Éditeur(s) : Amer Geophysical Union
Résumé : This study focuses on the improved estimation of mesoscale surface ocean circulation obtained by merging TOPEX/Poseidon (T/P) and ERS-1 and -2 altimeter measurements between October 1992 and May 1998. Once carefully intercalibrated and homogenized, these data are merged through an advanced global objective analysis method that allows us to correct for residual long wavelength errors and uses realistic correlation scales of ocean dynamics, The high-resolution (0.25 degrees x 0.25 degrees) merged T/P + ERS-1 and -2 sea level anomaly maps provide more homogeneous and reduced mapping errors than either individual data set and more realistic sea level and geostrophic velocity statistics than T/P data alone. Furthermore, the merged T/P + ERS-1 and -2 maps yield eddy kinetic energy (EKE) levels 30% higher than maps of T/P alone. They also permit realistic global estimates of east and north components of EKE and their seasonal variations, to study EKE sources better. A comparison of velocity statistics with World Ocean Circulation Experiment surface drifters in the North Atlantic shows very good agreement. Comparison with contemporary current meter data in various oceanic regimes also produces comparable levels of energy and similar ratios of northward and eastward energy, showing that the maps are suitable to studying anisotropy. The T/P + ERS zonal and meridional components of the mapped currents usually present comparable rms variability, even though the variability in the Atlantic is more isotropic than that in the Pacific, which exhibits strong zonal changes. The EKE map presents a very detailed description, presumably never before achieved at a global scale. Pronounced seasonal changes of the EKE are found in many regions, notably the northeastern Pacific, the northeastern and northwestern Atlantic, the tropical oceans, and the zonally extended bands centered near 20 degrees S in the Indian and western Pacific Oceans and at 20 degrees N in the northwestern nl Pacific.
Journal Of Geophysical Research-oceans (0148-0227) (Amer Geophysical Union), 2000-08 , Vol. 105 , N. C8 , P. 19477-19498

Droits : 2000 AGU
http://archimer.ifremer.fr/doc/00079/19033/16617.pdf
DOI:10.1029/2000JC900063
http://archimer.ifremer.fr/doc/00079/19033/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: In Guadeloupe and Martinique, two French Overseas Departments, colorectal cancer (CRC) has become an essential public health issue. However, little is known about CRC characteristics and the p53 status in these populations, particularly in Guadeloupe, whereas certification of a cancer registry has been recently validated. METHODS: This was a descriptive retrospective study of 201 patients who, between 1995 and 2000, underwent surgery for CRC in the Guadeloupe Teaching Hospital (GlpeTH; 83 patients) and in the Martinique Teaching Hospital (MqueTH; 118 patients). The clinicopathological features and the p53 expression, evaluated with immunohistochemistry, were compared at the time of diagnosis. A relationship between these parameters and the p53 expression was also studied. Data were analysed, using the SPSS computer software version 17.0. RESULTS: No statistical difference was found between the two groups of patients regarding age (p = 0.60), percentage of young patients (<=50 years; p = 0.94)), sex (p = 0.47), histological type (p = 0.073) and tumour sites (p = 0.65), although the GlpeTH patients were diagnosed with more distal colon cancers (54.2%) than the Mque TH patients (47.4%). By contrast, a significant difference was found regarding the tumour grade (p < 0.0001), the pTNM stage (p = 0.045) and the pT stage (p < 0.0001). Regarding p53 expression, solely for the MqueTH patients, nuclear expression was associated with pTNM, the percentage of p53 negative tumours increasing with the progression of the pTNM stages (p = 0.029). CONCLUSIONS: For the first time, this study reveals discrepancies in clinicopathological features and in the p53 status between the two groups of patients. The GlpeTH patients were diagnosed with more moderated CRCs but with few CRCs at pTNM IV stage. By contrast, the MqueTH patients were diagnosed with more differentiated tumours, but with many more CRCs at pTNM IV stage. This paradox may be due to differences in tumour location (distal vs proximal), multiplicity of the genetic profiles of patients, or patients getting treatment elsewhere. Although our study is limited due to its small size, it emphasizes the originality of our results.
ISSN: 1472-6890

inserm-00971313
http://www.hal.inserm.fr/inserm-00971313
http://www.hal.inserm.fr/inserm-00971313/document
http://www.hal.inserm.fr/inserm-00971313/file/1472-6890-14-12.pdf
DOI : 10.1186/1472-6890-14-12

