Éditeur(s) : HAL CCSD IRMA
Résumé : International audience
Colloque trajectorien à la mémoire de G. Reeb et J.L. Callot, Strasbourg/Obernai
Strasbourg, Obernai, France

hal-01529544
https://hal.univ-antilles.fr/hal-01529544

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
PURPOSE: Dairy farming is a risk factor for the development of chronic obstructive pulmonary disease (COPD). We assessed the prevalence of farming-induced COPD (FI-COPD) using a new screening device, and we analyzed symptoms and occupational risk factors. METHODS: We performed on-site screening study of bronchial obstruction using an electronic mini-spirometer (EMS) on an entire population of dairy farmers (n = 147) from two villages in Brittany, France. Suspected bronchial obstruction (FEV1/FEV6 <0.8) was confirmed with standardized lung function tests (FEV1/FVC ≤0.7). We assessed past medical histories, respiratory symptoms, and occupational tasks of subjects with bronchial obstruction; asthmatics were defined as atopic and/or reversible; smoking-induced COPD patients were defined as non-reversible, non-atopic with smoking histories (≥5 PY); and FI-COPD patients were defined as non-reversible, non-atopic, and non-smokers. RESULTS: Using the EMS, 30.6% (n = 45) of dairy farmers were suspected of bronchial obstruction and underwent standardized spirometry. The FEV1/FEV6 ratio and FEV1/FVC ratio were in good agreement (r² = 0.66, P < 0.0001). The prevalence of confirmed bronchial obstruction was 9.5% (n = 14), which included 4 asthmatics, 3 smoking-induced COPD subjects, and 7 FI-COPD subjects. All the COPD patients were GOLD Stage II, and none were aware of their respiratory disease. Foddering duration was significantly higher in FI-COPD subjects compared with non-obstructive subjects, with 44 versus 17 min/day, respectively. CONCLUSIONS: The EMS was a convenient mean of screening for bronchial obstruction, especially in on-site settings, and allowed us to diagnose FI-COPD in a non-spontaneously complaining dairy farmer population. Foddering was considered a significant risk factor.
ISSN: 0340-0131

hal-00872929
https://hal.archives-ouvertes.fr/hal-00872929
DOI : 10.1007/s00420-011-0708-6
PUBMED : 21986906

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In this work we perform a statistical analysis of global solar radiation measured at two sites, 38 km distant from, in Guadeloupe, French West Indies. We have established a correlation model based on the coefficient of variation assuming a time scale separation. The coefficient of variation is calculated on minutes interval with data measured at 1 Hz. This analysis highlight the dynamic correlation that can occur between measurements from two different sites with a time step of one second. From this results, knowing the coefficient of variation on a site we have established a new correlation model on this parameter for another site. A diagram linking the standard deviation on both sites, for a given coefficient of variation is proposed for correlated and non-correlated cases. More over this analysis put in evidence the existence of a threshold time under which there is no significant correlation. This model can be useful in choosing new sites of production not only for establishing correlation from on site to another, but also in optimizing the geographical distribution of the solar farms within the territory.
ISSN: 0960-1481

Droits : http://hal.archives-ouvertes.fr/licences/copyright/
hal-01099045
https://hal.archives-ouvertes.fr/hal-01099045
https://hal.archives-ouvertes.fr/hal-01099045/document
https://hal.archives-ouvertes.fr/hal-01099045/file/Article%20Foison_2014.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
Rencontres européennes d'Analyse Non Standard,
Luminy - Marseille, France

