Résumé : The main aim of the CAMP project (2009-2011) is to estimate the efficient connectivity between the Marine Protected Areas (MPA) of the South-West Indian Ocean (SWIO). For that purpose, we use a population genetics approach on 3 reef fishes: Epinephelus merra, Lutjanus kasmira et Myripristis berndti. The overall goal of the project is to provide new elements to MPA managers that will contribute to design the best network of MPAs in the SWIO. In the first year of the project, most of the time was spent to sample fishes. Based on collaborations with 5 international and national partners, we succeed to sample more than 1100 fishes within 12 sites of the SWIO. More than 850 of the 1100 fishes were already sequenced. The development of third microsatellite libraries is under-going and should be available for the 2nd part of the year 2010. The second year of the project (2010) will focus on the end of the sampling in the SWIO as well as doing most of the genetic analysis of the samples collected in 2009 (microsatellit analysis) and in 2010 (mtDNA sequencing). At the end of the second year, we expect to be able to do a first regional analysis of the genetic structure of these reef fishes population. Then, in 2011, the project team will elaborate some recommendations to MPAs managers on the basis of the whole genetic dataset
L’objectif principal du projet CAMP (2009-2011) est d’estimer la connectivité effective entre les Aires Marines Protégées (AMP) du sud ouest de l’océan Indien (SOOI) par le biais de la génétique des populations de 3 modèles biologiques : Epinephelus merra, Lutjanus kasmira et Myripristis berndti. L’objectif final est de fournir des éléments de réflexion aux gestionnaires afin de contribuer significativement au dessin du réseau des AMPs dans le SOOI. La première année du projet a été consacrée essentiellement à l’échantillonnage. Basé sur une coopération avec nos 5 partenaires nationaux et internationaux, cet échantillonnage a permis de collecter plus de 1100 échantillons de tissus de ces 3 espèces de poissons répartis dans 12 sites du SOOI. Sur ces 1100 poissons, plus de 850 séquences d’ADN mitochondrial ont d’ores et déjà été effectuées. En parallèle, le développement des banques microsatellites pour les 3 espèces est en cours et devrait être disponible pour à la mi 2010. La deuxième année du projet (2010) aura pour objectif de poursuivre l’échantillonnage sur l’ensemble du SOOI et de réaliser les analyses microsatellites des échantillons collectés en 2009 ainsi que les séquences des échantillons collectés en 2010. Au terme de cette deuxième année, une analyse de la structure génétique de ces populations de poissons de récifs pourra être menée, suivie en 2011 de l’élaboration d’aides à la gestion sur la base de l’ensemble des données acquises dans le cadre de ce projet.

Droits : 2010 Ifremer
http://archimer.ifremer.fr/doc/00100/21086/18710.pdf
http://archimer.ifremer.fr/doc/00100/21086/

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Functional traits provide insight into a variety of ecological questions, yet the optimal sampling method to estimate the community-level distribution of plant functional trait values remains a subject of debate, especially in species-rich forests. 2. We present a simulation analysis of the trait distribution of a set of nine completely sampled permanent plots in the lowland rain forests of French Guiana. 3. Increased sampling intensity consistently improved accuracy in estimating community-weighted means and variances of functional trait values, whereas there was substantial variation among functional traits and minor differences among sampling strategies. 4. Thus, investment in intensified sampling yields a greater improvement in the accuracy of estimation than does an equivalent investment in sampling design complication. 5. Notably, 'taxon-free' strategies frequently had greater accuracy than did abundance-based strategies, which had the additional cost of requiring botanical surveys. 6. We conclude that there is no substitute for extensive field sampling to accurately characterize the distribution of functional trait values in species-rich forests.
ISSN: 0269-8463

hal-01536541
https://hal.archives-ouvertes.fr/hal-01536541
PRODINRA : 343202
DOI : 10.1111/1365-2435.12433

