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) : Edp Sciences S A
Résumé : Reared sea bass were submitted to six stressful situations: hyperoxia with or without hypercapnia, increased stocking density in an open flow or recirculating system, transfer to another tank and nodavirus injection. The potentially negative impact of these factors on the lives of sea bass was investigated by measuring 9 water parameters and 19 fish parameters including total serum protein (TSP). TSP has already been used to evaluate stress. The present study investigates data of previous and new experiments, concentrating on the potential use of TSP as a routine indicator to assess welfare in sea bass reared on fish farms. In the current experiment, oxygen and carbon dioxide were seen to affect levels of TSP, but alterations were too erratic to enable proper comparison, probably because they are normal components of the fish environment and become toxic only by dose increase. TSP decreased when stocking density increased. After transfer to another tank, TSP decreased to 14% for three weeks and then increased during the fourth week through compensative overproduction, before returning to normal levels after 2 months. The results confirmed that transfer is an important stress factor for fish, with cumulative effects for successive transfers. TSP alteration of nodavirus-injected fish depends on the type of symptoms, which can be divided into 3 groups: (i) dying fish, in which TSP increased sharply due to over-production of protein involved in non-specific defences and inflammation, then decreased dramatically before death; (ii) whirling fish, a group that included both fish that later died, in which TSP decreased, and fish that subsequently survived, in which TSP increased due to development of specific immunity; and (iii) asymptomatic fish, in which TPS was similar to control levels and which were probably insensitive to nodavirus and/or had developed defences. In this paper, different mechanisms of TSP alteration are proposed and the interest of TSP as a field parameter is discussed. TSP is a non-destructive parameter that is robust, easy to measure everywhere and cheap, representing a suitable way of monitoring the overall welfare of fish by its regular increase. It can be used only as a "warning" of poor rearing conditions, however, and further investigations would be needed to identify the specific stress or health disorder.
Aquatic Living Resources (0990-7440) (Edp Sciences S A), 2011-04 , Vol. 24 , N. 2 , P. 121-127

Droits : EDP Sciences, IFREMER, IRD 2011
http://archimer.ifremer.fr/doc/00043/15382/12740.pdf
DOI:10.1051/alr/2011130
http://archimer.ifremer.fr/doc/00043/15382/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Because many biological processes related to the dynamics of infectious diseases are caused by complex interactions between the environment, the host(s) and the agent(s), the necessity to address the methodological implications of this inherent complexity has recently emerged in epidemiology. Most epidemiologists now acknowledge that most human infectious diseases are likely to have complex dynamics. However, this knowledge still percolates with difficulty in their statistical "modus operandi". Indeed, for the study of complex systems, the traditional first-line statistical toolbox of epidemiologists (mainly built around the Generalized Linear Model family), despite its undeniable practicality and robustness, has structural limitations deprecating its usefulness. Three major sources of complexity neglected or not taken into account by this first-line statistical toolbox and having deep statistical implications are the multi-level organization of data, the non-linear relationships between variables and the complex interactions between variables. Three promising candidates to incorporate along with traditional tools for a new first-line statistical toolbox more suitable to apprehend these sources of complexity are the generalized linear mixed models, the generalized additive models, and the structural equation models. The aforementioned methodologies have the advantage to be generalizations of GLM models and are relatively easy to implement. Their assimilation and implementation would thus be greatly facilitated for epidemiologists. More globally, this text underlines that an improved use of other methods as such described here compared to traditional ones has to be performed to better understand the complexity challenging epidemiologists every day. This is particularly true in the field of infectious diseases for which major public health challenges will have to be addressed in the coming decades.
ISSN: 1567-1348

inserm-00872354
http://www.hal.inserm.fr/inserm-00872354
http://www.hal.inserm.fr/inserm-00872354/document
http://www.hal.inserm.fr/inserm-00872354/file/main_document.pdf
DOI : 10.1016/j.meegid.2013.09.006

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Development of hepatocellular carcinoma (HCC) is a complex and progressive disease that involves cycles of liver cell death, inflammation, and tissue regeneration/remodelling. Chemokines and chemokine receptors play numerous and integral roles in the disease progression of HCC. Here we investigated the novel chemokine receptor CXCR7/RDC1 in HCC progression, its two known ligands CXCL12 and CXCL11, as well as the other CXCL12 receptor, CXCR4. Our results show that in a cohort of 408 human HCCs, CXCR7 and CXCL11 were significantly higher in tumours compared to normal liver controls (5- and 10-fold, respectively). Immunohistochemical (IHC) staining on human HCC sections confirmed that both CXCL11 and CXCR7 were much higher in cancer tissues. Furthermore, IHC staining revealed that CXCR7 protein was only expressed in endothelial cells whereas CXCL11 exhibited a much broader tissue expression. At the cellular level we observed that in vitro, human microvascular endothelial cells (HMEC-1) up-regulated CXCR7 under hypoxic and acidic pH conditions, which are well known characteristics of the HCC tumour micro-environment. As for its ligand, we observed that IFNγ robustly induced CXCL11 in hepatic stellate cells, hepatocytes, and HMEC-1s. In addition, in the mouse Diethylnitrosamine model of hepatocarcinogenesis we observed a very strong induction of CXCR7 and CXCL11 transcripts, confirming that CXCR7/CXCL11 up-regulation is conserved between human and mice liver cancer. Altogether, our results strongly support the hypothesis that the CXCL11/CXCR7 pathway is involved HCC progression.
ISSN: 0959-8049

