Éditeur(s) : Actes du 6e colloque national BRG, La Rochelle, 2-3-4 octobre 2006
Résumé : Previous studies have shown heritable variation in larval developmental traits in the Pacific oyster Crassostrea gigas. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors, specific to hatcheries, were examined: the effect of discarding the smallest larvae (i.e. culling) and the effect of temperature (20°C versus 26°C). A mixed-family approach was used in order to infer the genetic composition of larval populations and family assignment, limiting possible environmental bias and allowing the study of a relatively large number of families using a limited number of larval tanks. Our results show that three multiplexed highly polymorphic microsatellite markers are a powerful tool for family assignment and, consequently, for the study of bivalve larvae genetics. Culling, by selective sieving of the smallest larvae is an advantageous practice at a phenotypic scale as it reduced variance in larval size, variance of developmental rate and time to settlement. Culling of 50% of the larval population only led to 15% less spat, showing a positive phenotypic correlation between larval growth and settlement success. However, culling represents a substantial risk for diversity loss, because it increases the variance of reproductive success among parental oysters. The effective population sizes of early settling cohorts of settlement were lower than those of later ones. Our results show that the settlement of slow growing larvae significantly contributes to minimizing the variability of reproductive success and therefore to maximizing genetic diversity. These results corroborate the low estimations of variability of broodstocks sampled in several French commercial hatcheries, relative to natural populations. The genetic composition of the larval population and the resulting spat was significantly different between the two tested temperatures, revealing genotype x environment interaction for survival. Similarly, genotype x environment interaction was also observed for larval growth as a higher temperature exerted a positive influence on the expression of genetic variability for this trait. Consequently, we can conclude that a temperature of 26°C coupled with culling, to common practice in oyster hatcheries, is likely to amplify the selection pressure for fast growing larvae. To test for this hypothesis, we compared larval developmental traits in the progeny of a hatchery broodstock closed for 7 generations, with the progeny of wild oysters and the two possible hybrids. Our results show that selection of fast growing larvae can counteract presumed inbreeding depression, due to higher mean relatedness among hatchery broodstock than in the wild. Genetic effects of intensive rearing conditions at larval stage are significant and should be taken into account in hatchery practices, especially in terms of genetic diversity management.
Afin d'étudier les conséquences génétiques des pratiques de production en écloserie d'huître creuse, deux facteurs ont été examinés : l'élimination des petites larves et la température. Nos résultats montrent que l'assignation de parenté par marqueurs microsatellites est un outil performant pour les études génétiques en phase larvaire de familles élevées en mélange. Bien qu'avantageux d'un point de vue phénotypique, le tamisage sélectif représente un risque de perte de diversité. La fixation des larves à croissance lente permet en effet de minimiser la variabilité du succès reproducteur et de fait, de maximiser la variabilité génétique. Ces résultats corroborent les estimations de variabilité sur les stocks d'écloseries françaises où l'on constate une diversité allélique inférieure à celle de populations issues du milieu naturel. La température exerce également une influence sur la précocité de l'expression de la variabilité génétique pour la croissance larvaire. Ainsi une température élevée associée à une procédure de tamisage peut amplifier l'effet sélectif. Enfin, la sélection de larves à croissance rapide semble démontrée, s'opposant à la dépression de consanguinité présumée. Les conditions d'élevage peuvent donc avoir un effet génétique significatif qui devrait être pris en considération dans les pratiques d'écloserie, notamment dans la gestion de la diversité génétique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-1505.pdf
http://archimer.ifremer.fr/doc/00000/1505/

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : This paper will analyze the tourism image the municipal and state tourism offices of Guanajuato, Mexico, a World Heritage site, aim to project through their promotional materials: a small, colonial city, whose streets are shown as empty, cobble-stoned, and set in romantic light. The "city of Cervantes in the Americas" (a title bestowed by UNESCO in 2005 to honor the theatrical tradition of Cervantes plays in Guanajuato) appears to want to set forth an image of tranquility and spaciousness, while the reality is much different: Guanajuato's mainly narrow and windy streets typically bustle, plazas and gardens are full of activity, in short, the town is alive, yet its projected image lacks liveliness. Furthermore, although it is a World Heritage site, Guanajuato has thus far not used that brand to its advantage; instead, Guanajuato has recently had a variety of slogans to promote itself, seemingly at the whim of officials. Through interviews with tourism officials and a selection of collected tourism materials, I show how the city has yet to establish a “coherent” brand, and is going through various phases of place marketing at once.
Cette étude analyse l'image touristique et le projet touristique des municipalités et des offices de tourisme de l'État de Guanajuato, au Mexique. La «ville de Cervantès dans les Amériques" (un titre décerné par l'UNESCO en 2005 pour honorer la tradition théâtrale de Cervantès joue dans Guanajuato) semble vouloir assoir une image de tranquillité et d'espace, alors que la réalité est bien différente: l’image projetée de la ville de Guanajuato est loin de refléter la vie animée des places et jardins, des ruelles étroites coloniales. Force est de constater que la ville n’a pas encore su tirer profit de sa reconnaissance en tant que site du patrimoine mondial. Les slogans évoluent au gré des fonctionnaires qui organisent en charge de ce secteur. Par le biais d'entrevues avec des fonctionnaires du tourisme et une sélection de matériaux recueillis tourisme, l’auteure montre comment la ville passe par différentes phases marketing sans avoir établie une image cohérente de la destination.
Guanajuato
Mexique

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.3882
http://journals.openedition.org/etudescaribeennes/3882