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Society's needs for a network of in situ ocean observing systems cross many areas of earth and marine science. Here we review the science themes that benefit from data supplied from ocean observatories. Understanding from existing studies is fragmented to the extent that it lacks the coherent long-term monitoring needed to address questions at the scales essential to understand climate change and improve geo-hazard early warning. Data sets from the deep sea are particularly rare with long-term data available from only a few locations worldwide. These science areas have impacts on societal health and well-being and our awareness of ocean function in a shifting climate. Substantial efforts are underway to realise a network of open-ocean observatories around European Seas that will operate over multiple decades. Some systems are already collecting high-resolution data from surface, water column, seafloor, and sub-seafloor sensors linked to shore by satellite or cable connection in real or near-real time, along with samples and other data collected in a delayed mode. We expect that such observatories will contribute to answering major ocean science questions including: How can monitoring of factors such as seismic activity, pore fluid chemistry and pressure, and gas hydrate stability improve seismic, slope failure, and tsunami warning? What aspects of physical oceanography, biogeochemical cycling, and ecosystems will be most sensitive to climatic and anthropogenic change? What are natural versus anthropogenic changes? Most fundamentally, how are marine processes that occur at differing scales related? The development of ocean observatories provides a substantial opportunity for ocean science to evolve in Europe. Here we also describe some basic attributes of network design. Observatory networks provide the means to coordinate and integrate the collection of standardised data capable of bridging measurement scales across a dispersed area in European Seas adding needed certainty to estimates of future oceanic conditions. Observatory data can be analysed along with other data such as those from satellites, drifting floats, autonomous underwater vehicles, model analysis, and the known distribution and abundances of marine fauna in order to address some of the questions posed above. Standardised methods for information management are also becoming established to ensure better accessibility and traceability of these data sets and ultimately to increase their use for societal benefit. The connection of ocean observatory effort into larger frameworks including the Global Earth Observation System of Systems (GEOSS) and the Global Monitoring of Environment and Security (GMES) is integral to its success. It is in a greater integrated framework that the full potential of the component systems will be realised. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.
Progress In Oceanography (0079-6611) (Pergamon-elsevier Science Ltd), 2011-10 , Vol. 91 , N. 1 , P. 1-33

Droits : 2011 Published by Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00044/15557/15923.pdf
DOI:10.1016/j.pocean.2011.05.001
http://archimer.ifremer.fr/doc/00044/15557/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
1. The Before-After Control-Impact Paired Series (BACIPS) design distinguishes natural spatial and temporalvariability from variation induced by an environmental impact (or intervention) of interest. BACIPS is a powerfultool to derive inferences about interventions when classic experimental approaches (e.g. which rely on spatialreplicates and random assignment of treatments) are not feasible or desirable. Previously applied BACIPSdesigns generally assume that effects are sudden, constant and long-lived: that is, that systems exhibit ‘stepchanges’in response to interventions. However, complex ecological interactions or gradual interventions maycreate delayed and/or progressive responses, potentially impeding the reliability of classic (step-change) analyses.2. We propose a novel approach, the Progressive-Change BACIPS, which generalizes and expands the scope ofBACIPS analyses.We evaluate the relative performance of this approach using both simulated and real data thatexhibit step-change, linear, asymptotic and sigmoid responses following an intervention.We quantify the statisticalpower and accuracy of the Progressive-Change BACIPS under varying initial population densities, intensityof spatial sampling, effect sizes and number of sampling dates After the intervention.3. We show that Progressive-Change BACIPS identified the correct model among the set of candidate modelsunder most conditions and led to accurate estimates of the parameters that were used to generate the simulateddata. When data were sparse, and the dynamics complex, simpler (more parsimonious) models were favouredover the more complex models that actually generated the simulated data. Application of the Progressive-Change BACIPS to existing data sets from the literature led to strong support for specific models (over alternatives)and led to more specific inferences than possible under the classic BACIPS approach.4. The Progressive-Change BACIPS proposed here is more flexible than the original BACIPS formulationbecause the data are used to inform the form of the final model, rather than having the form of the modelimposed on the data. This leads to better estimates of the effects of environmental impacts and the time-scalesover which they operate. As a result, the Progressive-Change BACIPS should be applicable to a wide range ofstudies and should help improve investigation of time-dependent effects. R code to perform Progressive-ChangeBACIPS analysis is provided.
ISSN: 2041-210X

hal-01416668
https://hal-univ-perp.archives-ouvertes.fr/hal-01416668
DOI : 10.1111/2041-210X.12655