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of expression quantitative trait locus (eQTL) analyses were also replicated with a Gene Expression Omnibus (GEO) data set. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. RESULTS: Five ancestry-related SNPs were identified as cis-eQTLs in the DNA polymerase beta (POLB) gene (false discovery rate [FDR]<0.01). The homozygous/heterozygous genotypes containing the African allele showed higher POLB expression than the homozygous white allele genotype (P<.001). A replication study using a GEO data set validated all 5 eQTLs and also showed a statistically significant difference in POLB expression based on genetic ancestry (P=.002). An association was observed between these eQTLs and OS (P<.037; FDR<0.0363) as well as DFS (P=.018 to.0629; FDR<0.079) for oral cavity and laryngeal cancer patients treated with platinum-based chemotherapy and/or radiotherapy. Genotypes containing the African allele were associated with poor OS/DFS in comparison with homozygous genotypes harboring the white allele. CONCLUSIONS: Analyses show that ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparities in patients diagnosed with oral cavity and laryngeal cancer. (C) 2016 American Cancer Society.
ISSN: 0008-543X

hal-01519253
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519253
DOI : 10.1002/cncr.30457
PUBMED : 27906459

Éditeur(s) : NRC
Résumé : Universal kriging was used to model the spatio-temporal variability in the acoustic density of tuna aggregations recorded during star echosounding surveys around moored fish aggregating devices (FADs) in Martinique (Lesser Antilles). The large-scale deterministic drift in the tuna spatial distribution was modeled using an advection-diffusion equation applied to animal grouping. Residuals from the drift were modeled as a random component with small-scale spatial correlation. An estimation variance formula was derived from this deterministic-statistical mixed model to assess the mean precision of density estimates of daytime tuna aggregation. The mean relative error obtained with our star design for daytime surveys was 24%. The methodology was applied to estimate daily maxima of tuna biomass around moored FADs during four monthly sea cruises. The daily peak of tuna biomass aggregated around moored FADs was 9 t on average (standard deviation = 4). Estimation variances for different survey designs were compared for optimizing sampling strategy.
La distribution spatiale d'agrégations de thons autour de dispositifs de concentration de poissons (DCP) ancrés a été étudiée en Martinique (Petites Antilles) au moyen de parcours acoustiques en étoile. Les densités acoustiques géoréférencées attribuées aux thons ont été analysées à l'aide d'un modèle de krigeage universel. Une tendance à large échelle a été identifiée dans la distribution spatiale des thons. Cette tendance a été modélisée de façon déterministe au moyen d'une équation d'advection–diffusion appliquée aux groupes d'animaux. Les résidus de la tendance ont été modélisés comme une composante aléatoire du modèle, spatialement corrélée à faible échelle. De ce modèle, qui contenant une composante déterministe et une composante statistique, a été déduite une formule permettant de calculer la variance d'estimation de la densité diurne moyenne de l'agrégation de thons autour des DCP. L'erreur relative moyenne commise sur l'estimation de la densité de thons lors d'un parcours en étoile diurne a été estimée à 24 %. Cette méthode a été appliquée afin d'estimer les maxima journaliers de biomasse de l'agrégation de thons observés lors de quatre campagnes en mer mensuelles successives autour des DCP ancrés. La biomasse maximale de thons agrégée autour des DCP ancrés durant une phase diurne était en moyenne de 9 t (écart type : 4). Les variances d'estimation obtenues avec différents parcours acoustiques ont été comparées afin d'optimiser la stratégie d'échantillonnage.
Canadian journal of fisheries and aquatic sciences (0706-652X) (NRC), 2008-06 , Vol. 65 , N. 6 , P. 1193-1205

Droits : 2008 National Research Council Canada
http://archimer.ifremer.fr/doc/2008/publication-4559.pdf
DOI:10.1139/F08-050
http://archimer.ifremer.fr/doc/00000/4559/