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Afin de comprendre en quoi la patrimonialisation est susceptible de révéler un lien avec la notion politique et institutionnelle de développement, nous étudions les modalités savantes de fabrication du site de Teotihuacán, son insertion dans un récit national puis les formes de son internationalisation par le biais de son inscription, en 1987, sur la liste du patrimoine mondial de l’Unesco. Nous détaillons les liens entre l’archéologie nationale et l’anthropologie historique, ainsi que leur rapport à l’espace et aux territoires des cultures précolombiennes. Ainsi l' étude révèle que le lien historique avec le passé des populations précolombiennes mis au jour par la patrimonialisation du site a permis le rapprochement des deux composantes de l’identité mexicaine contemporaine, indienne et hispanique. Nous présentons ensuite, à partir de l’œuvre poétique d’Octavio Paz, les convergences entre le contenu historique et le contenu culturel dont les représentations du site sont porteuses. On montre ainsi que Teotihuacán a pris place dans un vaste territoire mental, culturel et mémoriel, servant à la constitution d’un projet pour le futur.
To understand to what extent the heritage fabrication may reveal a link with the political and institutional notion of development, we study the learned modalities of making the site of Teotihuacán, its insertion in the national narrative then the forms of its internationalization by means of its registration, in 1987, on the UNESCO World Heritage List. We analyze the links between national archaeology and historic anthropology, as well as their relationship in the space and in the territories of the pre-Colombian cultures. The historical linkage between the contemporary Mexico with the past of the pre-Columbian populations revealed by the archaeological exploration of the site has made possible the reconciliation of both components of the contemporary Indian and Hispanic Mexican identity. From the Octavio Paz’s poetic work, we underline the convergences between the historic and the cultural contents whose representations carried by the site. We show that Teotihuacán took place in a wide mental, cultural and memory territory, being of use to the constitution of a project for future.
Mexique

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.6953
http://journals.openedition.org/etudescaribeennes/6953

Éditeur(s) : HAL CCSD
Résumé : International audience
The Heliosat-II method was developed to process Meteosat satellite images in order to assess the solar irradiation at surface. It is modified for its use with GOES satellite images in order to estimate the solar irradiation over French Guiana.Modifications include a change in the calibration formula, in the calculation of the cloud albedo, and in the values of the Linke turbidity factor. These modifications allow the improvement of the performances of the Heliosat-II model in Intertropical zones in French Guiana. The outcomes were compared to coincident measurements of hourly irradiation performed by ground stations.The results show that the use of the maximum apparent albedo as the cloud albedo (ρcmax), along with a fixed value of the Linke turbidity factor produces the best results; the bias was less than 23.61 Wh/m2 (5% of the mean value of the measurements) overall, and the RMSE was less than 109.39 W/m2 (24%) overall when using hourly values. In the case of daily means, the RMSE drops to less than 10.08 W/m2 (10%) overall, whereas the overall bias remains unchanged, as expected. The model performs better in clear skies than in cloudy skies. The results suggest that the Linke turbidity factor used in the Heliosat-II method does not reproduce well the attenuation of the solar radiation in French Guiana. The results were compared to those obtained from Heliosat II method and Meteosat images (HelioClim-3 database) and we found a better accuracy for GOES satellite data, which exhibits smaller viewing angle. The use of the Heliosat II method with GOES images allows assessment of the SSI with a good accuracy and high temporal and spatial resolutions.
Canadian Journal of Remote Sensing

meteo-01304576
https://hal-meteofrance.archives-ouvertes.fr/meteo-01304576
DOI : 10.1080/07038992.2015.1040876

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Plant litter diversity effects on decomposition rates are frequently reported, but with a strong bias towards temperate ecosystems. Altered decomposition and nutrient recycling with changing litter diversity may be particularly important in tree species-rich tropical rainforests on nutrient-poor soils. Using 28 different mixtures of leaf litter from 16 Amazonian rainforest tree species, we tested the hypothesis that litter mixture effects on decomposition increase with increasing functional litter diversity. Litter mixtures and all single litter species were exposed in the field for 9 months using custom-made microcosms with soil fauna access. In order to test the hypothesis that the long-term presence of tree species contributing to the litter mixtures increases mixture effects on decomposition, microcosms were installed in a plantation at sites including the respective tree species composition and in a nearby natural forest where these tree species are absent. We found that mixture decomposition deviated from predictions based on single species, with predominantly synergistic effects. Functional litter diversity, defined as either richness, evenness, or divergence based on a wide range of chemical traits, did not explain the observed litter mixture effects. However, synergistic effects in litter mixtures increased with the long-term presence of tree species contributing to these mixtures as the home field advantage hypothesis assumes. Our data suggest that complementarity effects on mixed litter decomposition may emerge through long-term interactions between aboveground and belowground biota.
ISSN: 0029-8549

hal-01032393
https://hal.archives-ouvertes.fr/hal-01032393
DOI : 10.1007/s00442-011-1966-4

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
ObjectivesTo compare the efficacy, in current clinical practice, of ă first regimens containing abacavir with lamivudine (ABC/3TC) or ă tenofovir with emtricitabine (TDF/FTC) in patients with baseline viral ă load 100000 HIV-1 RNA copies/mL. ă MethodsUsing a prospective cohort, we selected all patients starting a ă first HIV regimen based either on ABC/3TC or on TDF/FTC. The propensity ă score (PS) method was used to limit the indication bias due to the ă observational nature of the data. Adjusting and weighting methods via PS ă were used to compare the effectiveness of a first regimen containing ă ABC/3TC or TDF/FTC. The primary outcome was treatment failure by month ă 12 (M12). ă ResultsOverall, 2781 patients started an antiretroviral (ARV) regimen ă with ABC/3TC or TDF/FTC each in combination with efavirenz, boosted ă atazanavir or boosted darunavir. Among the 2472 uncensored patients ă before M12, 962 (39%) had a baseline viral load 100000 copies/mL of ă whom 294 were in treatment failure at or before M12. Our analyses showed ă no difference between ABC/3TC and TDF/FTC in the risk of treatment ă failure at M12 in patients starting an ARV regimen with a high viral ă load (100000 copies/mL). ă ConclusionsUsing a large prospectively collected cohort of patients ă seeking care in France, we found no evidence that ABC/3TC based regimens ă led to more failures than TDF/FTC based ones in patients with high ă baseline viral loads.
ISSN: 1464-2662

hal-01482656
https://hal.archives-ouvertes.fr/hal-01482656
DOI : 10.1111/hiv.12306