hal-01535423
https://hal.univ-antilles.fr/hal-01535423

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Orogenic lherzolites exhibit a specific (although reproducible) platinum-group element signature characterized by slight positive deviations of Pd/Ir, Rh/Ir and Ru/Ir ratios from the canonical chondritic model. Such a signature was alternatively considered to be a compositional feature of the primitive upper mantle or resulting from sulfide melt addition by refertilisation reactions in the continental lithosphere. To shed additional light on this conundrum, the distribution of PGE in FON B 93, an unserpentinized, fertile (3.24% Al2O3) orogenic lherzolite (French Pyrenees) used as in-house standard by our group, has been studied to different scales, from the bulk rock to trace minerals. In addition to new ICPMS analyses after separation into Nis and Te coprecipitation, its whole-rock PGE concentrations were redetermined by three different laboratories using very precise ID-ICP-MS methods after digestion of the sample in Carius tube at T=250 degrees C and 320 degrees C or in high-pressure asher (HPA-S). The four methods produce reproducible Ru, Rh and Pd contents (7.1 +/- 0.18 ppb; 1.43 +/- 0.05 ppb; 7.1 +/- 0.30 ppb) whereas the non-ID NiS-fire assay method underestimates the Os and Ir concentrations by c.a. 10 and 15% compared to ID-ICP-MS analyses (4.40 +/- 0.07 and 4.00 +/- 0.17 ppb, respectively). Platinum was the most difficult to analyse. If performed on powder aliquots smaller than 3 g, the ID-ICP-MS analyses generate strong nugget effects while the non-ID NiS-fire assay method yields statistically lower (but highly reproducible) Pt concentrations (6.92 +/- 0.26 ppb). These features reflect the strong partitioning of Pt into trace phases that SEM and laser ablation-ICP-MS analyses on thin sections identify as both high-temperature Pt-Ir-Os alloys and Pt-(Pd) tellurides of likely subsolidus origin; ten to fifteen grains ranging in maximum dimension from a few micrometres to a few hundreds of nanometers, were identified by standard polished thin section. LA-ICP-MS data on base metal sulfides (25 grains analysed), coupled with the whole-rock S concentration (277 +/- 10 ppm) and modal composition of the BMS (90% pentlandite+accessory pyrite and secondary pyrrhotite + 10% chalcopyrite) allowed the contribution of the BMS phase to the PGE budget of FON B 93 to be estimated. Except Pt that exhibits a 95% deficit in the BMS phase, the PGE concentrations measured by ID-ICP-MS can be balanced by BMS while Al-spinel is a negligible contributor, accounting for less than 0.5% of the Ru budget. The occurrence of Pt in trace phases may bias the whole-rock Pt concentrations because 1) mechanical collection of Pt-rich trace phases remains problematic with the Nis button, and 2) Pt-Ir-Os alloys may be prone to digestion problems in conventional Carius tube procedures. Since they could be stable at mantle depth, such refractory alloys that contain Os and Ir may also have enhanced the heavy PGEs/light PGEs fractionation. Our observations likely pertain to orogenic lherzolites as a whole because BMS assemblages in these mantle rocks record evolution at low sulfur fugacity, which prevents Pt-Ir-Os alloy from entering the Mss in the mantle; moreover, at subsolidus temperature, pentlandite, the major BMS, cannot accommodate 0 valence state Pt.
ISSN: 0009-2541

hal-00411486
https://hal.archives-ouvertes.fr/hal-00411486
DOI : 10.1016/j.chemgeo.2007.06.030

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Isotopic fractionation of tritium is a highly relevant issue in radiation protection and requires certain radioecological considerations. Sound evaluation of this factor is indeed necessary to determine whether environmental compartments are enriched/depleted in tritium or if tritium is, on the contrary, isotopically well-distributed in a given system. The ubiquity of tritium and the standard analytical methods used to assay it may induce biases in both the measurement and the signification that is accorded to the so-called fractionation: based on an exhaustive review of the literature, we show how, sometimes large deviations may appear. It is shown that when comparing the non-exchangeable fraction of organically bound tritium (neOBT) to another fraction of tritium (e.g. tritiated water) the preparation of samples and the measurement of neOBT reported frequently led to underestimation of the ratio of tritium to hydrogen (T/H) in the non-exchangeable compartment by a factor of 5 % to 50 %. In the present study, corrections are proposed for most of the biological matrices studied so far. Nevertheless, the values of isotopic fractionation reported in the literature remain difficult to compare with each other, especially since the physical quantities and units often vary between authors. Some improvements are proposed to better define what should encompass the concepts of exchangeable and non-exchangeable fractions.
ISSN: 0160-4120

hal-01117744
https://hal.archives-ouvertes.fr/hal-01117744
https://hal.archives-ouvertes.fr/hal-01117744/document
https://hal.archives-ouvertes.fr/hal-01117744/file/Article%20review%20discrimination%20isotopique-envoy%C3%A9.pdf
DOI : 10.1016/j.envint.2013.12.020