Éditeur(s) : HAL CCSD
Résumé : The bacterial microbiota of ants (Hymenoptera: Formicidae) is known to have a defensive role in social insects, particularly for leaf-cutting ants (Formicidae: Attini) due to the use of antimicrobial molecules produced by cuticular actinobacteria. In this thesis, we studied the bacterial microbiota of ants in French Guyana using different approaches based on natural products chemistry and molecular ecology. The first chapter describes the isolation, identification, culture and biological evaluations of 43 cuticular actinobacteria. Antagonism bioassays of isolated strains and antibiotic activities of the culture extracts against human pathogens are presented as well as the identification of an antimicrobial cyclic dipeptide (Cyclo (LPro-LPhe)) isolated from a strain close to Streptomyces thioluteus. Moreover, the implementation of molecular networks applied to UPLC/MS/MS analysis of actinobacterial cocultures allowed us to explore the diversity of metabolites produced under these conditions. The second chapter presents a methodological study to evaluate the capacity of four DNA extraction methods, in terms of richness and composition of the cuticular bacterial microbiota, in high-throughput sequencing from Atta cephalotes and Pseudomyrmex penetrator. The results of metabarcoding highlight two methods of extraction and reveal inter- and intraspecific differences in the composition of cuticular bacterial communities. Finally, chapter three describes the composition of the cuticular bacterial microbiota of Camponotus femoratus and Crematogaster levior in ant garden and the results reveal the acquisition in the environment of a part of the microbiota. In parallel, metabolomic analyses of ant’s cuticle show, on the contrary, a greater specificity related to the ant species. Future researches focusing on statistical analysis strategies combining metabarcoding and metabolomics data are discussed.
Le microbiote bactérien cuticulaire des fourmis (Hymenoptera : Formicidae) est connu pour avoir un rôle défensif chez ces insectes sociaux, notamment chez les fourmis attines (Formicidae : Attini) grâce l’utilisation de molécules antimicrobiennes produites par des actinobactéries cuticulaires. Dans le cadre de cette thèse, nous avons étudié le microbiote bactérien des fourmis de Guyane en utilisant différentes approches en chimie des produits naturels et en écologie moléculaire. Le premier chapitre décrit l’isolement, l’identification, la culture et l’évaluation biologique de 43 actinobactéries cuticulaires de fourmis de Guyane. Les tests d’antagonismes des souches isolées et l’activité antibiotique des extraits de culture contre des micro-organismes pathogènes humains sont présentés ainsi que l’identification d’un dipeptide cyclique (Cyclo(LPro-LPhe)) antimicrobien qui a été isolé à partir d’une souche proche de Streptomyces thioluteus. Par ailleurs, la mise en œuvre de réseaux moléculaires appliqués à une analyse par UPLC/MS/MS de cocultures d’actinobactéries a permis d’explorer la diversité des métabolites produits dans ces conditions. Le deuxième chapitre présente une étude méthodologique pour comparer quatre méthodes d’extraction d’ADN, en termes de richesse et de composition du microbiote bactérien cuticulaire, par séquençage haut débit à partir des espèces Atta cephalotes et Pseudomyrmex penetrator. Les résultats du métabarcoding ADN mettent en lumière deux méthodes d’extraction et révèlent des différences inter- et intraspécifiques dans la composition des communautés bactériennes cuticulaires. Enfin, le chapitre trois décrit la composition du microbiote bactérien cuticulaire des espèces Camponotus femoratus et Crematogaster levior dans les jardins de fourmis. Les résultats soulignent l’acquisition d’une partie du microbiote dans l’environnement. En parallèle l’analyse métabolomique des cuticules montre à contrario une plus grande spécificité liée à l’espèce de fourmi. Les recherches futures axées sur les stratégies d’analyses statistiques combinant le métabarcoding et la métabolomique sont discutées.
https://tel.archives-ouvertes.fr/tel-01537793

NNT : 2017YANE0003
tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793/document
https://tel.archives-ouvertes.fr/tel-01537793/file/thesecarolinebirer.pdf

Éditeur(s) : HAL CCSD Hindawi Publishing Corporation
Résumé : During the 1982-1984 bradyseismic crises in the Campi Flegrei area (Italy), the University of Wisconsin deployed a network of seismological stations to record local earthquakes. In order to analyse the potential of the recorded data in terms of tomographic imaging, a blind test was recently set up and carried out in the framework of a research project. A model representing a hypothetical 3D structure of the area containing the Campi Flegrei caldera was also set up, and a synthetic dataset of time arrivals was in turn computed. The synthetic dataset consists of several thousand P- and S-time arrivals, computed at about fourteen stations. The tomographic inversion was performed by four independent teams using different methods. The teams had no knowledge of either the input velocity model or the earthquake hypocenters used to create the synthetic dataset. The results obtained by the different groups were compared and analysed in light of the true model. This work provides a thorough analysis of the earthquake tomography potential of the dataset recording the seismic activity at Campi Flegrei in the 1982-1984 period. It shows that all the tested earthquake tomography methods provide reliable low-resolution images of the background velocity field of the Campi Flegrei area, but with some differences. However, none of them succeeds in detecting the hypothetical structure details (i.e. with a size smaller than about 1.5-2 km), such as a magmatic chamber 4 km deep and especially the smaller, isolated bodies, which represent possible magmatic chimneys and intrusions.
ISSN: 1687-885X

hal-00795584
https://hal.archives-ouvertes.fr/hal-00795584
DOI : 10.1155/2012/505286