Résumé : Le statut de département français fait de l’île de la Martinique une des régions ultra périphériques (RUP) de l’Union européenne. L’activité des navires de pêche qui exploitent sa ZEE s’inscrit dans le cadre de la politique commune des pêches de l’Union européenne, et la gestion des ressources partagées avec d’autres pays s’exerce dans le cadre des organisations internationales de pêche afférentes. Avec 1098 navires de pêche dont 1074 de moins de 10 mètres, la flotte de la Martinique représentait en 2009 16% de la flotte française. L’absence de données halieutiques depuis les évaluations de Gobert en 1989 a été identifiée à de nombreuses reprises comme un élément critique pour le suivi de l’évolution des activités de pêche et des ressources exploitées, ainsi que pour la définition de politiques de gestion durable de ce secteur économique. L’objectif de cette étude pilote était de tester la mise en place d’un système d’informations relatif aux activités de pêche maritime en Martinique, et d’étudier les conditions scientifiques et techniques d’une pérennisation d’un tel dispositif. Ce projet mené sur la période 2008-2010 avait pour objectif d’une part de consolider les connaissances en termes d’effort de pêche, de captures et de suivi socio-économique des différentes composantes de la pêche martiniquaise, et d’autre part de réaliser des synthèses sous forme d’indicateurs à destination des partenaires du projet (Direction des pêches maritimes et de l’aquaculture, Conseil régional de Martinique, Comité régional des pêches maritimes et des élevages marins de Martinique). Ce travail a été mené considérant le contexte particulier de la pêche martiniquaise qui cumule les difficultés inhérentes à une pêcherie artisanale en milieu tropical : utilisation de nombreux engins, exploitation à partir d’une centaine de ports/abris une ressource très diversifiée, débarquement de faibles quantités de produits à toutes heures de la journée, faible disponibilité des patrons, très polyvalents dans leur activité en mer comme à terre, pour remplir des documents statistiques. Le projet a permis de tester différentes méthodes d’enquêtes dans les ports et de sondages téléphoniques utilisables dans ce contexte. La confrontation de ces méthodes et de leurs résultats a permis de mettre en évidence certains biais associés à la difficulté de respecter les règles du tirage statistique des unités d’échantillonnage. Il est ainsi apparu que les enquêtes sur les points de débarquement pouvaient surévaluer l’effort de pêche et les débarquements. En effet, ces enquêtes méconnaissent les navires inactifs parqués hors des ports. De plus, les retours de pêche avec des prises faibles ou nulles échappent en partie aux observateurs en raison de la brièveté du séjour du patron dans le port au terme de sa marée. Des sondages téléphoniques couvrant une période de sept jours ont été menés, afin de prendre en compte le cycle hebdomadaire d’organisation de la pêche et de la commercialisation du poisson. Ces sondages permettent de s’affranchir des contraintes spatiales (éloignement et mauvaise accessibilité de certains lieux de débarquement) et temporelles (fin de semaine, jours fériés, débarquements de nuit), dans la mesure où ils peuvent être établis sur la base d’un registre complet des patrons-armateurs. Au cours de l’étude pilote, le plan d’échantillonnage a pu être suivi à 70 % (navires tirés au hasard figurant dans le plan). Dans 27 % des cas, l’observateur a du substituer l’unité d’échantillonnage, selon les règles imposées par le plan. En outre 2 % des sondages prévus au plan n’ont pas pu être réalisés en raison d’un refus. L’inconvénient majeur attribué à la méthode des sondages téléphoniques est l’impossibilité de vérifier les déclarations de personnes interviewées. Une comparaison entre ces déclarations et des pesées effectuées par les observateurs sur les points de débarquement a permis de décrire les divergences entre les deux modes de collecte des données. Cette analyse a également montré que si la collecte des données au débarquement offre la garantie d’une observation directe, elle peut également manquer une partie du produit de la pêche : langoustes déposées en vivier en pleine eau avant l’entrée dans le port, poisson non débarqué pour satisfaire la commande d’un client, lots de poissons remis aux haleurs de sennes de plage, débarquement sur un premier point avant le site enquêté, etc. Il est apparu qu’une collecte de données fiables ne peut se faire sans une bonne information des professionnels et leur participation volontaire à l’établissement des statistiques. La collecte des données dans un cadre qui garantit l’anonymat du pêcheur est également une condition inhérente à la réussite d’un observatoire. Par ailleurs, bon nombre d’informations portant par exemple sur l’activité en mer (dimension des engins, temps de pose, zone de pêche, etc.) invérifiables sur le lieu de débarquement peuvent être recueillies dans des conditions analogues par téléphone. Pendant la réalisation du projet pilote, 90,4 % des pêcheurs contactés par téléphone ont répondu sans réticence aux observateurs. Ceux qui ont refusé de répondre ou qui n’ont jamais décroché le téléphone (erreur de numéro ou refus) représentent 3 % des patrons-armateurs des navires figurant au fichier flotte national. Les pêcheurs qui n’ont pas régulièrement répondu aux observateurs représentent 6,6 % des effectifs. Pour valider les données collectées par enquêtes téléphoniques, leurs résultats ont été comparés par différentes méthodes à ceux des enquêtes au débarquement en vue d’identifier et de quantifier des biais éventuels. Aucune surévaluation ou sous-évaluation systématique par les enquêtes téléphoniques n’a été décelée au cours de ces travaux, certaines valeurs pouvant être plus élevées et d’autres moins. Les écarts non formellement expliqués ont été considérés comme une sous-évaluation par les enquêtes téléphoniques. Ceux-ci s’élèveraient à 20 % pour l’estimation du nombre de sorties et à 30 % pour celle des prises par sortie. Malgré la prise en compte de ces écarts, les estimations faites en 2009 et 2010 indiquent une régression des débarquements et de l’effort de pêche depuis l’évaluation réalisée en 1987 par le Pôle de recherche océanographique et halieutique Caraïbes. Un second niveau de validation a consisté à vérifier cette décroissance de la pêche en confrontant les informations obtenues par la présente étude pilote à des données d’origines différentes : étude des comportements alimentaires par l’Institut de veille sanitaire, étude de la consommation des ménages par l’INSEE, évolution des données d’importation des Douanes, données de vente de matériel de pêche par la coopérative d’avitaillement des pêcheurs de la Martinique (COOPEMAR). Toutes ces données font ressortir une baisse de la consommation de poisson par habitant depuis la fin des années 1980 et une augmentation des importations de produits de la mer. La pêche martiniquaise n’étant pas exportatrice, ces données donnent également un signal de diminution de la pêche martiniquaise au cours des 25 dernières années. Les données collectées à l’occasion de cette étude pilote suggèrent que la régression de la pêche martiniquaise au cours des dernières décennies serait le résultat de deux causes majeures : - la surpêche des ressources de fond sur le plateau insulaire. Ces ressources subissent une forte pression de pêche, entre autres de la part des pêcheurs les plus âgés qui n’ont plus les capacités physiques de pratiquer une activité loin des côtes. Un quart des patrons-armateurs ont aujourd’hui l’âge de la retraite et relèvent près de la moitié des nasses mouillées sur le plateau insulaire. Ces pêcheurs à l’activité peu flexible sont contraints de la poursuivre en raison de la faiblesse de leur pension de retraite. Une réduction de la pression de pêche sur le plateau insulaire par le départ effectif de ces pêcheurs favoriserait certainement, après quelques années, un retour à la situation décrite il y a 25 ans, qui permettait un débarquement annuel d’espèces issues du plateau insulaire d’environ 1 000 tonnes de plus que la production actuelle. - la concurrence des importations, en particulier des produits congelés, est certainement en partie la cause de la régression de la pêche des pélagiques hauturiers, malgré le développement des dispositifs de concentration de poissons (DCP) qui sont à l’origine d’environ 30 % des débarquements de la pêche de l’île. Face aux importations, la commercialisation de la pêche locale est encore peu structurée avec plus de 49 sites de vente répartis sur le territoire, généralement peu achalandés en raison des faibles prises irrégulières des pêcheurs artisans. Les espaces de vente sont encore peu équipés et rarement aux normes. C’est ainsi que plus de quarante pour cent des tables de vente sont en bois. Plusieurs options sont actuellement examinées pour améliorer la fiabilité et la précision des données collectées par le SIH sans augmenter leurs coûts de collecte. Le traitement des données collectées sur quelques années permettra d’affiner les critères de stratification de la population afin d’améliorer la précision des données. Compte tenu de l’éparpillement des points de débarquement et de la faible fréquence de sortie des navires de pêche, une optimisation du travail de terrain des observateurs doit être faite. L’objectif de ces enquêtes de terrain doit être de : - servir de témoin pour la validation des enquêtes téléphoniques. Pour cela, il faudra rechercher les sousensembles communs aux enquêtes téléphoniques et aux observations sur le terrain afin qu’ils soient comparables ; - disposer d’une composition spécifique et en taille des débarquements qui soit si possible représentative de l’ensemble des débarquements ou au moins d’une part significative qui pourrait servir d’indicateur de l’évolution de la pêche et des ressources exploitées. Afin d’optimiser les déplacements des observateurs sur le terrain, les données des enquêtes téléphoniques peuvent être utilisées pour identifier par semestre les 50 à 100 sites et tranches horaires de cinq heures au sein desquels les fréquences de retours de pêche sont les plus élevées. L’étude pilote a montré que, par ce procédé, le nombre de retours échantillonnés s’élève en moyenne à 3,5. Les échantillonnages biologiques des débarquements permettant de décrire leur composition spécifique et en taille sont réalisés par photographie lorsque l’engin utilisé capture un grand nombre d’espèces différentes (nasses, filets de fond, senne de plage...). Par ce procédé, il est possible de réduire la durée des échantillonnages de près de trois quarts du temps nécessaire aux mensurations directes, et ainsi de moins gêner le débarquement et la vente du poisson. Ce procédé permet également d’avoir une traçabilité des échantillonnages; il offre notamment la possibilité de revenir sur les identifications en cas de doute. Cette méthode, aujourd’hui bien rodée, devrait permettre d’améliorer la qualité des travaux sur la biodiversité de la faune marine.