Éditeur(s) : HAL CCSD Integrated Ocean Drilling Program
Résumé : Integrated Ocean Drilling Program (IODP) Expedition 325, designed to investigate the fossil reefs on the shelf edge of the Great Barrier Reef, was the fourth expedition to utilize a mission-specific platform and was conducted by the European Consortium for Ocean Research Drilling (ECORD) Science Operator (ESO). The objectives of Expedition 325 were to establish the course of sea level change, define sea-surface temperature variations, and analyze the impact of these environmental changes on reef growth and geometry for the region over the period of 20-10 ka. To meet these objectives, a succession of fossil reef structures preserved on the shelf edge seaward of the modern barrier reef were cored from a dynamically positioned vessel in February-April 2010. A total of 34 boreholes across 17 sites were cored in depths ranging from 42.27 to 167.14 meters below sea level (lowest astronomical tide taken from corrected EM300 multibeam bathymetry data). Borehole logging operations in four boreholes provided continuous geophysical information about the drilled strata. The cores were described during the Onshore Science Party (OSP) at the IODP Bremen Core Repository (Germany) in July 2010, where minimum and some standard measurements were made. Preliminary postcruise dating of core catcher samples and initial observations of the cores made during the OSP confirm that coral reef material ranging in age from >30,000 to 9,000 calendar years before present (years before 1950 AD) was recovered during Expedition 325. Further postcruise research on samples taken during the OSP is expected to fulfill the objectives of the expedition.
ISSN: 1930-1014

hal-00855800
https://hal.archives-ouvertes.fr/hal-00855800

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
This paper presents a comparison of models for extreme rainfall and flood values. Based on a large set of thousands of rainfall and discharge data, the French ExtraFlo project showed that design estimate of extreme values based on the fitting of a distribution on a limited sample of maximum values is very inaccurate when only a few decades of observation are available. Some interesting alternatives are possible, using a regional approach, or historical data when available, or simulation methods, or sedimentological or geochemical signatures of flood deposits.
Cette communication présente les principaux résultats du projet ExtraFlo sur l'estimation des pluies et crues extrêmes. A partir d'un jeu de données conséquent de plusieurs milliers de stations, une procédure d'inter-comparaison a permis d'évaluer les performances d'une trentaine d'implémentations différentes issues de différentes combinaisons (modèle probabiliste, méthode d'estimation, cadre local / régional / mixte local et régional). Le projet ExtraFlo a permis de mettre en évidence le manque de robustesse des approches basées sur le traitement statistique d'une série de quelques dizaines d'années d'observation. Des alternatives intéressantes existent, basées sur l'exploitation des records de pluie et de débit à l'échelle d'une région, de la collecte de données historiques quand cela est possible, de méthodes de simulation basées sur le couplage d'un générateur d'averses avec un modèle hydrologique pour la transformation des pluies en débit, ou des traces morphologiques laissées par les crues anciennes.
ISSN: 0018-6368

hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341/document
https://hal.archives-ouvertes.fr/hal-01128341/file/ly2014-pub00041933.pdf
DOI : 10.1051/lhb/2014010

