine Protected Areas: A Network Perspective offers invaluable insights into the role of MPAs in preserving the welfare and long-term viability of our world’s oceans.
Management of Marine Protected Areas: A Network Perspective

ISBN : 978-1-119-07577-6
hal-01562040
https://hal-univ-perp.archives-ouvertes.fr/hal-01562040

Éditeur(s) : HAL CCSD Elsevier Science
Résumé : International audience
Some anthropogenic noise is now considered pollution, with evidence building that noise from human activities such as transportation, construction and exploration can impact behaviour and physiology in a broad range of taxa. However, relatively little research has considered the effects of repeated or chronic noise; extended exposures may result in habituation or sensitisation, and thus changes in response. We conducted a field-based experiment at Moorea Island to investigate how repeated exposure to playback of motorboat noise affected a coral reef fish (Dascyllus trimaculatus). We found that juvenile D. trimaculatus increased hiding behaviour during motorboat noise after two days of repeated exposure, but no longer did so after one and two weeks of exposure. We also found that naïve individuals responded to playback of motorboat noise with elevated ventilation rates, but that this response was diminished after one and two weeks of repeated exposure. We found no strong evidence that baseline blood cortisol levels, growth or body condition were affected by three weeks of repeated motorboat-noise playback. Our study reveals the importance of considering how tolerance levels may change over time, rather than simply extrapolating from results of short-term studies, if we are to make decisions about regulation and mitigation.
ISSN: 0013-9327

Droits : http://creativecommons.org/licenses/by/
hal-01357915
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01357915/file/1-s2.0-S0269749116304468-main.pdf
DOI : 10.1016/j.envpol.2016.05.058

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Thermoelastic behavior of different marble types was analyzed using computational modeling and experimental measurements. Eight marble samples with different composition, grain size, grain boundary geometry, and texture were investigated. Calcitic and dolomitic marbles were considered. The average grain size varies from 75 μm to 1.75 mm; grain boundary geometry differs from nearly equigranular straight grain boundaries to inequigranular-interlobate grain boundaries. Four typical marble texture types were observed by EBSD measurements: weak texture; strong texture; girdle texture and high-temperature texture. These crystallographic orientations were used in conjunction with microstructure-based finite element analysis to compute the thermoelastic responses of marble upon heating. Microstructural response maps highlight regions and conditions in the marble fabric that are susceptible to degradation phenomena. This behavior was compared to the measured thermal expansion behavior, which shows increasing residual strains upon repetitive heating-cooling cycles. The thermal expansion behavior as a function of temperature changes can be classified into four categories: (a) isotropic thermal expansion with small or no residual strain; (b) anisotropic thermal expansion with small or no residual strain; (c) isotropic thermal expansion with a residual strain; and (d) anisotropic thermal expansion with residual strain. Thermal expansion coefficients were calculated for both simulated and experimental data and also modeled from the texture using the MTEX software. Fabric parameters control the amount and directional dependence of the thermal expansion. Marbles with strong texture show higher directional dependence of the thermal expansion coefficients and have smaller microstructural values of the maximum principal stress and strain energy density, the main precursors of microcracking throughout the marble fabric. In contrast, marbles with weak texture show isotropic thermal expansion behavior, have a higher propensity to microcracking, and exhibit higher values of maximum principal stress and strain energy density. Good agreement between the experimental and computational results is observed, demonstrating that microstructure-based finite-element simulations are an excellent tool for elucidating influences of rock fabric on thermoelastic behavior.
ISSN: 1866-6280

hal-00858095
https://hal.archives-ouvertes.fr/hal-00858095
DOI : 10.1007/s12665-013-2406-z