Droits : 2013 Ifremer
http://archimer.ifremer.fr/doc/00156/26762/24850.pdf
http://archimer.ifremer.fr/doc/00156/26762/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The development of inflammatory granulomas around infected Kupffer cells is necessary for hepatic parasite clearance during visceral leishmaniasis. Invariant NKT (iNKT) cells are predominant T cells in the mouse liver and can synthesize large quantities of IL-4 and IFN-γ, two cytokines involved in granuloma formation. This study analyzed the role of iNKT cells in the hepatic immune response during Leishmania donovani infection, using a murine model of wild-type (WT) and iNKT cell-deficient (Jα18⁻/⁻) C57BL/6 mice sacrificed 15, 30 or 60 days post-infection. We recorded hepatic parasite loads, cytokine expression, and analyzed granulomatous response by immunohistochemistry and hepatic immune cell infiltration by flow cytometry. Whereas WT animals rapidly controlled the infection and developed an inflammatory response associated with a massive influx of iNKT cells observed by flow cytometry, Jα18⁻/⁻ mice had significantly higher parasitic loads on all time points. This lack of control of parasite burden was associated with a delay in granuloma maturation (28.1% of large granulomas at day 60 versus 50.7% in WT). Cytokine transcriptome analysis showed that mRNA of 90/101 genes encoding chemokines, cytokines and their receptors, was underexpressed in Jα18⁻/⁻ mice. Detection of IL-4 and TNF-α by ELISA in liver extracts was also significantly lower in Jα18⁻/⁻ mice. Consistent with flow cytometry analysis, cytokinome profile in WT mice showed a bias of expression towards T cell-chemoattractant chemokines on D15, and displayed a switch towards expression of granulocytes and/or monocytes -chemoattractant chemokines on D60. In Jα18⁻/⁻ mice, the significantly lower expression of CXCL5, MIP-2 and CCL2 mRNA was correlated with a defect in myeloperoxidase positive-cell attraction observed by immunohistochemistry and with a lower granulocyte and monocyte infiltration in the liver, as shown by flow cytometry. These data indicate that iNKT cells play a role in early and sustained pro-inflammatory cytokine response warranting efficient organization of hepatic granulomas and parasite clearance.
ISSN: 1932-6203