Éditeur(s) : Institut national agronomique Paris Grignon
Résumé : The flat oyster Ostrea edulis L. is the indigenous oyster of the Atlantic as well as the Mediterranean coasts of Europe. Its commercial exploitation dates back to Antiquity but its breeding is now threatened by two parasitic protozoa, among which Bonamia ostreae. Various aspects of the genetics of this species' natural and farmed populations have been studied with the aid of microsatellite markers. At first, the implementation and the screening of two partial genomic libraries made it possible to identify 28 new microsatellite loci. Analysis of the segregation of 12 of these loci and of two enzymatic loci shows that most microsatellite loci are transmitted in a Mendelian way, but some loci have significant segregation distortions. Moreover, seven linkage groups, of which four contain at least two markers, were identified in Ostrea edulis. The genetic variability of three populations selected for one or two generations for resistance to Bonamia ostreae was analysed with the aid of 5 microsatellite loci. In spite of the absence of genealogical data, we have shown that these selected populations were descended from a very low number of founding genitors (from 3 to 15 depending on the population) and for two populations, we were able to reconstruct the genealogy and the relationships between the individuals were identified. These selected populations have, in addition to a very low genetic variability, real and at times high levels of consanguinity. These results have a significant implication for the continuation of the selection programme (consanguinity management, augmentation of genetic variability by introducing wild genitors). The geographical structuring of the genetic variability of natural populations of Ostrea edulis has been analysed with the aid of 5 microsatellite loci on a sampling covering almost the entire distribution area of the species (from Norway to the Adriatic Sea). The results are consistent with those published in the literature and using enzymatic markers. The populations show a low level of differentiation that could correspond to a model of isolation by distance. The Atlantic populations, which have a reduced polymorphism, could be descended from post-glacial recolonisation from Mediterranean populations that had survived the glaciations of the Quaternary Period. The current distribution of flat oyster populations is surely also subject to anthropogenic activities. Finally, the genetic bases of the heterozygosis-growth correlation were studied in a natural population with the aid of enzymatic and microsatellite markers. Although leads favouring the direct contribution of enzymatic loci have been found, biases in the sampling design make it impossible to come to a formal conclusion. However, this study has made it possible to show that the capture of individuals over a short period (around ten days) leads to a sampling of a population descended from a very low number of founding genitors, in contradiction with the generally accepted idea that marine bivalve populations are large panmictic populations with significant, efficient numbers. These results confirm in a natural population the observations of a significant reduction of efficient sizes in hatchery populations.
L'huître plate Ostrea edulis L. est l'huître indigène des côtes européennes aussi bien atlantiques que méditerranéennes. Son exploitation commerciale remonte à l'Antiquité mais son élevage est aujourd'hui menacé par deux protozoaires parasites dont Bonamia ostreae. Différents aspects de la génétique des populations naturelles et cultivées de cette espèce ont été étudiés à l'aide de marqueurs microsatellites. Dans un premier temps, la réalisation et le criblage de deux banques génomiques partielles ont permis l'identification de 28 nouveaux locus microsatellites. L'analyse de la ségrégation de 12 de ces locus et de deux locus enzymatiques montre que la plupart des locus microsatellites sont transmis de façon mendélienne, mais certains locus présentent des distorsions de ségrégation importantes. Par ailleurs, sept groupes de liaison dont quatre contiennent au moins deux marqueurs ont été identifiés chez Ostrea edulis. La variabilité génétique de trois populations sélectionnées depuis une ou deux générations pour une résistance à Bonamia ostreae a été analysée à l'aide de 5 locus microsatellites. Malgré l'absence de données généalogiques, nous avons montré que ces populations sélectionnées étaient issues d'un très faible nombre de géniteurs fondateurs (de 3 à 15 selon les populations) et pour deux populations, la généalogie a pu être reconstituée et les liens de parenté entre les individus ont été identifiés. Ces populations sélectionnées présentent, outre une très faible variabilité génétique, des niveaux de consanguinité réels et parfois élevés. Ces résultats ont une implication importante pour la continuation du programme de sélection (gestion de la consanguinité, augmentation de la variabilité génétique par introduction de géniteurs sauvages). La structuration géographique de la variabilité génétique des populations naturelles d'Ostrea edulis a été analysée à l'aide de 5 locus microsatellites sur un échantillonnage couvrant presque toute l'aire de répartition de l'espèce (de la Norvège à la Mer Adriatique). Les résultats sont cohérents avec ceux publiés dans la littérature et utilisant des marqueurs enzymatiques. Les populations montrent un niveau de différenciation faible qui pourrait correspondre à un modèle d'isolement par la distance. Les populations atlantiques, qui présentent un polymorphisme réduit, pourraient être issues de recolonisation post-glaciaire à partir de populations méditerranéennes ayant survécu aux glaciations du Quaternaire. La répartition actuelle des populations d'huître plate est certainement aussi soumise aux actions anthropiques. Enfin, les bases génétiques de la corrélation hétérozygotie-croissance ont été étudiées dans une population naturelle à l'aide de marqueurs enzymatiques et microsatellites. Bien que des pistes en faveur de la contribution directe des locus enzymatiques aient été trouvées, des biais dans le dispositif expérimental ne permettent pas de conclure de façon formelle. Cependant, cette étude a permis de montrer que le captage d'individus sur une faible période (une dizaine de jours) conduit à l'échantillonnage d'une population issue d'un nombre très réduit de géniteurs fondateurs, en contradiction avec l'idée reçue que les populations de bivalves marins sont de larges populations panmictiques à effectif efficace important. Ces résultats confirment dans une population naturelle les observations de réduction importante des tailles efficaces dans des populations d'écloserie.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1998/these-1919.pdf
http://archimer.ifremer.fr/doc/00000/1919/