Éditeur(s) : HAL CCSD
Résumé : Karstic aquifers represent the most important fresh water reservoirs in many regions of the world like the Mediterranean Basin. However, because of complex processes of karstification, those aquifers are highly heterogeneous at all spatial scales and vulnerable to contamination. In this dissertation, we studied the potential of gravimetry and ambient seismic noise for hydrological modeling in karstic areas.The dolomitic area surrounding the “GEK” observatory in the Durzon catchment on the Larzac plateau, in France, is the preferred site for these studies. Inside the observatory, a superconducting gravimeter dedicated to hydrology has continuously measured gravity changes since 2011 with high precision, undertaken for the first time on a karst. From this gravity monitoring, we made conceptual hydrological models which laid the foundation of 1-D flow physical models. Indeed, gravimetry is an integrative hydro-geophysical method which allows 1) to consider the epikarst, locally heterogeneous as an equivalent tabular medium and 2) to define the types of transfer (fast & slow) occurring at the site. Especially, the lack of fast transfer through the GEK epikarst was precisely quantified for the first time at the field scale (~100m). Gravity-driven water mass balance with local meteorological data (evapotranspiration from a flux tower and precipitation) allowed setting the bottom outlet of the model to 1 mm.day-1. This flow has proved to be representative of the low-flow discharge at the only spring which represents all groundwater outflows from the catchment. This result supposes the homogeneity of the dolomitic epikarst almost at the basin scale. Model parameters were next calibrated using one year of ambient seismic noise monitored at two stations. Phase velocity changes obtained by cross-correlating the noise between 6 and 8 Hz were used as a ”timer” to follow the water infiltration between a depth of 30 and 60 meters. Thus, monitoring seismic velocity changes using ambient seismic noise demonstrates great potential for the study of deep and complex critical zones and could fill the instrumental gap currently existing in hydrology.Time-lapse gravity measurements with a spring-based portable gravimeter have also demonstrated the different behavior of two epikarsts and their variability at the scale of a few hundred meters. Monthly measurements around the observatory revealed the spatial homogeneity of this dolomitic epikarst: all the stations showed the same water storage changes. On the contrary, seasonal surface to depth gravity measurements along the underground passage of the Saint-Ferréol sinkhole, in limestone, have shown fast transfer and strong spatial variability of water storage. Lithology is then expected to play a part in the epikarst capacity to retain water. The precision needed to measure the weak hydrological induced signals during those surveys required robust methodology and an ambient temperature effect on measurements with spring-based gravimeter was observed in the field and quantified in the laboratory.
Les aquifères karstiques représentent des ressources en eau essentielles dans de nombreuses régions du monde comme le bassin Méditerranéen. Cependant, de par les processus complexes de karstification, ces aquifères sont hétérogènes à de nombreuses échelles et vulnérables. Dans cette thèse, nous étudions le potentiel de la gravimétrie et du bruit sismique ambiant pour la modélisation hydrologique en milieu karstique.Le site dolomitique de l’observatoire « GEK », sur le bassin du Durzon dans le Larzac, est le site d’étude privilégié de ces travaux. Dans l’observatoire, un gravimètre supraconducteur dédié à l’hydrologie mesure depuis 2011 les variations de gravité en continu et à une très haute précision, pour la première fois sur un karst. Des modèles hydrologiques conceptuels ont été réalisés à partir de cette surveillance gravimétrique et ont permis de poser les bases de modèles physiques d’écoulements 1-D. En effet la gravimétrie, intégratrice, permet 1) de considérer l’épikarst localement hétérogène comme un milieu tabulaire équivalent et 2) de définir les types de transfert à l’œuvre sur le site. En particulier, l’absence de transfert rapide dans l’épikarst a été quantifiée avec précision pour la première fois à l’échelle du terrain (~100m). A l’aide de données météorologiques locales, un bilan de masse précis a permis de définir le flux en limite inférieure du modèle à 1 mm.jour-1. Ce flux s’est montré représentatif du débit de basses-eaux de la source drainant l’ensemble du bassin. Ce résultat suppose une homogénéité de l’épikarst dolomitique quasiment à l’échelle du bassin. Les paramètres des modèles physiques ont ensuite pu être calibrés à l’aide d’un an d’intercorrélation du bruit sismique ambiant entre deux stations. Les variations de vitesses de phase obtenues entre 6 et 8Hz nous ont servi de « chronomètre » pour suivre l’infiltration entre 30 et 60m de profondeur. La surveillance passive des variations de vitesses sismiques par intercorrélation du bruit sismique ambiant montre ainsi un fort potentiel pour l’étude des zones critiques profondes et complexes à l’échelle du terrain et peut combler la lacune instrumentale qui existe actuellement en hydrologie.Des campagnes répétées de mesures avec un gravimètre portable à ressort ont également mis en évidence le fonctionnement différent de deux épikarsts et leur variabilité à l’échelle de la centaine de mètres. Des mesures mensuelles autour de l’observatoire ont mis en évidence l’homogénéité spatiale de cet épikarst dolomitique : toutes les stations ont les mêmes variations temporelles de stock d’eau. Au contraire, des mesures saisonnières en surface et en profondeur le long de la galerie souterraine calcaire de l’abîme de Saint-Ferréol ont montré une variabilité spatiale forte du stockage ainsi que du transfert rapide. La lithologie de l’épikarst est donc suspectée de jouer un rôle dans sa capacité de stockage. Lors de ces campagnes, la faiblesse du signal recherché a nécessité une méthodologie précautionneuse et un effet de température sur les mesures des gravimètres relatifs à ressort a été observé sur le terrain et quantifié en laboratoire.
https://tel.archives-ouvertes.fr/tel-01649606