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A new method was proposed to determine the nitrogen content of nitrocelluloses (NCs). It is based on the finding of a linear relationship between the nitrogen content and the molar ratio of nitrite-to-nitrate ions released after alkaline hydrolysis. Capillary electrophoresis was used to monitor the concentration of nitrite and nitrate ions. The influences of hydrolysis time and molar mass of NC on the molar ratio of nitrite-to-nitrate ions were investigated, and new insights into the understanding of the alkaline denitration mechanism of NCs, underlying this analytical strategy is provided. The method was then tested successfully with various explosive and non-explosive NC-containing samples such as various daily products and smokeless gunpowders. Inherently to its principle exploiting a concentration ratio, this method shows very good repeatability in the determination of nitrogen content in real samples with relative standard deviation (n=3) inferior to 1.5%, and also provides very significant advantages with respect to sample extraction, analysis time (1h for alkaline hydrolysis, 3min for electrophoretic separation), which was about 5 times shorter than for the classical Devarda's method, currently used in industry, and safety conditions (no need for preliminary drying NC samples, mild hydrolysis conditions with 1M sodium hydroxide for 1h at 60°C).
Journal of Hazardous Materials

hal-01103120
https://hal.archives-ouvertes.fr/hal-01103120
PUBMED : 25562808

Éditeur(s) : HAL CCSD
Résumé : Given the technological development of embedded satellite sensors, the potential of available satellite images increases so that the question now arises of their most efficient exploitation possible. This is the purpose of the CARTAM-SAT project to fluidize the processing workflow from satellite images to users. The thesis is part of this framework.Processing operations relating to images have evolved over the years. Low-resolution images were processed by a so-called pixel approach while the high-resolution has allowed the development of a so-called object approach. The latter focuses on analysing not about the isolated pixels, but about groups of pixels representative of concrete objects on the ground. Thus, in principle, these are groups of pixels with a domain-specific remote sensing semantics.Along with satellite imagery, knowledge representation has evolved. The standards of representation have benefited from the expansion of the web to give rise to standards like OWL. This one is widely based on description logics that allow the use of automated reasoners able to infer implicit knowledge.This thesis is at the junction of these two sciences and provides an ontological approach for analysing satellite images. The aim is to formalize different types of knowledges and conceptualizations implicitly used by image processing programs and by remote sensing experts, and then reasoning automatically on an image description to obtain one semantic interpretation.This general principle may have numerous technical variations. The implementation consisted in a prototype combining a satellite image analysis library and an ontology-based reasoner. The implementation proposed in the thesis allows to explore four technical variations of the principle that lead to discussions on the complementarity of pixel and object analysis paradigms, the representation of some of the spatial relations and the role of knowledge in relation to processing.
Étant donnée l'évolution technologique des capteurs embarqués à bord des satellites, le potentiel d'images satellitaires accessible s'accroît de telle manière que se pose maintenant la question de son exploitation la plus efficace possible. C'est l'objectif du projet CARTAM-SAT que de fluidifier la chaîne de traitement depuis les satellites jusqu'aux utilisateurs des images. La thèse s'inscrit dans ce cadre. Les traitements relatifs aux images ont évolué au cours des années. Les images basse résolution étaient traitées par une approche dite pixel alors que la haute résolution a permis le développement d'une approche dite objet. Cette dernière s'attache à analyser non plus des pixels isolés, mais des groupes de pixels représentatifs d'objets concrets sur le terrain. Ainsi, en principe, ces groupes de pixels sont dotés d'une sémantique propre au domaine de la télédétection. La représentation des connaissances a évolué parallèlement aux images satellitaires. Les standards de représentation ont profité de l'expansion du web pour donner naissance à des standards comme OWL. Celui-ci repose en grande partie sur les logiques de description qui permettent l'utilisation de raisonneurs automatiques capables d'inférer une connaissance implicite.Cette thèse se place à la jonction de ces deux sciences et propose une approche ontologique d'analyse des images satellitaires. Il s'agit de formaliser différents types de connaissances et de conceptualisations implicitement utilisés par les logiciels de traitement d'image et par les experts en télédétection, puis de raisonner automatiquement sur la description d'une image pour en obtenir une interprétation sémantique.Ce principe général est susceptible de nombreuses déclinaisons techniques. La mise en œuvre a consisté en la réalisation d'un prototype alliant une bibliothèque d'analyse d'images satellitaires et un raisonneur basé sur les ontologies. L'implémentation proposée dans la thèse permet d'explorer quatre déclinaisons techniques du principe qui mènent à des discussions sur la complémentarité des paradigmes d'analyse pixel et objet, la représentation de certaines relations spatiales et la place de la connaissance par rapport aux traitements.
https://tel.archives-ouvertes.fr/tel-00998692