Éditeur(s) : HAL CCSD National Institute of Environmental Health Sciences
Résumé : International audience
Safe drinking water is essential for well-being. Although microbiological contamination remains the largest cause of water-related morbidity and mortality globally, chemicals in water supplies may also cause disease, and evidence of the human health consequences is limited or lacking for many of them. We aimed to summarize the state of knowledge, identify gaps in understanding, and provide recommendations for epidemiological research relating to chemicals occurring in drinking water. Assessing exposure and the health consequences of chemicals in drinking water is challenging. Exposures are typically at low concentrations, measurements in water are frequently insufficient, chemicals are present in mixtures, exposure periods are usually long, multiple exposure routes may be involved, and valid biomarkers reflecting the relevant exposure period are scarce. In addition, the magnitude of the relative risks tends to be small. Research should include well-designed epidemiological studies covering regions with contrasting contaminant levels and sufficient sample size; comprehensive evaluation of contaminant occurrence in combination with bioassays integrating the effect of complex mixtures; sufficient numbers of measurements in water to evaluate geographical and temporal variability; detailed information on personal habits resulting in exposure (e.g., ingestion, showering, swimming, diet); collection of biological samples to measure relevant biomarkers; and advanced statistical models to estimate exposure and relative risks, considering methods to address measurement error. Last, the incorporation of molecular markers of early biological effects and genetic susceptibility is essential to understand the mechanisms of action. There is a particular knowledge gap and need to evaluate human exposure and the risks of a wide range of emerging contaminants.
ISSN: 0091-6765

hal-01118530
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118530
PUBMED : 24380896
DOI : 10.1289/ehp.1206229
PUBMEDCENTRAL : PMC3948022

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
: Indoor dust samples cannot always be analyzed immediately after collection. However, little information is currently available on how storage conditions may affect measurements. This study was designed to determine how sample storage conditions may affect the concentration of semi-volatile organic compounds (SVOCs) in the dust. A composite dust was prepared using a Standard Reference Material (SRM 2585) with real indoor dust samples. The composite dust was stored in various types of packaging, at different temperatures (-18°C, 5°C, 20°C and 35°C) and in different light conditions. The concentration of SVOCs was measured after various storage durations. No effect on SVOC concentrations was observed for the composite dust stored in an amber glass vial at -18°C for 36 months. At 5°C, 20°C and 35°C, losses occurred for the more volatile compounds. The experimental storage conditions clearly showed that temperature and duration affected the concentrations of SVOCs in the composite dust. The type of packaging material (polyethylene zip bag or polyethylene garbage bag) did not seem to have a systematic effect on the preservation of SVOCs in the composite dust. Maximum storage duration times are proposed for each compound at various temperatures. For most compounds, samples can be stored for two months at 20°C. For samples that cannot be analyzed immediately, we recommend to store them in the dark at -18°C to ensure a good recovery of all tested compounds. This article is protected by copyright. All rights reserved.
ISSN: 0905-6947

inserm-00866171
http://www.hal.inserm.fr/inserm-00866171
DOI : 10.1111/ina.12066
PUBMED : 24033516