NNT : 2016MONTT128
tel-01649606
https://tel.archives-ouvertes.fr/tel-01649606
https://tel.archives-ouvertes.fr/tel-01649606/document
https://tel.archives-ouvertes.fr/tel-01649606/file/2016_FORES_archivage.pdf

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (similar to 9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.
ISSN: 0012-9658

hal-01032424
https://hal.archives-ouvertes.fr/hal-01032424

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Few studies have considered using environmental amenities to explain social health inequalities.Nevertheless, Green spaces that promote good health may have an effect on socioeconomic health inequalities. In developed countries, there is considerable evidence that green spaces have a beneficial effect on the health of urban populations and recent studies suggest they can have a positive effect on pregnancy outcomes. To investigate the relationship between green spaces and the spatial distribution of infant mortality taking account neighborhood deprivation levels. METHODS: The study took place in Lyon metropolitan area, France. All infant deaths that occurred between 2000 and 2009 were geocoded at census block level. Each census block was assigned greenness and socioeconomic deprivation levels. The spatial--scan statistic was used to identify high risk cluster of infant mortality according to these neighborhood characteristics. RESULTS: The spatial distribution of infant mortality was not random with a high risk cluster in the south east of the Lyon metropolitan area (p<0.003). This cluster disappeared (p=0.12) after adjustment for greenness level and socioeconomic deprivation, suggesting that these factors explain part of the spatial distribution of infant mortality. These results are discussed using a conceptual framework with 3 hypothetical pathways by which green spaces may have a beneficial effect on adverse pregnancy outcomes: (i) a psychological pathway, (ii) a physiological disruption process and (iii) an environmental pathway. CONCLUSIONS: These results add some evidence to the hypothesis that there is a relationship between access to green spaces and pregnancy outcomes but further research is required to confirm this.
BMC Pregnancy and Childbirth

hal-00876083
https://hal.archives-ouvertes.fr/hal-00876083
https://hal.archives-ouvertes.fr/hal-00876083/document
DOI : 10.1186/1471-2393-13-191

Éditeur(s) : HAL CCSD Springer International Publishing
Résumé : The intensive farming practices that have been developed over the past 60 years are based mainly on the use of chemical inputs such as fertilisers and pesticides, mechanical tillage and monoculture. The limitations of these methods are now clear: long-term degradation of soil fertility, impacts on the environment and human health, high consumption of fossil fuels, low efficiency of inputs and threats to food security in a context of climate change. Would farming practices that rely on the activation of ecological processes be an alternative to achieve a balance between high productivity and environmental preservation? While many studies suggest a positive relationship between soil biodiversity and ecosystem services, there is considerable debate on the form such agricultural systems should take. This study reviewed the state of current knowledge and identified aspects requiring further research to achieve the aim of sustainable intensification of agriculture. The following major points emerged: 1) Most studies focused on the evaluation of individual practices. However, changes in farmers’ cropping practices to take advantage of soil biodiversity services would need to manage not only the interactions between various practices but also the trade-off between the technical and socio economic constraints of cropping systems. Advances in agricultural system design approaches may help to ensure appropriate trade-offs. 2) More attention should be given to drawing on knowledge from different sources: laboratory studies focusing on the ecological functions of soil biodiversity, experimental surveys on farmers’ fields to rank the farming practices and processes to be included in site-specific models, and on- station experiments to test hypotheses and acquire additional reference material. 3) Whereas advances in technical and scientific knowledge provide an increasing number of relevant indicators for characterizing biodiversity and ecological functions, studies are rarely targeted at the development of indicators that are accessible to farmers or their technical advisors. The lack of indicators accessible to grassroots players for evaluating the impacts of their decisions on soil biodiversity remains a serious obstacle to the development of innovative agro-ecological systems.
Sustainable Agriculture Reviews 14

ISBN : 978-3-319-06015-6
hal-01268743
https://hal.archives-ouvertes.fr/hal-01268743
DOI : 10.1007/978-3-319-06016-3_5
PRODINRA : 270786