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : This paper presents the background for the calculation of physical properties of an aggregate from constituent crystal properties and the texture of the aggregate in a coherent manner. Emphasis is placed on the important tensor properties of 2nd and 4th rank with applications in rock deformation, structural geology, geodynamics and geophysics. We cover texture information that comes from pole figure diffraction and single orientation measurements (electron backscattered diffraction or EBSD, electron channelling pattern, Laue pattern, optical microscope universal-stage). In particular, we provide explicit formulae for the calculation of the averaged tensor from individual orientations or from an orientation distribution function (ODF). For the latter we consider numerical integration and an approach based on the expansion into spherical harmonics. This paper also serves as a reference paper for the mathematical tensor capabilities of the texture analysis software MTEX, which is a comprehensive, freely available MatLab toolbox that covers a wide range of problems in quantitative texture analysis, for example, ODF modelling, pole figure to ODF inversion, EBSD data analysis and grain detection. MTEX offers a programming interface which allows the processing of involved research problems as well as highly customizable visualization capabilities; MTEX is therefore ideal for presentations, publications and teaching demonstrations.
Deformation Mechanisms, Rheology and Tectonics: Microstructures, Mechanics and Anisotropy

hal-00688833
https://hal.archives-ouvertes.fr/hal-00688833

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Prediction of ice mass flow and associated dynamics is pivotal at a time of climate change. Ice flow is dominantly accommodated by the motion of crystal defects – the dislocations. In the specific case of ice, their observation is not always accessible by means of the classical tools such as X-ray diffraction or transmission electron microscopy (TEM). Part of the dislocation population, the geometrically necessary dislocations (GNDs) can nevertheless be constrained using crystal orientation measurements via electron backscattering diffraction (EBSD) associated with appropriate analyses based on the Nye (1950) approach. The present study uses the Weighted Burgers Vectors, a reduced formulation of the Nye theory that enables the characterization of GNDs. Applied to ice, this method documents, for the first time, the presence of dislocations with non-basal or Burgers vectors. These or dislocations represent up to of the GNDs observed in laboratory-deformed ice samples. Our findings offer a more complex and comprehensive picture of the key plasticity processes responsible for polycrystalline ice creep and provide better constraints on the constitutive mechanical laws implemented in ice sheet flow models used to predict the response of Earth ice masses to climate change.
ISSN: 0012-821X

hal-01685565
https://hal.archives-ouvertes.fr/hal-01685565
DOI : 10.1016/j.epsl.2017.06.020

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
Antisynthetase syndrome is an inflammatory myopathy frequently associated with pulmonary manifestations, especially interstitial lung diseases, and uncommonly pulmonary hypertension. In the context of a suggestive clinical and radiological picture, positive anti-RNA synthetase antibodies confirm the diagnosis. Anti-Jo1, anti-PL7, and anti-PL12 antibodies are the more commonly encountered. The presence of a number of extra-thoracic manifestations in association with pulmonary disease may suggest the diagnosis. These include: myalgia or muscular deficit, Raynaud's phenomenon, polyarthritis, fever, mechanics hands. Serum creatine kinase levels are usually increased. Electromyogram, muscular magnetic resonance imaging or muscle pathology are not mandatory to make the diagnosis. There is a high variability in symptoms and severity, between patients but also during the course of the disease in the same patient. The presence of an interstitial lung disease is a major prognostic factor and an indication for more intensive treatment, principally with systemic corticosteroids with or without immunosuppressive drugs. Improving respiratory physicians’ knowledge of this disease, which is often revealed by its pulmonary manifestations, should help diagnosis, therapeutic management, and possibly prognosis.
Le syndrome des antisynthétases correspond à une myopathie inflammatoire fréquemment associée à une atteinte pulmonaire, surtout parenchymateuse (pneumopathie infiltrante diffuse) et plus rarement vasculaire (hypertension pulmonaire). Devant un tableau clinique et radiologique évocateur, la présence d’anticorps anti-ARNt synthétases signe le diagnostic. Les plus fréquents de ces auto-anticorps sont les anti-Jo1, les anti-PL7 et les anti-PL12. De nombreuses manifestations cliniques extrathoraciques associées à l’atteinte pulmonaire peuvent orienter le diagnostic : myalgies ou déficit musculaire, phénomène de Raynaud, polyarthrite, fièvre et « mains de mécaniciens ». Une augmentation des créatine-phospho-kinases est quasi constante. Le recours à l’électromyogramme, à l’imagerie musculaire par résonance magnétique ou à l’histologie n’est pas systématique. Néanmoins, il existe une grande variabilité des symptômes et de leur sévérité d’un patient à l’autre ou au long de l’évolution de la maladie. L’atteinte pulmonaire est un facteur pronostic majeur et incite à traiter de manière intensive les patients, principalement par corticothérapie systémique, voire d’emblée par association corticoïdes et immunosuppresseurs. Mieux connaître cette pathologie qui est souvent de révélation pneumologique permettrait d’améliorer le diagnostic et la prise en charge thérapeutique, voire même le pronostic.
ISSN: 0761-8425