Éditeur(s) : HAL CCSD National Institute of Environmental Health Sciences
Résumé : International audience
Background: Glycol ethers (GE) are widely used organic solvents. Despite the potential neurotoxicity of several families of organic solvents, little is known about the impact of GE on the neurodevelopment of infants and children. Objectives: We investigated the relation between urinary concentrations of GE metabolites in pregnant women and neurocognitive abilities in their 6-year-old children in the PELAGIE mother-child cohort. Methods: Five GE metabolites were measured in first morning void urine samples of 204 French pregnant women in early pregnancy (<19 weeks of gestation). Psychologists assessed the neurocognitive abilities of their 6-year-old children with the Wechsler Intelligence Scale for Children IV (WISC) and the Developmental Neuropsychological Assessment (NEPSY). We analyzed the results with linear (WISC) and Poisson regression models (NEPSY), adjusted for potential confounders, including child's stimulation at home. Results: GE metabolites were detected in 90-100% of maternal urine samples. The WISC Verbal Comprehension score was significantly lower for children with the highest tertile of urinary phenoxyacetic acid (PhAA) [beta (third vs. first tertile)=-6.53; 95% CI: -11.44, -1.62]. Similarly, the NEPSY Design Copying subtest score was lower in those with the highest tertile of urinary ethoxyacetic acid (EAA) [beta (third vs. first tertile)=-0.11; 95% CI: -0.21, 0.00]. The other GE metabolites we studied were not significantly associated with WISC or NEPSY scores. Conclusions: Prenatal urine concentrations of two GE metabolites were associated with lower WISC Verbal Comprehension Index scores and NEPSY Design Copying subscale scores, respectively, at age 6 years. PhAA is the primary metabolite of 2-phenoxyethanol (EGPhE), which is commonly found in cosmetics, and precursors of EAA are frequently used in cleaning agents. Additional research is needed to confirm our findings and further explore potential effects of prenatal GE exposures on neurocognitive performance in children.
ISSN: 0091-6765

hal-01519256
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519256
DOI : 10.1289/EHP39
PUBMED : 27740510

Éditeur(s) : Inter-Research
Résumé : The Biocean database was designed to collate the extremely large volume of data collected from different deep-sea ecosystem studies conducted by Ifremer's department of 'Environnement Profond' (Deep-Sea Environment). This database comes in a 6-application package: 2 of them are used on research vessels to collect operational data, whereas the others are used to link with a core database back on land. The latter are used to: (1) manage taxonomic nomenclature, (2) monitor the identification of faunal collections, (3) fill in chemical analyses results or measurement data files and (4) add or extract data from the database. Biocean was designed to facilitate ecosystem studies in the deep sea. It represents an important new resource for deep-sea ecologists and will have wide applications in biogeography and biodiversity studies at Ifremer, but also for the international community, as faunal data are linked to the Census of Marine Life information system OBIS (Ocean Biogeographic Information System). Biogeographical analyses of Biocean data recovered through the OBIS portal evidence an evolution in the deep-sea sampling strategies more focused in limited areas and is intended to reveal ecosystems functioning.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2006-07 , Vol. 316 , P. 215-224

Droits : 2006 Inter-Research
http://archimer.ifremer.fr/doc/2006/publication-1581.pdf
http://archimer.ifremer.fr/doc/00000/1581/

Éditeur(s) : HAL CCSD Ferrata Storti Foundation
Résumé : International audience
BACKGROUND: Abnormal interactions between red blood cells, leukocytes and endothelial cells play a critical role in the occurrence of the painful vaso-occlusive crises associated with sickle cell disease. We investigated the interaction between circulating leukocytes and red blood cells which could lead to aggregate formation, enhancing the incidence of vaso-occlusive crises. DESIGN AND METHODS: Blood samples from patients with sickle cell disease (n=25) and healthy subjects (n=5) were analyzed by imaging and classical flow cytometry after density gradient separation. The identity of the cells in the peripheral blood mononuclear cell layer was determined using antibodies directed specifically against white (anti-CD45) or red (anti-glycophorin A) blood cells. RESULTS: Aggregates between red blood cells and peripheral blood mononuclear cells were visualized in whole blood from patients with sickle cell disease. The aggregation rate was 10-fold higher in these patients than in control subjects. Both mature red blood cells and reticulocytes were involved in these aggregates through their interaction with mononuclear cells, mainly with monocytes. The size of the aggregates was variable, with one mononuclear cell binding to one, two or several red blood cells. Erythroid Lu/basal cell adhesion molecule and α(4)β(1) integrin were involved in aggregate formation. The aggregation rate was lower in patients treated with hydroxycarbamide than in untreated patients. CONCLUSIONS: Our study gives visual evidence of the existence of circulating red blood cell-peripheral blood mononuclear cell aggregates in patients with sickle cell disease and shows that these aggregates are decreased during hydroxycarbamide treatment. Our results strongly suggest that erythroid Lu/basal cell adhesion molecule proteins are implicated in these aggregates through their interaction with α(4)β(1) integrin on peripheral blood mononuclear cells.
ISSN: 0390-6078

inserm-00821120
http://www.hal.inserm.fr/inserm-00821120
http://www.hal.inserm.fr/inserm-00821120/document
http://www.hal.inserm.fr/inserm-00821120/file/1841.full.pdf
DOI : 10.3324/haematol.2010.026294