NNT : 2013MON20059
tel-00998692
https://tel.archives-ouvertes.fr/tel-00998692
https://tel.archives-ouvertes.fr/tel-00998692/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In order to perform a human and ecological risk assessment of pharmaceutical products (PPs) in natural waters, it is necessary to accurately quantify a broad variety of PPs at low concentrations. Although numerous currently implemented analytical methodologies, less is known about the preservation of PPs in natural water samples within the period before analysis (holding time, storage conditions). This paper is the first literature review about the stability of PPs in natural waters (surface and groundwaters) during sample storage. The current work focuses on a comparison of the performances of the available preservation techniques (filtration, container materials, storage temperature, preservative agents, etc.) for PPs in samples. All 58 reviewed PPs may be successfully stabilized during 7 days in surface waters by at least one appropriate methodology regarding temperature, acidic and non-acidic preservatives. When temperature is not a sufficient preservation parameter f! or some PPs (hormones and fluoxetine) its combination with the addition of chemical agents into the samples may prolong the integrity of the PPs during storage in surface water. There is a strong need to use standard protocols to assess and compare the stability of PPs in environmental water matrices during storage as well as during analytical preparation or analysis (European criteria 2002/657/EC). Since the stability of PPs during sample storage is a critical parameter that could call into question the quality of the data provided for the concentrations, the design of stability studies should rigorously take into account all critical parameters that could impact the concentrations of the PPs with time.
Talanta

insu-00839186
https://hal-insu.archives-ouvertes.fr/insu-00839186
DOI : 10.1016/j.talanta.2013.01.042

Éditeur(s) : HAL CCSD
Résumé : International audience
Anwendungen des infinitesimalmathematik
Oberwolfach, Germany

hal-01535427
https://hal.univ-antilles.fr/hal-01535427

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
ISSN: 0764-4442

hal-01529508
https://hal.univ-antilles.fr/hal-01529508

Éditeur(s) : Academic Press Inc Elsevier Science
Résumé : Several Vibrio species are known to be pathogenic to the Pacific oyster Crassostrea gigas. Survival varies according to pathogen exposure and high mortality events usually occur in summer during gametogenesis. In order to study the effects of gametogenetic status and ploidy (a factor known to affect reproduction allocation in oysters) on vibriosis survival, we conducted two successive experiments. Our results demonstrate that a common bath challenge with pathogenic Vibrio splendidus and Vibrio aestuarianus on a mixture of mature, spawning and non-mature oysters can lead to significant mortality. Previous bath challenges, which were done using only non-mature oysters, had not produced mortality. Immunohisto-chemical analyses showed the affinity of Vibrio for gonadic tissues, highlighting the importance of sexual maturity for vibriosis infection processes in oysters. Mortality rate results showed poor repeatability between tanks, however, in this bath challenge. We then tested a standardized and repeatable injection protocol using two different doses of the same combination of two Vibrio species on related diploid and triploid oysters at four different times over a year. Statistical analyses of mortality kinetics over a 6-day period after injection revealed that active gametogenesis periods correspond to higher susceptibility to vibriosis and that there is a significant interaction of this seasonal effect with ploidy. However, no significant advantage of triploidy was observed. Triploid oysters even showed lower survival than diploid counterparts in winter. Results are discussed in relation to differing energy allocation patterns between diploid and triploid Pacific oysters. (C) 2010 Elsevier Inc. All rights reserved.
Journal Of Invertebrate Pathology (0022-2011) (Academic Press Inc Elsevier Science), 2011-02 , Vol. 106 , N. 2 , P. 179-191