hal-00682463
https://hal.archives-ouvertes.fr/hal-00682463
DOI : 10.1016/j.ejca.2011.06.044
PUBMED : 21778049

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Generation and emplacement of felsic magmas in the Paleoproterozoic Baoulé-Mossi domain, West African Craton does not match the apparent peaks of global crust generation identified between ca. 2900–2600, 1900–1600 and 1200–900 Ma. In contrast, across the Baoulé-Mossi domain, the emplacement of felsic intrusions ranges from ca. 2300 to 2000 Ma. It has proven difficult to place this magmatism within a robust geodynamic framework due to the lack of accurate geochronological data from across the West African Craton. The present study addresses this issue by presenting eighty-four new felsic intrusions zircon ion microprobe and LA-ICP-MS U-Pb ages from areas that up until now have not been targeted for geochronology. The new dataset, when fully integrated with existing age data, reveals a craton-wide diachronous geochronological pattern characterized by a magmatic front that migrated westward. This migration proceeded at a rate of 35 km per million years, with an apparent offset of the initiation and cessation of felsic magmatic activity between the east and west of approximately 50 million years. The new data also show that although the entire Baoulé-Mossi domain was subject to continuous magmatic activity for at least 150 million years, this magmatic activity displays a rather different record in the eastern and western portions of the domain. The differences are expressed as a westward migration of the magmatic activity, cessation of activity around ca. 2100 Ma (easternmost portion) and ca. 2050 Ma (westernmost portion) and a higher incidence of inherited ages in the westernmost portion when compared to the easternmost region. In addition, the new U-Pb data identify some of the oldest felsic intrusions in the region, including a granite from Burkina Faso (2265 ± 17 Ma) and a diorite porphyry (2216 ± 5 Ma) in southern Mali. This study also reveals inherited Archean zircon cores from across southern Mali. The combination of the new data presented here, along with previously published data, suggests that the Baoulé-Mossi domain formed from the accretion of two major crustal blocks. The Archean inherited ages open a window for further investigation of the interaction between the Archean Kénéma-Man and the Paleoproterozoic Baoulé-Mossi domains.
ISSN: 0301-9268

hal-01623272
https://hal.archives-ouvertes.fr/hal-01623272
DOI : 10.1016/j.precamres.2017.07.036

Éditeur(s) : HAL CCSD Wiley
Résumé : The intensification of the hydrological cycle, with an observed and modeled increase in drought incidence and severity, underscores the need to quantify drought effects on carbon cycling and the terrestrial sink. FLUXNET, a global network of eddy covariance towers, provides dense data streams of meteorological data, and through flux partitioning and gap filling algorithms, estimates of net ecosystem productivity (FNEP), gross ecosystem productivity (P), and ecosystem respiration (R). We analyzed the functional relationship of these three carbon fluxes relative to evaporative fraction (EF), an index of drought and site water status, using monthly data records from 238 micrometeorological tower sites distributed globally across 11 biomes. The analysis was based on relative anomalies of both EF and carbon fluxes and focused on drought episodes by biome and climatic season. Globally P was ≈50% more sensitive to a drought event than R. Network-wide drought-induced decreases in carbon flux averaged −16.6 and −9.3 g C m−2 month−1 for P and R, i.e., drought events induced a net decline in the terrestrial sink. However, in evergreen forests and wetlands drought was coincident with an increase in P or R during parts of the growing season. The most robust relationships between carbon flux and EF occurred during climatic spring for FNEP and in climatic summer for P and R. Upscaling flux sensitivities to a global map showed that spatial patterns for all three carbon fluxes were linked to the distribution of croplands. Agricultural areas exhibited the highest sensitivity whereas the tropical region had minimal sensitivity to drought. Combining gridded flux sensitivities with their uncertainties and the spatial grid of FLUXNET revealed that a more robust quantification of carbon flux response to drought requires additional towers in all biomes of Africa and Asia as well as in the cropland, shrubland, savannah, and wetland biomes globally.
ISSN: 1354-1013

hal-01032076
https://hal.archives-ouvertes.fr/hal-01032076
DOI : 10.1111/j.1365-2486.2009.01991.x