Éditeur(s) : HAL CCSD
Résumé : International audience
OBJECTIVES: Semen composition is influenced by HIV-1 infection, yet the impact of semen components on HIV infection of primary target cells has only been studied in samples from HIV-uninfected donors. DESIGN: We compared the effect of seminal plasma from chronically HIV-infected (SP+) versus uninfected donors (SP-) on HIV-1 infection of PBMCs and CD4+T cells. METHODS: Primary cells were infected with HIV-1 in the presence of SP+ or SP- and analyzed for infection level, metabolic activity, HIV receptor expression, proliferation and activation. SP+ and SP- were compared for infection-enhancing peptides, cytokines and prostaglandin E2 levels. RESULTS: SP- efficiently enhanced HIV-1 R5 infection of CD4+ T cells, whereas SP+ enhancing activity was significantly reduced. RANTES concentrations were elevated in SP+ relative to SP-, while the concentrations of infectivity-enhancing peptides (SEVI, SEM1, SEM2) were similar. CCR5 membrane expression levels were reduced on CD4+T cells shortly post-exposure to SP+ compared with SP- and correlated to R5-tropic HIV-1 infection levels, and CCR5 ligands' concentrations in semen. SP+ and SP- displayed similar enhancing activity on PBMC infection by X4-tropic HIV-1. Addition/depletion of RANTES from seminal plasmas modulated their effect on PBMC infection by R5-tropic HIV-1. CONCLUSIONS: Semen from HIV-infected donors exhibit a significantly reduced enhancing potential on CD4+ T cell infection by R5-tropic HIV-1 when compared with semen from uninfected donors. Our data indicate that elevated seminal concentrations of RANTES in HIV+ men can influence the ability of semen to enhance infection.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives 4.0 License, where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially. http://creativecommons.org/licenses/by-nc-nd/4.0
AIDS

hal-01274885
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01274885
DOI : 10.1097/QAD.0000000000001048
PUBMED : 26854806

Éditeur(s) : ICES 2008 Annual Science Conference, 22-26 september 2008, HALIFAX, CANADA
Résumé : While the majority of small-scale coastal fisheries are found in developing nations, a considerable number exist in developed nations as well. Indeed, small-scale fisheries are strongly represented in all European Union (EU) Member States, 81% and 87% of the EU 25 whole fleet is composed of vessels less than 12 and 15 meters long respectively. In 2000, European regulation established a fisheries data collection framework including economic information requirements in order to provide the scientific basis for the implementation of the Common Fisheries Policy. This paper presents the methodology designed to collect the relevant economic data and characterize the status of the French fleets from an economic perspective. Based on stratified sampling plan including the following of small-scale fleets, data collection by field survey is based on a single questionnaire for all the fleets, whatever the size of the vessel, the gear used, the fishing area or the species targeted. It provides a large data set including earnings and costs but also capital, employment, fishing activity figures. Statistical analysis through a revenue model gives the basis for a re-assessing of the small-scale fisheries contribution to national production. Economic indicators such as gross added value, revenues, and direct employment are derived from the data set. The significant role of small scale fisheries in the French fishing sector is established and the impact of the rising fuel costs in fisheries is discussed.

Droits : 2008 ICES
http://archimer.ifremer.fr/doc/00059/16998/14500.pdf
http://archimer.ifremer.fr/doc/00059/16998/

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Humans may be exposed via their environment to multiple chemicals as a consequence of human activities and use of synthetic products. Little knowledge is routinely generated on the hazards of these chemical mixtures. The metabolomic approach is widely used to identify metabolic pathways modified by diseases, drugs, or exposures to toxicants. This review, based on the state of the art of the current applications of metabolomics in environmental health, attempts to determine whether metabolomics might constitute an original approach to the study of associations between multiple, low-dose environmental exposures in humans. Studying the biochemical consequences of complex environmental exposures is a challenge demanding the development of careful experimental and epidemiological designs, in order to take into account possible confounders associated with the high level of interindividual variability induced by different lifestyles. The choices of populations studied, sampling and storage procedures, statistical tools used, and system biology need to be considered. Suggestions for improved experimental and epidemiological designs are described. Evidence indicates that metabolomics may be a powerful tool in environmental health in the identification of both complex exposure biomarkers directly in human populations and modified metabolic pathways, in an attempt to improve understanding the underlying environmental causes of diseases. Nevertheless, the validity of biomarkers and relevancy of animal-to-human extrapolation remain key challenges that need to be properly explored.
ISSN: 1093-7404