Droits : 2010 Elsevier Inc. All rights reserved.
http://archimer.ifremer.fr/doc/00030/14108/11368.pdf
DOI:10.1016/j.jip.2010.09.003
http://archimer.ifremer.fr/doc/00030/14108/

Résumé : The goal of this study was to provide economic data to align Ifremer's research programme with the global socio-economic context, which is the crux of this work. Although the economies of the French Overseas Departments and Territories are poorly understood in mainland France, a brief macroeconomic analysis shows that they have the following main features: steady, but unbalanced growth, as indicated by high unemployment rates and low trade indices, and an overdeveloped services sector. This situation can be explained by an economic growth regime specific to the French overseas regions. It is based on, for the most part, public subsidies, a voluntary strategy promoted by the public authorities to raise the standards of living in the overseas regions.
L'objet de cette étude est de fournir des éléments économiques qui permettent de mettre en parallèle la démarche de programmation de recherche de l'IFREMER et le contexte socio-économique d'ensemble dans lequel cette recherche s'insère. Si l'économie des DOM-TOM reste méconnue en métropole, une analyse macroéconomique rapide montre bien quelles en sont les caractéristiques principales : une croissance soutenue mais très déséquilibrée comme l'attestent un taux de chômage élevé et un taux de couverture des importations dérisoire, l'existence d'un secteur tertiaire qualifié parfois d'"hypertrophié"... Cette situation s'explique par un mode de croissance spécifique à l'outre-mer français. Il repose pour une large part sur l'intervention financière publique, qui elle-même découle de la volonté exprimée par les pouvoirs publics de promouvoir un rattrapage rapide des niveaux de vie ultramarins. [OCR NON CONTRÔLE]

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1991/rapport-4094.pdf
http://archimer.ifremer.fr/doc/00000/4094/

Éditeur(s) : HAL CCSD
Résumé : National audience
Le standard d’eau de rivière naturelle SLRS-5 (NRC-CNRC) est uneréférence de contrôle qualité en analyse d’eau de routine pour la communautéinternationale. Dix laboratoires français étudiant les élémentsmajeurs et en trace dans les solutions naturelles (groupe de travail del’atelier du CNRS « Isotrace ») valident leurs mesures avec les 19 élémentscertifiés par le producteur. Or, d’autres éléments non certifiés sontrégulièrement analysés par ces laboratoires qui ont comparé et compilé2 années de leurs mesures sur ce standard d’eau. La plupart desmesures sont réalisées par ICP-MS (Inductively Coupled Plasma Mass-Spectrometry).Dans un premier temps, il a été vérifié que les résultats obtenus étaientcohérents pour les éléments certifiés par le producteur. Ainsi Ba présenteune valeur compilée de 14,2 1,4 g/l (330 mesures issues de 9laboratoires participants) en accord avec la valeur certifiée de 14 0,5g/l.Ensuite, des valeurs moyennes et leurs incertitudes associées sont proposéespour des éléments non certifiés par NRC-CNRC tels que le siliciumet 35 éléments en trace (terres rares, Ag, B, Bi, Cs, Ga, Ge, Li, Nb,P, Rb, Rh, Re, S, Sc, Sn, Th, Ti, Tl,W, Y et Zr). Le rapport isotopique deSr est aussi proposé à partir de mesures par TIMS (Thermo IonisationMass Spectrometry).Il apparaît que les mesures individuelles et compilées varient dequelques ng/l à 2400 g/l avec des incertitudes associées comprisesentre 2 et 240%. Les fortes incertitudes associées ne sont pas proportionnellesaux concentrations puisque certaines mesures s’accordent mêmeà de faibles teneurs tels que Bi (0,9 0,3 ng/l valeur compilée). Danscertains cas, un ou deux laboratoires ont caractérisé l’élément impliquantmoins de mesures et une incertitude associée plus élevée quelleque soit la concentration en l’élément. C’est le cas, par exemple, de Ge(0,015 0,014 g/l valeur compilée) caracterisé par seulement 2 laboratoires(34 mesures) et de P (8,19 3,40 g/l) issu de 8 mesuresd’un seul laboratoire. Les terres rares et onze autres éléments (B, Bi,Cs, Li, Rb, Si, Th, Ti, Tl, Y et Zr) ont été déterminés par au moins 3laboratoires différents et apportent des informations complémentairesessentielles à l’utilisation
24 ème Réunion des sciences de la Terre 2014
Pau, France