Éditeur(s) : HAL CCSD American Arachnological Society
Résumé : To obtain a reliable description of spider communities, robust sampling protocols are crucial. However, it remains unclear if descriptions of spider communities in tropical habitats require both day and night sampling. Here we tested whether sampling both day and night in high and low vegetation strata would lead to better diversity estimates of spider communities than sampling at only one period of the day. We determined spider taxonomic diversity in a network of 12 plots in French Guiana along a vegetation gradient. We found high alpha diversity of spiders as expected for a tropical area at every site. We showed strong differences in spider alpha and beta diversity between high and low vegetation strata, while they were similar between day and night sampling. Our results suggest that collecting spiders at only one period is sufficient to describe the diversity of spider communities across land use types in the neotropics.
ISSN: 0161-8202

hal-01535342
https://hal.archives-ouvertes.fr/hal-01535342
PRODINRA : 346667

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA) is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP) based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening
ISSN: 1932-6203

hal-01163756
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163756
DOI : 10.1371/journal.pone.0128188
PUBMED : 26053379

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : Public Library Science
Résumé : Background: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques - including site-based monitoring, genetic analyses, mark-recapture studies and telemetry - can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings: To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine-to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance: The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework - including maps and supporting metadata - will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.
Plos One (1932-6203) (Public Library Science), 2010-12 , Vol. 5 , N. 12 , P. -

Droits : 2010 Plos One
http://archimer.ifremer.fr/doc/00028/13926/11308.pdf
DOI:10.1371/journal.pone.0015465
http://archimer.ifremer.fr/doc/00028/13926/

Éditeur(s) : HAL CCSD
Résumé : International audience
ABSTRACT :A satellite retrieval of surface solar irradiance (SSI) based on GOES satellite data is presented and validated for the French Guiana with three years of in situ measurements from six ground stations. We propose a particle filter approach combining GOES satellite observations and in situ data. We propose an original observation function based on a joint probability distribution and taking advantages of the characteristics of both the involved type of data. The statistical results are compared with those of existing estimation methods and they are found to be in accordance with them. The daily bias ranges from -12 W/m² (-6% of the mean of measurements) to 12 W/m² (6%), depending on the stations. The daily root mean square difference ranges between 23 W/m² (10%) and 27 W/m² (15%). The correlation coefficient is close to 0.92. There is no seasonal climatic effect on the method, the bias and RMSD remain similar for both the rainy and the dry season, but better correlation is observed in the rainy season than in the dry season. Uncertainties are mainly due to the presence of specific tropical atmospheric conditions during the dry season. The method has been tested through various tests: cross-validation scheme has highlighted the potential generalization of the model in a temporal dimension; the ability of the method to effectively duplicate anomalies in surface solar irradiance time series has also been tested. The robustness of the results shows the interest of the method compared to other existing estimation methods. Because of its simplicity of implementation this method opens new prospects in estimating surface solar irradiance. It is concluded that using a particle filter and original observation function method allow a high-quality surface solar irradiance estimation in French Guiana.RESUMEUne méthode d'estimation de l'irradiance solaire de surface (SSI) à partir de données satellites GOES est présentée et validée par comparaison avec trois années de mesures in situ provenant de six stations météorologiques de Guyane Française. Dans cet article, nous proposons une approche par filtre particulaire combinant observations du satellite GOES et données in situ. Nous proposons une fonction d'observation originale basée sur une distribution de probabilité conjointe des deux types de données. Les résultats statistiques sont conformes à ceux des méthodes existantes. Le biais journalier varie de -16 W / m² (-7% de la moyenne des mesures) à 12 W / m² (6%). L'erreur quadratique moyenne (RMSD) est comprise entre 23 W / m² (10%) et 27 W / m² (15%). Le coefficient de corrélation est de 0,92. La méthode est peu sensible aux variations climatiques saisonnières, le biais et RMSD restent similaires en saison des pluies comme en saison sèche, mais une meilleure corrélation est observée pendant la saison des pluies. Les incertitudes sont principalement dues à la présence de conditions atmosphériques tropicales spécifiques en saison sèche. La méthode a été soumise à différents tests : un processus de validation croisée a mis en évidence la possible généralisation du modèle dans une dimension temporelle, la capacité du modèle à reproduire efficacement des anomalies dans les séries temporelles d'irradiance solaire de surface a aussi été testée. La robustesse des résultats obtenus montrent l'intérêt du modèle par rapport aux autres méthodes d'estimation existantes. A cause de sa simplicité de mise en oeuvre cette méthode ouvre de nouvelles perspectives en matière d'estimation de l'irradiance solaire au sol. Nous concluons que l'utilisation d'un filtre particulaire combinée à une fonction d'observation originale permet une estimation de haute qualité de l'irradiance solaire au sol en Guyane Française.
Canadian Journal of Remote Sensing

meteo-01304574
https://hal-meteofrance.archives-ouvertes.fr/meteo-01304574
DOI : 10.1080/07038992.2015.1040150