hal-00696897
https://hal.archives-ouvertes.fr/hal-00696897
https://hal.archives-ouvertes.fr/hal-00696897/document
https://hal.archives-ouvertes.fr/hal-00696897/file/Invariant_NKT_Cells_Drive-accepted.pdf
DOI : 10.1371/journal.pone.0033413

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background: The impact of hepatitis B virus (HBV) genomic variability on the measurement of HBsAg level has been poorly evaluated. Objective: This study was designed to compare the performance of all the available assays measuring HBsAg level in this setting. Study design: A large selection of wild type HBV genotypes (n = 184) and HBsAg strains harboring mutations in the S gene (n = 81) from clinical samples was studied with three HBsAg quantification assays: Architect HBsAg (Abbott), LiaisonXL Murex HBsAg Quant (DiaSorin) and the Elecsys HBsAgII (Roche). Results: The overall percentage of positive results was 99.2% for Abbott, 98.9% for DiaSorin and 98.1% for Roche. Abbott and Roche assays provided an excellent concordance in HBsAg quantification (global mean bias of -0.006 logIU/mL). By contrast, DiaSorin underestimated HBsAg level with values 0.112 logIU/ml and 0.103 logIU/ml lower than Abbott and Roche, respectively. By contrast, DiaSorin slightly over quantified gtC(2.5% over the expected value) while Abbott provided values 6.2% lower than expected and 16.2% lower than what observed for the other genotypes. HBsAg quantitative assays were influenced by HBs protein substitutions irrespective to the genotype but no specific protein pattern that would particularly impair the quantification by one technique has been identified. However, Roche seemed to be particularly impacted by substitutions at 145 residue: 75% of under quantified samples carried a substituted 145 residue. Conclusion: This head-to-head comparison indicates a good correlation between all current systems used to quantify HBsAg but clearly shows an influence of both the genotype and the presence of "a" determinant variants in the absolute quantification of HBsAg. While these discrepancies may not translate into major clinical consequence, they may explain an absence of detection of weak concentration of HBsAg on some systems. (C) 2017 Elsevier B.V. All rights reserved.
ISSN: 1386-6532

hal-01588395
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01588395
DOI : 10.1016/j.jcv.2017.02.001
PUBMED : 28189936

Éditeur(s) : Elsevier
Résumé : Because Vibrio aestuarianus is known to cause serious infections in Pacific oyster Crassostrea gigas, a real-time PCR assay was developed targeting the dnaJ gene of this bacterium. Only V. aestuarianus strains isolated from C. gigas mortality events in different geographic areas and the reference strain tested positive, whereas no amplification products was obtained with type strains belonging to 23 other species of Vibrio. Sensitivity and reproducibility of the method were assessed using either seawater or oyster homogenate samples spiked with one V aestuarianus strain. All these samples were stored at -20 degrees C in order to mimic retrospective or grouped natural sample analysis without quantification bias due to prolonged freezing. Analysis of standard curves revealed excellent correlation values between light microscopy cell enumerations and PCR Threshold Cycle (Ct) values, and acceptable PCR reaction efficiencies for all type of samples. Quantification curves of both sample types were equivalent, with a detection level as low as 1.6 V. aestuarianus cells in the PCR reaction tube, corresponding to 1.6.10(2) cells ml(-1) and 1.6.10(2) cells mg(-1) in seawater and entire oyster samples, respectively, taking into account the dilution factor used for appropriate template DNA preparation. Comparison of PCR assay reproducibility according to the complexity of samples revealed that seawater samples gave more reproducible quantification measures than samples from oyster homogenate, with precision of measured Ct values inferior to 0.4 and 0.6 respectively at 99% confidence. Use of the real-time PCR assay allowed us to monitor V. aestuarianus load in oysters naturally infected with this pathogen. Furthermore, we were able to detect V aestuarianus in samples of seawater in which oysters had been reared and in algal cultures used for feeding oysters. Because of the rapidity and reliability of the real-time PCR assay method used in this study, just a few hours are needed compared with the two days required using the classic culture method, this technique will be particularly valuable in mollusc pathology laboratories, for monitoring the source and course of infections by V. aestuarianus in pathogenesis and epidemiologic studies, as well as for designing appropriate prophylactic control measures. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Microbiological Methods (0167-7012) (Elsevier), 2009-05 , Vol. 77 , N. 2 , P. 191-197