insu-01080879
https://hal-insu.archives-ouvertes.fr/insu-01080879

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : Ten international laboratories participated in an inter-laboratory comparison of a fossil bone composite with the objective of producing a matrix and structure-matched reference material for studies of the bio-mineralization of ancient fossil bone. We report the major and trace element compositions of the fossil bone composite, using in-situ method as well as various wet chemical digestion techniques. For major element concentrations, the intra-laboratory analytical precision (%RSDr) ranges from 7 to 18%, with higher percentages for Ti and K. The %RSDr are smaller than the inter-laboratory analytical precision (%RSDR; <15-30%). Trace element concentrations vary by similar to 5 orders of magnitude (0.1 mg kg(-1) for Th to 10,000 mg kg(-1) for Ba). The intra-laboratory analytical precision %RSDr varies between 8 and 45%. The reproducibility values (%RSDR) range from 13 to <50%, although extreme value >100% was found for the high field strength elements (Hf, Th, Zr, Nb). The rare earth element (REE) concentrations, which vary over 3 orders of magnitude, have %RSDr and %RSDR values at 8-15% and 20-32%, respectively. However, the REE patterns (which are very important for paleo-environmental, taphonomic and paleo-oceanographic analyses) are much more consistent. These data suggest that the complex and unpredictable nature of the mineralogical and chemical composition of fossil bone makes it difficult to set-up and calibrate analytical instruments using conventional standards, and may result in non-spectral matrix effects. We propose an analytical protocol that can be employed in future inter-laboratory studies to produce a certified fossil bone geochemical standard. (C) 2007 Elsevier B.V. All rights reserved.
ISSN: 0003-2670

hal-00407629
https://hal.archives-ouvertes.fr/hal-00407629
DOI : 10.1016/j.aca.2007.08.015

Éditeur(s) : HAL CCSD Elsevier
Résumé : We describe, test, and explain the relative effectiveness of six thermal and microwave techniques of absolute palaeointensity determination applied to lava samples from Mount Etna (Sicily) that acquired their thermoremanence (TRM) in a known geomagnetic field. The application of a single alternating field demagnetisation treatment prior to each measurement in a standard Thellier experiment is demonstrated to be beneficial: increasing the quality of the results and making the analysis simpler. A new quasi-perpendicular (QP) method dramatically improves the linearity of Arai plots by reducing or altogether eliminating non-ideal effects due to multidomain (MD) grains. Two broad types of sample were encountered by this study and the QP method is the only one capable of producing accurate measurements from them both. Its ease of use, speed, and increased reliability should allow it to replace standard double heating methods in studies such as these where laboratory alteration can be detected by other means than pTRM checks. The results of experiments performed using a microwave palaeointensity system provide further proof that the microwave (de)magnetisation process is equivalent to conventional thermal excitation. They also demonstrate that microwave experiments are subject to the same risks as conventional experiments when performed on samples containing MD grains. The behaviour of the samples in both the thermal and microwave experiments is in good agreement with a recently proposed model of MD TRM which is based on first-order symmetry of the remagnetisation process.
ISSN: 0012-821X

hal-00407671
https://hal.archives-ouvertes.fr/hal-00407671
DOI : 10.1016/j.epsl.2007.03.016