Éditeur(s) : HAL CCSD
Résumé : National audience
We propose a method to solve the problem of clustering individuals described by mixed variables structured in blocks. It is a hierarchical method with two levels similar to Hierarchical Principal Component Analysis presented by Wold, based on the mixed topology maps (MTM). The first step consists in establishing, for each block of mixed variables, a clustering representing a synthesis of local individuals at the block level. The second step is to re-apply MTM on the weighted results of the first level. We obtain a global clustering of individuals, consensus among the partitions from level 1. The proposed method is illustrated on data from the national survey in the French housing stock carried out in 2003-2005 by the Observatory for Indoor Air Quality (OQAI).
Fouille de Données Complexes, complexité liée aux données multiples et massives (FDC)
bordeaux, France

hal-00748841
https://hal.archives-ouvertes.fr/hal-00748841
https://hal.archives-ouvertes.fr/hal-00748841/document

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
STUDY QUESTION: Is prenatal exposure to persistent organic pollutants (POPs) associated with variations of sex hormone levels in cord blood? SUMMARY ANSWER: Prenatal exposure to a number of POPs is associated with a disruption of hormone levels in cord blood, with sex specificities. WHAT IS KNOWN ALREADY: Epidemiological studies have reported disorders of reproductive health, in relation with POPs exposure during early life and the endocrine disruption properties of these chemicals have been suggested as possible mechanisms. STUDY DESIGN, SIZE, DURATION: A subset of 282 mother-child pairs was selected from the prospective population-based PELAGIE birth cohort (n = 3421, 2002-2006, Brittany, France). Pregnant women were recruited before 19 weeks of gestation and followed until delivery. PARTICIPANTS/MATERIALS, SETTING, METHODS: Sex hormone levels including sex hormone-binding globulin (SHBG), estradiol (E2), total testosterone (T), free testosterone (fT = T/SHBG) and the aromatase index (AI = T/E2) were measured in 282 cord blood samples. Anti-Müllerian hormone (AMH) was measured in male newborns only. Pesticide concentrations of α-endosulfan, β-hexachlorocyclohexane (β-HCH), γ-HCH, dieldrin, pp'-dichlorodiphenyldichloroethylene (p,p'-DDE), hexachlorobenzene (HCB), heptachlor epoxide (HCE), as well as PCBs (congeners 153, 187 and the sum of anti-estrogenic PCBs 118, 138, and 170) and decabrominated diphenyl ether (BDE209) were also measured in cord blood. Associations between sex hormones and POPs exposure were explored using multiple linear regressions adjusted for potential confounders. MAIN RESULTS AND THE ROLE OF CHANCE: High PCB levels were associated with an increase of SHBG (P-trend extless 0.01) and AMH (P-trend extless 0.05) and a decrease of fT (P-trend extless 0.05) and AI (P-trend extless 0.01). High pesticide levels, particularly α-endosulfan and HCE, were associated with an increase of SHBG (P extless 0.05) and E2 (P extless 0.01) and a decrease of fT (P extless 0.05) and AI (P extless 0.01). Several of these associations were stronger, or specific, among male or female newborns. The associations were not altered in the sensitivity analyses. LIMITATIONS, REASONS FOR CAUTION: The study population was of relatively small sample size, and some compounds rarely detected in cord blood. The high level of correlation between POPs makes it difficult to identify the most contributing POPs. Hormone measurements were performed at birth (in cord blood) and may not adequately represent the infant endocrine system. Multiple statistical testing may have led to false-positive associations. WIDER IMPLICATIONS OF THE FINDINGS: Our results are in discordance with those reported in the only published study of the kind but in accordance with studies about prenatal exposure to other endocrine disruptors such as phthalates. These findings may help understanding the pathways involved in adverse reproductive outcomes associated with POPs exposure. STUDY FUNDING/COMPETING INTERESTS: The PELAGIE cohort is funded by Inserm, French Ministry of Health, French Ministry of Labor, InVS, ANR, ANSES, and French Ministry of Ecology. None of the authors has any competing interest to declare
ISSN: 0268-1161

hal-01220641
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01220641
DOI : 10.1093/humrep/dev260
PUBMED : 26493407