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6447.pdf
DOI:10.1016/j.mimet.2009.01.021
http://archimer.ifremer.fr/doc/00000/6447/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Mapping forest aboveground biomass (AGB) has become an important task, particularly for the reporting of carbon stocks and changes. AGB can be mapped using synthetic aperture radar data (SAR) or passive optical data. However, these data are insensitive to high AGB levels (>150 Mg/ha, and >300 Mg/ha for P-band), which are commonly found in tropical forests. Studies have mapped the rough variations in AGB by combining optical and environmental data at regional and global scales. Nevertheless, these maps cannot represent local variations in AGB in tropical forests. In this paper, we hypothesize that the problem of misrepresenting local variations in AGB and AGB estimation with good precision occurs because of both methodological limits (signal saturation or dilution bias) and a lack of adequate calibration data in this range of AGB values. We test this hypothesis by developing a calibrated regression model to predict variations in high AGB values (mean >300 Mg/ha) in French Guiana by a methodological approach for spatial extrapolation with data from the optical geoscience laser altimeter system (GLAS), forest inventories, radar, optics, and environmental variables for spatial inter-and extrapolation. Given their higher point count, GLAS data allow a wider coverage of AGB values. We find that the metrics from GLAS footprints are correlated with field AGB estimations (R 2 =0.54, RMSE=48.3 Mg/ha) with no bias for high values. First, predictive models, including remote-sensing, environmental variables and spatial correlation functions, allow us to obtain "wall-to-wall" AGB maps over French Guiana with an RMSE for the in situ AGB estimates of ~51 Mg/ha and R²=0.48 at a 1-km grid size. We conclude that a calibrated regression model based on GLAS with dependent environmental data can produce good AGB predictions even for high AGB values if the calibration data fit the AGB range. We also demonstrate that small temporal and spatial mismatches between field data and GLAS footprints are not a problem for regional and global calibrated regression models because field data aim to predict large and deep tendencies in AGB variations from environmental gradients and do not aim to represent high but stochastic and temporally limited variations from forest dynamics. Thus, we advocate including a greater variety of data, even if less precise and shifted, to better represent high AGB values in global models and to improve the fitting of these models for high values.
ISSN: 0303-2434

Droits : http://creativecommons.org/licenses/by/
hal-01381116
https://hal.archives-ouvertes.fr/hal-01381116
https://hal.archives-ouvertes.fr/hal-01381116/document
https://hal.archives-ouvertes.fr/hal-01381116/file/Fayad2016a.pdf
DOI : 10.1016/j.jag.2016.07.015

Éditeur(s) : Amer Geophysical Union
Résumé : Sea surface salinity (SSS) measured from space by the Soil Moisture and Ocean Salinity (SMOS) mission is validated in the subtropical North Atlantic Ocean. 39 transects of ships of opportunity equipped with thermosalinographs (TSG) crossed that region from 2010 to 2012, providing a large database of ground truth SSS. SMOS SSS is also compared to Aquarius SSS. Large seasonal biases remain in SMOS and Aquarius SSS. In order to look at the capability of satellite SSS to monitor spatial variability, especially at scales less than 300 km (not monitored with the Argo network), we first apply a monthly bias correction derived from satellite SSS and In Situ Analysis System (ISAS) SSS differences averaged over the studied region. Ship SSS averaged over 25 km is compared with satellite and ISAS SSS. Similar statistics are obtained for SMOS, Aquarius and ISAS products (root mean square error of about 0.15 and global correlation coefficient r of about 0.92). However, in the above statistics, SSS varies due to both large scale and mesoscale (here, for scales around 100 km) variability. In order to focus on mesoscale variability, we consider SSS anomalies with respect to a monthly climatology. SMOS SSS and Aquarius SSS anomalies are more significantly correlated (r > 0.5) to TSG SSS anomaly than ISAS. We show the effective gain of resolution and coverage provided by the satellite products over the interpolated in situ data. We also show the advantage of SMOS (r=0.57) over Aquarius (r=0.52) to reproduce SSS mesoscale features.
Journal Of Geophysical Research-oceans (0148-0027) (Amer Geophysical Union), 2014-12 , Vol. 119 , N. 12 , P. 8878-8896

Droits : 2014. American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00210/32150/34082.pdf
DOI:10.1002/2013JC009610
http://archimer.ifremer.fr/doc/00210/32150/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Measuring functional or phylogenetic diversity is the object of an active literature. The main issues to address are relating measures to a clear conceptual framework, allowing unavoidable estimation-bias correction and decomposing diversity along spatial scales. We provide a general mathematical framework to decompose measures of species-neutral, phylogenetic or functional diversity into α and β components. We first unify the definitions of phylogenetic and functional entropy and diversity as a generalization of HCDT entropy and Hill numbers when an ultrametric tree is considered. We then derive the decomposition of diversity. We propose a bias correction of the estimates allowing meaningful computation from real, often undersampled communities. Entropy can be transformed into true diversity, that is an effective number of species or communities. Estimators of α- and β-entropy, phylogenetic and functional entropy are provided. Proper definition and estimation of diversity is the first step towards better understanding its underlying ecological and evolutionary mechanisms.
ISSN: 2041-210X

hal-01502645
https://hal-agroparistech.archives-ouvertes.fr/hal-01502645
DOI : 10.1111/2041-210X.12323