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
French Guiana is a South American French territory, where HIV prevalence consistently exceeds 1% in the adult population. In the only correctional facility, HIV prevalence fluctuates at around 4%.
After describing the population of HIV-positive inmates, we aimed to evaluate mortality after release from the correctional facility, and to identify its predictive factors.
Outside North American settings, data on treatment outcome and vital status of HIV-positive former inmates are scarce. There were no data in French Guiana. Filling this gap represents a basis for potential improvements.
All HIV-infected adults released from an incarceration of 30 days or more, between 2007 and 2013, were enrolled in a retrospective cohort study. Mortality was described over time, one to seven years following release, using Kaplan-Meier estimates. Factors associated with mortality were identified through a non-parametric survival regression model.
147 former inmates were included. The male to female ratio was 4.4. The median age was 37.3 years. The majority were migrants, 25.8% were homeless, 70.1% suffered from substance abuse, with 34.0% of crack-cocaine users. On admission, 78.1% had an early HIV-stage infection (CDC-stage A), with a median CD4 count of 397.5/mm3, 34.0% had one comorbidity, mainly hypertension. Upon release, 50.3% were on ART. Reasons for not being treated were not fulfilling the criteria for 74.6%, and refusing for 15.1%. Before release, 84.5% of the patients on ART had a viral load≤200cp/ml. After release, 8.2% of the cohort had died, with a crude incidence of 33.8/1000 person-years. All recorded deaths were males, with an incidence of 42.2/1000 person-years. Comparing with the age-specific mortality rates for males in French Guiana, the standardized mortality ratio was 14.8. In multivariate analysis, factors associated with death were age and CD4 count before release.
Despite access to ART while incarcerated, with good virological outcome, the post-release mortality was very high for males, almost 15 times what is observed in the general male population living in French Guiana, after age standardization. Access to ART in correctional facilities may be a necessary, but not sufficient condition to protect male inmates from death after release.
ISSN: 1932-6203

inserm-01519987
http://www.hal.inserm.fr/inserm-01519987
http://www.hal.inserm.fr/inserm-01519987/document
http://www.hal.inserm.fr/inserm-01519987/file/2017%2C%20Huber%20-%20Mortality%20HIV%20prisoners%20after%20release.pdf
DOI : 10.1371/journal.pone.0175740.t002

Éditeur(s) : HAL CCSD
Résumé : International audience
NSS'88
Amherst, United States