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper deals with image processing. This study takes place in a segmentation process based on texture analysis. We use the multifractal ap-proach to characterize the textures. More precisely we study a particular multi-fractal spectrum called the large deviation spectrum. We consider two statistical methods to numerically compute this spectrum. The resulting spectrum, com-puted by both methods over an image, is a one dimension spectrum. In the scope of this article, we extend these methods in order to obtain a two dimen-sions spectrum which could be assimilated to an image. This 2D spectrum al-lows a local characterization of the image singularities while a 1D spectrum is a global characterization. Moreover, the computation of the spectrum requires the use of a measure. We introduce here a pre processing based on the gradient to improve the measure. We show results on both synthetic and real world images. Finally, we remark that the resulting 2D spectrum is close to the resulting im-age of an edge detection process while edge detection using one dimension spectrum requires post processing methods. This statement will be used for fu-ture works.
SITIS Proceedings
Hammamet, Tunisia

hal-00602273
https://hal.archives-ouvertes.fr/hal-00602273

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Estimating how topography is maintained provides insights into the different factors responsible for surface deformations and their relative roles. Here, we develop a new and simple approach to assess the degree of isostatic compensation of continental topography at regional scale from GOCE gravity gradients. We calculate the ratio between the radial gradient observed by GOCE and that calculated from topography only. From analytical and statistical formulations, simple relationships between this ratio and the degree of compensation are obtained under the Airy–Heiskanen isostasy hypothesis. Then, a value of degree of compensation at each point of study area can be easily deduced. We apply our method to the Alaska-Canada Cordillera and validate our results by comparison with a standard isostatic gravity anomaly model and additional geophysical information for this area. Both our GOCE-based results and the isostatic anomaly show that Airy–Heiskanen isostasy prevails for the Yukon Plateau whereas additional mechanisms are required to support topography below the Northwest Territories Craton and the Yakutat collision zone.
ISSN: 0956-540X

hal-01467540
https://hal.archives-ouvertes.fr/hal-01467540
https://hal.archives-ouvertes.fr/hal-01467540/document
https://hal.archives-ouvertes.fr/hal-01467540/file/cadioGJI2016.pdf
DOI : 10.1093/gji/ggw281

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Few studies have considered using environmental amenities to explain social health inequalities.Nevertheless, Green spaces that promote good health may have an effect on socioeconomic health inequalities. In developed countries, there is considerable evidence that green spaces have a beneficial effect on the health of urban populations and recent studies suggest they can have a positive effect on pregnancy outcomes. To investigate the relationship between green spaces and the spatial distribution of infant mortality taking account neighborhood deprivation levels. METHODS: The study took place in Lyon metropolitan area, France. All infant deaths that occurred between 2000 and 2009 were geocoded at census block level. Each census block was assigned greenness and socioeconomic deprivation levels. The spatial--scan statistic was used to identify high risk cluster of infant mortality according to these neighborhood characteristics. RESULTS: The spatial distribution of infant mortality was not random with a high risk cluster in the south east of the Lyon metropolitan area (p<0.003). This cluster disappeared (p=0.12) after adjustment for greenness level and socioeconomic deprivation, suggesting that these factors explain part of the spatial distribution of infant mortality. These results are discussed using a conceptual framework with 3 hypothetical pathways by which green spaces may have a beneficial effect on adverse pregnancy outcomes: (i) a psychological pathway, (ii) a physiological disruption process and (iii) an environmental pathway. CONCLUSIONS: These results add some evidence to the hypothesis that there is a relationship between access to green spaces and pregnancy outcomes but further research is required to confirm this.
ISSN: 1471-2393

inserm-00878362
http://www.hal.inserm.fr/inserm-00878362
http://www.hal.inserm.fr/inserm-00878362/document
http://www.hal.inserm.fr/inserm-00878362/file/1471-2393-13-191.pdf
DOI : 10.1186/1471-2393-13-191

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND AND AIM: The impact of basal core promoter (BCP) and precore (PC) mutants of the hepatitis B virus (HBV) on liver disease severity remains controversial. The aim of the present study was to screen BCP and PC mutations in 252 HBV surface antigen (HBsAg) positive carriers in France and to assess relationships between these mutations and severe fibrosis. METHODS: Direct sequencing of the precore/core gene was used to detect A1762T/G1764A and G1757A mutations in the BCP and G1896A and G1899A mutations in the PC region. RESULTS: The prevalences of A1762T/G1764A, G1757A, G1896A, and G1899A mutations were 34.1%, 38.7%, 54.9%, and 29.3% (P < 0.001), respectively. The independent predictors of severe fibrosis (>/=F3 Metavir) were older age (P < 0.001), male gender (P = 0.012), elevated alanine aminotransferase (P < 0.001), and the double A1762T/G1764A mutant with no other mutations (P = 0.011). Interestingly, the association of the G1899A mutation with the double A1762T/G1764A mutant significantly counteracted the deleterious effect of the sole double A1762T/G1764A mutant (odds ratio [OR] = 0.28 vs. OR = 3.55, respectively, P = 0.028). CONCLUSIONS: Patients with the A1762T/G1764A mutation have a higher risk of severe fibrosis. The G1899A mutation is a protective factor against severe fibrosis that counteracted the deleterious effect of the A1762T/G1764A mutation. Finally, host phenotypic and HBV genotypic markers independently predict fibrosis severity.
Journal of gastroenterology and hepatology

hal-01477209
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477209
DOI : 10.1111/jgh.13338
PUBMED : 26992056