Éditeur(s) : HAL CCSD
Résumé : International audience
OBJECTIVES: To detect new hazards ("signals"), occupational health monitoring systems mostly rest on the description of exposures in the jobs held and on reports by medical doctors; these are subject to declarative bias. Our study aims to assess whether job-exposure matrices (JEMs) could be useful tools for signal detection by improving exposure reporting. METHODS: Using the French national occupational disease surveillance and prevention network (RNV3P) data from 2001 to 2011, we explored the associations between disease and exposure prevalence for 3 well-known pathology/exposure couples and for one debatable couple. We compared the associations measured when using physicians' reports or applying the JEMs, respectively, for these selected diseases and across non-selected RNV3P population or for cases with musculoskeletal disorders, used as two reference groups; the ratio of exposure prevalences according to the two sources of information were computed for each disease category. RESULTS: Our population contained 58,188 subjects referred with pathologies related to work. Mean age at diagnosis was 45.8 years (95% CI 45.7; 45.9), and 57.2% were men. For experts, exposure ratios increase with knowledge on exposure causality. As expected, JEMs retrieved more exposed cases than experts (exposure ratios between 12 and 194), except for the couple silica/silicosis, but not for the MSD control group (ratio between 0.2 and 0.8). CONCLUSIONS: JEMs enhanced the number of exposures possibly linked with some conditions, compared to experts' assessment, relative to the whole database or to a reference group; they are less likely to suffer from declarative bias than reports by occupational health professionals.
International Archives of Occupational and Environmental Health

hal-01560279
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560279
DOI : 10.1007/s00420-017-1215-1
PUBMED : 28299449

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999 15-19 octobre 1999
Résumé : The development of the FAD gave rise to technical problems owing to their conception, their setting spot and of their utilisation. Failings generated by the unreliability of components or the uncertain repair precariousness, those can prove to be here more and more expensive with the progression of the ageing of devices and reasons of their loss. For as various domains that aerospace or the fishing deck layout, the engineering has functional analysis tools that permit to reduce conception uncertainties of systems by the mean of a hierarchical classification of function values of components. The application of one of these techniques, the FMEA, Failure Mode and Effects Analysis, to the study of reasons of FAD loss in La Reunion describes perfectly everything that this type of method can bring to the appraisal in fishing technology. This preventive analysis method assess the potential risks integrates perfectly in the mind of a precaution approach as it would agree to see to apply to the FADs and to their exploitation.Original Abstract: Le developpement des DCP a entraine l'apparition de problemes techniques, issus tant de leur conception, de leur lieu d'implantation que de leur utilisation. Defaillances generees par le manque de fiabilite des composants ou la precarite de reparations aleatoires, celles-ci peuvent s'averer de plus en plus couteuses au fur et a mesure du vieillissement des systemes et cause a terme de leur perte. Pour des domaines aussi divers que l'aerospatiale ou l'amenagement de pont de peche, l'ingenierie dispose d'outils d'analyse fonctionnelle qui, par le biais d'une hierarchisation des valeurs des fonctions de chaque element des systemes etudies, permettent de reduire les incertitudes de la conception. L'application d'une de ces techniques, l'Amdec, analyse des modes de defaillance et de criticite, a l'etude des causes des pertes de DCP a La Reunion illustre parfaitement tout ce que ce type de methode peut apporter a l'expertise en technologie des peches. Cette methode d'analyse preventive qui recense et met en evidence les risques potentiels s'integre parfaitement dans l'esprit d'une approche de precaution telle que celle qu'il conviendrait de voir appliquer aux DCP et a leur exploitation.

Droits : Ifremer
http://archimer.ifremer.fr/doc/00042/15289/12675.pdf
http://archimer.ifremer.fr/doc/00042/15289/

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : The sea surface salinity (SSS) measured from space by the Soil Moisture and Ocean Salinity (SMOS) mission has recently been revisited by the European Space Agency first campaign reprocessing. We show that, with respect to the previous version, biases close to land and ice greatly decrease. The accuracy of SMOS SSS averaged over 10 days, 100 x 100 km(2) in the open ocean and estimated by comparison to ARGO (Array for Real-Time Geostrophic Oceanography) SSS is on the order of 0.3-0.4 in tropical and subtropical regions and 0.5 in a cold region. The averaged negative SSS bias (-0.1) observed in the tropical Pacific Ocean between 5 degrees N and 15 degrees N, relatively to other regions, is suppressed when SMOS observations concomitant with rain events, as detected from SSM/Is (Special Sensor Microwave Imager) rain rates, are removed from the SMOS-ARGO comparisons. The SMOS freshening is linearly correlated to SSM/Is rain rate with a slope estimated to -0.14 mm(-1) h, after correction for rain atmospheric contribution. This tendency is the signature of the temporal SSS variability between the time of SMOS and ARGO measurements linked to rain variability and of the vertical salinity stratification between the first centimeter of the sea surface layer sampled by SMOS and the 5 m depth sampled by ARGO. However, given that the whole set of collocations includes situations with ARGO measurements concomitant with rain events collocated with SMOS measurements under no rain, the mean -0.1 bias and the negative skewness of the statistical distribution of SMOS minus ARGO SSS difference are very likely the mean signature of the vertical salinity stratification. In the future, the analysis of ongoing in situ salinity measurements in the top 50 cm of the sea surface and of Aquarius satellite SSS are expected to provide complementary information about the sea surface salinity stratification.
Ocean Science (1812-0784) (Copernicus Gesellschaft Mbh), 2013 , Vol. 9 , N. 1 , P. 183-192

Droits : Author(s) 2013. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00139/25073/23161.pdf
DOI:10.5194/os-9-183-2013
http://archimer.ifremer.fr/doc/00139/25073/