hal-01535426
https://hal.univ-antilles.fr/hal-01535426

Résumé : La distribution actuelle des espèces d’arbres des forêts tropicales humides amazoniennes est le résultat de processus dynamiques sur lesquels les perturbations passées, d’origine climatique ou anthropique, peuvent avoir jouées un rôle majeur. Des outils génétiques actuels associés à des méthodes d’analyses puissantes permettent d’inférer et de dater l’empreinte génomique des évènements démographiques subits par les populations naturelles. Le but de cette thèse est de contribuer à une vision d’ensemble de l’évolution démographique de la forêt tropicale humide du plateau des Guyanes pendant le Quaternaire. J’ai d’abord étudié les propriétés des microsatellites (répétitions simple de séquences, SSR) et les limites de leurs applications en tant que marqueurs moléculaires en phylogéographie. Plusieurs allèles SSR contenu dans diverses populations de trois genres d’arbres différents ont été séquencés et le polymorphisme, porté par chaque partie des fragments ADN contenant des SSR, a été étudié. J’ai observé que la quantité de variation génétique était aussi importante dans les régions encadrant le microsatellite que dans le SSR lui-même. Ces régions ont contribué significativement à l’information phylogénétique et ont parfois été la principale source de différenciation entre les individus et les populations. Cette expérience m’a permis de choisir la meilleure stratégie à adopter pour traiter les données de variation génétique des SSR dans des modèles démographiques. J’ai ensuite utilisé ces marqueurs SSR et des méthodes ABC pour étudier l’impact local des occupations humaines précolombiennes sur les forêts en Guyane française. Les changements démographiques subis par des populations de quatre espèces d’arbres ont été comparés entre cinq sites occupés et quatre sites non perturbés. Les perturbations naturelles et induites par l’homme ont contribué à la mise en place de la diversité observée actuellement, comme le suggère des signatures d’effet fondateur détectées sur les sites perturbés ou non. Néanmoins, la taille des populations fondatrices semble être proportionnelle à l’impact humain estimé, indiquant que les perturbations anthropique ont induit un remplacement des populations plus important que les processus écologiques naturels. Pour terminer, j’ai mené une étude de démographie comparative d’espèces d’arbres tropicaux à l’échelle régionale de la Guyane française. Cinq scénarios démographiques ont été testés pour neuf populations de huit espèces en utilisant des microsatellites nucléaires et des séquences chloroplastiques. Les changements démographiques les plus récents détectés convergent vers une signature générale d’expansion de la forêt humide depuis probablement la dernière glaciation. Cela peut suggérer, soit que la composition des forêts du plateau des Guyanes était différente, ou que le couvert forestier était moins étendu. Ce résultat constitue le premier indice de changement passé, probablement d’origine climatique, subi par les communautés forestières du plateau des Guyanes ; qui n’avait jusque-là pas pu être testé avec des méthodes standards en raison d’un manque de fossiles. En conclusion, j’ai recueilli des preuves génétiques que les perturbations, à différents échelles de temps, ont marqué la structure et la composition génétique des forêts du plateau des Guyanes. L’application de ces méthodes à d’autres régions Néotropicales pourrait contribuer, à l’avenir, à reconstruire l’histoire écologique de la forêt amazonienne de façon détaillée.
The current tree species distribution in Amazonian tropical rainforests is the outcome of dynamic processes in which past perturbations, climatic or anthropogenic, may have played a major role. Currently available genetic tools associated with powerful analytical methods allow inferring and dating the genomic imprint of demographic events undergone by natural populations. The aim of my thesis is to contribute to an overview of the demographic evolution of the tropical rainforest in the Guiana shield during the Quaternary. I have first studied the properties of microsatellites or Simple sequence repeat (SSR) and the limits in their applications as molecular markers in phylogeography. Several SSR alleles in multiple populations of three divergent tree genera have been sequenced and the sources of polymorphisms, carried by each portion of SSR-containing DNA amplicons, have been broken apart. I have observed that the amount of variation was as large in flanking regions as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations. This experiment allowed me to choose the best strategy to treat SSR variation in demographic modeling. I have subsequently used SSR markers and ABC methods to study the impact of pre-Columbian human settlements at the local level on rainforests in French Guiana. Demographic changes undergone by populations of four tree species were compared between five settled and four undisturbed sites. Both natural turnover and human-induced disturbances appeared as shaping currently observed genetic diversity, with signatures of founder effect both at disturbed and undisturbed sites. Nevertheless, the size of founding populations appeared to be proportional to the estimated human impact, suggesting that human-made disturbance caused deeper population turnover than background ecological processes. Finally, I have conducted a comparative demography study of tropical tree species at the regional level across French Guiana. Five demographic scenarios have been tested for nine populations from eight species using both nuclear microsatellites and chloroplastic sequences. The most recent demographic signals detected converge on a global signature of expansion of the rainforest since probably the last glaciation. This finding can suggest either that the composition of the Guiana shield rainforests was different, or that its global extent was smaller, during earlier epochs of the Pleistocene than today. This result is the first firm indication of changes undergone by the forest communities of the Guiana shield in the distant climatic past – something which could not be tested with standard methods due to almost complete lack of fossil evidence. In conclusion, I have gathered genetic evidence that disturbances, both in historical and geological times, have marked the structure and composition of forests in the Guiana shield.The extensive application of these methods to other regions of the Neotropics maycontribute, in the future, to the detailed reconstruction of the ecological history ofAmazonian forests.

http://www.theses.fr/2012AGUY0568/document