hal-00976116
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00976116/file/Potential_input_from_metabolomics_accepted.pdf
DOI : 10.1080/10937404.2013.860318

Éditeur(s) : HAL CCSD
Résumé : National audience
Designing systems able to interact with students in a natural manner is a complex and far from solved problem. A key aspect of natural interaction is the ability to understand and appropriately respond to human emotions. This paper details our response to the continuous Audio/Visual Emotion Challenge (AVEC'12) whose goal is to predict four affective signals describing human emotions. The proposed method uses Fourier spectra to extract multi-scale dynamic descriptions of signals characterizing face appearance, head movements and voice. We perform a kernel regression with very few representative samples selected via a supervised weighted-distance-based clustering, that leads to a high generalization power. We also propose a particularly fast regressor-level fusion framework to merge systems based on different modalities. Experiments have proven the efficiency of each key point of the proposed method and our results on challenge data were the highest among 10 international research teams.
IHM'14, 26e conférence francophone sur l'Interaction Homme-Machine
Lille, France

hal-01089628
https://hal.archives-ouvertes.fr/hal-01089628
https://hal.archives-ouvertes.fr/hal-01089628/document
https://hal.archives-ouvertes.fr/hal-01089628/file/p44-nicole.pdf

Éditeur(s) : HAL CCSD Wiley
Résumé :  
A digital land cover map of South America has been produced using remotely sensed satellite data acquired between 1995 and the year 2000. The mapping scale is defined by the 1 km spatial resolution of the map grid-cell. In order to realize the product, different sources of satellite data were used, each source providing either a particular parameter of land cover characteristic required by the legend, or mapping a particular land cover class. The map legend is designed both to fit requirements for regional climate modelling and for studies on land cover change. The legend is also compatible with a wider, global, land cover mapping exercise, which seeks to characterize the world's land surface for the year 2000. As a first step, the humid forest domain has been validated using a sample of high-resolution satellite images. The map demonstrates both the major incursions of agriculture into the remaining forest domains and the extensive areas of agriculture, which now dominate South America's grasslands.
ISSN: 1354-1013

hal-01032088
https://hal.archives-ouvertes.fr/hal-01032088
DOI : 10.1111/j.1529-8817.2003.00774.x

Éditeur(s) : Royal Soc
Résumé : Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.
Proceedings Of The Royal Society B-biological Sciences (0962-8452) (Royal Soc), 2013-11 , Vol. 280 , N. 1770 , P. 1-9

Droits : 2013 The Author(s) Published by the Royal Society. All rights reserved.
http://archimer.ifremer.fr/doc/00157/26814/24961.pdf
DOI:10.1098/rspb.2013.1876
http://archimer.ifremer.fr/doc/00157/26814/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adri-atic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
ISSN: 1932-6203

hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/file/journal.pone.0167441.pdf
DOI : 10.1371/journal.pone.0167441.s009

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Addressing data quality issues in information systems remains a challenging task. Many approaches only tackle this issue at the extract, transform and load steps. Here we define a comprehensive method to gain greater insight into data quality characteristics within data warehouse. Our novel architecture was implemented for an hydroecological case study where massive French watercourse sampling data are collected. The method models and makes effective use of spatial, thematic and temporal accuracy, consistency and completeness for multidimensional data in order to offer analysts a “data quality” oriented framework. The results obtained in experiments carried out on the Saône River dataset demonstrated the relevance of our approach
ISSN: 0098-3004

hal-01223918
https://hal.archives-ouvertes.fr/hal-01223918
https://hal.archives-ouvertes.fr/hal-01223918/document
https://hal.archives-ouvertes.fr/hal-01223918/file/final-cogeo.pdf
DOI : 10.1016/j.cageo.2015.09.012