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Satellite precipitation products are a means of estimating rainfall, particularly in areas that are sparsely equipped with rain gauges. The Guiana Shield is a region vulnerable to high water episodes. Flood risk is enhanced by the concentration of population living along the main rivers. A good understanding of the regional hydro-climatic regime, as well as an accurate estimation of precipitation is therefore of great importance. Unfortunately, there are very few rain gauges available in the region. The objective of the study is then to compare satellite rainfall estimation products in order to complement the information available in situ and to perform a regional analysis of four operational precipitation estimates, by partitioning the whole area under study into a homogeneous hydro-climatic region. In this study, four satellite products have been tested, TRMM TMPA (Tropical Rainfall Measuring Mission Multisatellite Precipitation Analysis) V7 (Version 7) and RT (real time), CMORPH (Climate Prediction Center (CPC) MORPHing technique) and PERSIANN (Precipitation Estimation from Remotely-Sensed Information using Artificial Neural Network), for daily rain gauge data. Product performance is evaluated at daily and monthly scales based on various intensities and hydro-climatic regimes from 1 January 2001 to 30 December 2012 and using quantitative statistical criteria (coefficient correlation, bias, relative bias and root mean square error) and quantitative error metrics (probability of detection for rainy days and for no-rain days and the false alarm ratio). Over the entire study period, all products underestimate precipitation. The results obtained in terms of the hydro-climate show that for areas with intense convective precipitation, TMPA V7 shows a better performance than other products, especially in the estimation of extreme precipitation events. In regions along the Amazon, the use of PERSIANN is better. Finally, in the driest areas, TMPA V7 and PERSIANN show the same performance.
ISSN: 2072-4292

meteo-01304579
https://hal-meteofrance.archives-ouvertes.fr/meteo-01304579
https://hal-meteofrance.archives-ouvertes.fr/meteo-01304579/document
https://hal-meteofrance.archives-ouvertes.fr/meteo-01304579/file/remotesensing-07-15831.pdf
DOI : 10.3390/rs71215831

Éditeur(s) : HAL CCSD
Résumé : From the protolanguage born with Homo erectus, the modern human language of Homo sapiens has naturally diversified into tonal, stress-timed, or syllable-timed languages, although the definition of the syllable has yet to be established. Thus for a French speaker, the transition from a language punctuated by the syllable to a language punctuated by the lexical stress will be a delicate point in learning oral English. For this purpose, we recommend the implementation of a reprogramming of the articulatory gesture in the brains as evidenced by articulatory phonology. Through the arched beam, Broca's area of the French-speaking learner will inhibit the French-related data to send to Wernicke's area new information regarding the reception / production of oral English.
A partir du protolangage né avec Homo erectus, le langage humain moderne d'Homo sapiens s'est naturellement diversifié en langues tonales, accentuelles, ou syllabiques, bien que la définition de la syllabe reste encore à établir. Ainsi pour un francophone, le passage d'une langue rythmée par la syllabe à une langue rythmée par l'accent lexical sera un point délicat de l'apprentissage de l'anglais oral. Pour ce faire, nous préconisons la mise en place d'une reprogrammation de la gestuelle articulatoire telle qu'elle a pu être mise en évidence par la phonologie articulatoire. Par le biais du faisceau arqué, l'aire de Broca de l'apprenant francophone inhibera les données liées au français pour envoyer à l'aire de Wernicke de nouvelles informations quant à la réception / production de l'anglais oral. Mots clés : neurodidactique, anglais oral, phonologie articulatoire, aires du langage, mémoire procédurale et à long terme. Abstract: From the protolanguage born with Homo erectus, the modern human language of Homo sapiens has naturally diversified into tonal, stress-timed, or syllable-timed languages, although the definition of the syllable has yet to be established. Thus for a French speaker, the transition from a language punctuated by the syllable to a language punctuated by the lexical stress will be a delicate point in learning oral English. For this purpose, we recommend the implementation of a reprogramming of the articulatory gesture in the brains as evidenced by articulatory phonology. Through the arched beam, Broca's area of the French-speaking learner will inhibit the French-related data to send to Wernicke's area new information regarding the reception / production of oral English.
https://hal.archives-ouvertes.fr/hal-01626540

hal-01626540
https://hal.archives-ouvertes.fr/hal-01626540
https://hal.archives-ouvertes.fr/hal-01626540/document
https://hal.archives-ouvertes.fr/hal-01626540/file/Neurodidactique%20%20Comment%20le%20cerveau%20d%27un%20apprenant%20francophone%20peut-il%20se%20programmer%20sur%20une%20langue%20accentuelle..pdf

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
In the mid-afternoon of 15 July 2007, during the Convective and Orographically induced Precipitation Study (COPS), in a very warm and dry environment, an isolated, short-lived, deep convective system developed over the southern Black Forest. Most of the high-resolution, convection-permitting models involved in COPS were unable to capture this event whereas the Meso-NH forecast was quite skilful. To assess the Meso-NH performance further, the model results were carefully checked against the various and numerous COPS observations. In full agreement with clear-air radar observations, model results underlined the triggering role of a low-level convergence line that developed in the lee of the Feldberg. The main departure from the observations was found to be in the low-level moisture fields, which appeared significantly moister in the model than in the observations and also slightly moister than in the other models. Sensitivity studies showed that this departure from the observations was strongly controlled by the initial surface moisture conditions. When the surface moisture was reduced by 20% or replaced by the value derived from a different analysis, the evolution of the planetary boundary layer was more accurately represented while the storm evolution was still correctly captured. These results demonstrate that the quality of the initial forecast cannot be ascribed to the moist bias of the model. It could therefore be hypothesized that the key parameters for a satisfactory forecast of this event lie more in the ability of the model to reproduce the dynamical forcing accurately than in the characteristics of the air-mass instability.
ISSN: 0035-9009

hal-00554400
https://hal.archives-ouvertes.fr/hal-00554400
DOI : 10.1002/qj.710

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