hal-01085369
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01085369
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01085369/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01085369/file/Manifestations%20pulmonaires%20du%20syndrome%20des%20antisynth%C3%A9tases_accepted.pdf
DOI : 10.1016/j.rmr.2014.07.013

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
BACKGROUND: Mutations in the telomerase complex (TERT and TR) are associated with pulmonary fibrosis and frequent hematologic manifestations. The aim of this study was to characterize the prognosis of lung transplantation in patients with TERT or TR mutations. METHODS: Patients with documented TERT or TR mutations who received a lung transplant between 2007 and 2013 in France were identified via an exhaustive search of the lung transplantation network, one expert genetic laboratory, and the clinical research network on rare pulmonary diseases. RESULTS: There were 9 patients (7 men) with TERT (n = 6) or TR (n = 3) mutations who received a single (n = 8) or a double (n = 1) lung transplant for pulmonary fibrosis. Median age was 50 years (range, 35-61 years) at diagnosis and 52 years (range, 37-62 years) at the time of lung transplantation. Thrombocytopenia was present in 7 patients before lung transplantation. After lung transplantation, 6 patients developed myelodysplasia and/or bone marrow failure, directly contributing to death in 4 cases. Anemia was observed in 9 patients, and neutropenia was observed in 3 patients. The median survival after lung transplantation was 214 days (range, 59-1,709 days). CONCLUSIONS: Patients with mutations of the telomerase complex are at high risk of severe hematologic complications after lung transplantation, in particular, bone marrow failure. Specific recommendations should be developed for appropriate guidance regarding hematologic risk assessment before transplantation and management of the post-transplantation immunosuppressive regimen.
ISSN: 1053-2498

hal-01146848
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146848
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146848/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146848/file/Severe%20hematological%20complications%20after%20lung%20transplantation_accepted.pdf
DOI : 10.1016/j.healun.2014.11.010

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The seismic (elastic) properties of the crust have been modelled using hypothetical polycrystals with typical crustal compositions and commonly measured petrofabrics. This modelling allows us to better evaluate and quantify the crustal contribution to splitting of teleseismic SKS-waves. Mafic rocks such as anorthosite or pyroxene-bearing gabbros have complex S-waves properties, i.e. with small shear-wave anisotropies (< 3%) and without clear relationships between the fast shear-wave polarization plane orientations and the fabric. On the other hand foliated felsic rocks such as gneisses or schists and mafic rocks such as amphibole-bearing gabbros are strongly birefringent (anisotropies greater than 5%) and exhibit clear relationships with the structure. Biotite and amphibole preferred orientations clearly play a major rote in shear-wave splitting in crustal rocks. We show strong correlations between the orientation of the foliation and the amplitude of the delay time. Maximum delay time is systematically observed for waves propagating parallel to the foliation. The fast shear-wave is furthermore polarized parallel to the foliation plane. We calculate a delay time of about 0.1-0.2 s per 10 km of crustal rocks.
ISSN: 0031-9201

hal-01389713
http://hal.univ-reunion.fr/hal-01389713
http://hal.univ-reunion.fr/hal-01389713/document
http://hal.univ-reunion.fr/hal-01389713/file/Barruol_SKS_crust_PEPI1993_hal.pdf
DOI : 10.1016/0031-9201(93)90161-2