Éditeur(s) : HAL CCSD
Résumé : International audience
To study social health inequalities, contextual data may constitute an appropriate alternative to individual socioeconomic characteristics, often hard to retrieve. Indices can be used to summarize the multiple dimensions of the neighborhood socioeconomic status. The main objectives of this work are to develop a statistical procedure to create a neighborhood socioeconomic index and to investigate the influence of the clustering method of the deprivation index on the measure of health inequalities. Our study setting is composed of three major French metropolitan areas: Lille, Lyon and Marseille. The statistical unit is the French census block. The methodology uses several successive principal components analyses to select variables and create the index. Deprivation categories are drawn with hierarchical clustering on principal components. Twenty socioeconomic variables are selected in the neighborhood deprivation index. An optimal clustering obtained by HC is in three classes and the clusters are ordered along the first axis of the PCA.
SFDS - 44èmes journées de Statistique - 2012
Bruxelles, Belgium

hal-00734769
https://hal.archives-ouvertes.fr/hal-00734769
https://hal.archives-ouvertes.fr/hal-00734769/document
https://hal.archives-ouvertes.fr/hal-00734769/file/submission_44.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Isotopes have been widely used for source identification since the early twentieth century. Recent advances in analytical techniques have increased the precision and the accuracy of isotope analysis. As a result, the use of isotopes has spread to several fields (e.g., ecology, food chemistry, archaeology, environmental health and pollution, and forensic sciences). This review examines the principal uses of stable-isotope analyses for tracing origins or sources, along with statistical methods employed for data interpretation, in recent papers (2007―09) dealing essentially with food authentication, ecology, environmental pollution and other applications, including geology, police forensics, hydrology and archaeometry. The main elements analyzed were H, C, N, O, S, Sr and Pb. For isotope-data interpretation, statistical methods appear to depend essentially on the field, the objectives of the study and the number of parameters. They were not often stated explicitly because the studies were exploratory and aimed primarily at assessing the relevance of the analytical techniques used to identify sources. We critically discuss the adequacy of these methods.
ISSN: 0165-9936

hal-00687383
https://hal.archives-ouvertes.fr/hal-00687383

Éditeur(s) : HAL CCSD
Résumé : International audience
Over the past decade, much attention has been devoted to the development of forest biomass estimation methods at a stand scale, leading to the establishment of allometric models (Chave et al., 2014). These allometric equations use a unique wood specific gravity value (WSG) per species, but neglect the within tree variations of WSG found by others (Wiemann & Williamson, 1989).The main objectives of this study are (1) to illustrate the diversity of radial (from pith to bark) and longitudinal (from bottom to top) patterns of WSG variation within and between species, (2) to highlight different trends of WSG radial variations and the possible misinterpretations of these trends due to the effect of heartwood and (3) to link these variations and patterns to the successional status of the species (from pioneer to sciaphilic species).We sampled 33 small trees (10 Wood sciences underpinning tropical ecology and management. International closing symposium of the XYLAREDD project.
Tervuren, Belgium

hal-01188894
https://hal-sde.archives-ouvertes.fr/hal-01188894

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: Although adverse birth outcomes have been associated with neighbourhood deprivation in urban areas, few studies have addressed this issue in rural zones. This study examines whether associations between neighbourhood deprivation and adverse birth outcomes differ in urban and rural contexts, while taking individual characteristics and spatial accessibility of prenatal care (SAPC) into account. METHODS: Pregnant women from a French mother-child cohort were recruited from 2002 to 2006 in Brittany. Their residential addresses were geocoded into their census blocks (the finest geographical resolution available). Deprivation was assessed at the same neighbourhood level. Models to assess the associations of deprivation, stratified by urban/rural status, with preterm delivery (PTD), with small for gestational age birth weight (SGA) and with small for gestational age head circumference at birth (SHC), estimated odds ratios (ORs), adjusted for maternal socioeconomic characteristics and SAPC. RESULTS: This study considered 2929 liveborn singleton pregnancies from 780 census blocks. Neighbourhood deprivation was associated with increased risks of SGA and SHC (P trend  extless 0.01 and 0.03 respectively), only among mothers residing in rural areas. Neighbourhood deprivation had statistically significantly heterogeneous effects on SGA and SHC according to the urban/rural status of maternal residence. CONCLUSION: These findings suggest that neighbourhood deprivation affects fetal growth differentially in urban and rural areas and that SAPC does not seem to be responsible for this difference. Comparison of these findings with the literature requires caution in the conceptualisation of urban and rural settings
ISSN: 0269-5022

hal-01187424
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187424
DOI : 10.1111/ppe.12208
PUBMED : 26186278