Éditeur(s) : HAL CCSD
Résumé : Modern measures of diversity satisfy reasonable axioms, are parameterized to produce diversity profiles, come with an effective number of species to simplify their interpretation, and estimators to apply them to real data. Generalized Simpson's entropy has all of these features and can be used as a measure of biodiversity. Moreover, unlike most commonly used diversity indices, it has unbiased estimator, which allows for robust estimation of the diversity of poorly sampled, rich communities.
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738

hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738/file/GSimpson.pdf

Éditeur(s) : IEEE Geoscience and Remote Sensing Society
Résumé : The Medium Resolution Imaging Spectrometer (MERIS) launched in March 2002 and has been providing images since June 2002. Before its launch, we had implemented a method to improve its resolution by merging its images with Landsat Enhanced Thematic Mapper images in order to preserve the best characteristics of the two images (spatial, spectral, temporal). We now present the results of this method for real MERIS images (level 1b and 2) in a coastal area. The robustness of the method is studied as well as the influence of the delay between the acquisitions of the two images.
IEEE Geoscience and Remote Sensing Letters (1545-598X) (IEEE Geoscience and Remote Sensing Society), 2006-04 , Vol. 3 , N. 2 , P. 227-231

Droits : 2006 IEEE
http://archimer.ifremer.fr/doc/2006/publication-2119.pdf
DOI:10.1109/LGRS.2005.861699
http://archimer.ifremer.fr/doc/00000/2119/

Éditeur(s) : Amer Geophysical Union
Résumé : We quantify, analyze, and characterize the frequency-dependent microseismic noise recorded by worldwide distributed seismic stations. Microseismic noise is generated through the interaction of ocean waves. It is the strongest ambient noise, and it is observed everywhere on Earth. We introduce a new approach which permits us to detect polarized signals in the time-frequency domain and which we use to characterize the microseismic noise. We analyze 7 years of continuous seismograms from the global GEOSCOPE network. Microseisms are dominated by Rayleigh waves, and we therefore focus on elliptically polarized signals. The polarized signals are detected in the time-frequency domain through a degree of polarization measure. We design polarization spectra and show that microseismic noise is more strongly polarized than noise in other frequency bands. This property is used to measure the directions of the polarized noise at individual stations as a function of time and frequency. Seasonal variations are found for the back azimuths and for the number of polarized signals at many stations. We show that the back azimuth directions are robust measurements that point toward the source areas computed from ocean wave models.
Geochemistry Geophysics Geosystems (1525-2027) (Amer Geophysical Union), 2011-07 , Vol. 12 , N. Q07014 , P. 14 p.

Droits : 2011. American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00041/15219/12713.pdf
DOI:10.1029/2011GC003661
http://archimer.ifremer.fr/doc/00041/15219/

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Résumé : Les graphes définis à partir de structures algébriques possèdent d’excellentes propriétés de symétries particulièrement intéressantes. L’exemple le plus flagrant est la notion de graphe de Cayley qui s’est révélée très riche non seulement du point de vue théorique mais aussi pratique par ses applications à de nombreux domaines incluant l’architecture des réseaux ou les machines parallèles. Néanmoins, la régularité des graphes de Cayley se révèle parfois être une limite étant donné qu’ils sont toujours sommet-transitifs et donc en particulier non pertinents pour générer des réseaux semiréguliers.Cette observation a motivé, en 2005, la définition d’une nouvelle classe de graphes définis à partir d’un groupe, appelés G-graphes. Ils possèdent aussi de nombreuses propriétés de régularité mais de manière moins restrictive.Cette thèse propose un nouveau regard sur cette classe de graphes par une approche plutôt orientée recherche opérationnelle alors que la grande majorité des études précédentes est dominée par des approches essentiellement algébriques. Nous-nous sommes alors intéressés à plusieurs questions :— La caractérisation des G-graphes : nous proposons des améliorations par rapport aux précédents résultats.— Identifier des classes de graphes comme des G-graphes grâce à des isomorphismes ou en utilisant le théorème de caractérisation.— Etudier la structure et les propriétés de ces graphes, en particulier pour de possibles applications aux réseaux : colorations semi-régulières, symétries et robustesse.— Une approche algorithmique pour la reconnaissance de cette classe avec notamment un premier exemple de cas polynomial lorsque le groupe est abélien.
Interactions between graph theory and group theory have already led to interesting results for both domains. Graphs defined from algebraic groups have highly symmetrical structure giving birth to interesting properties. The most famous example is Cayley graphs, which revealed to be particularly interesting both from a theoretical and a practical point of view due to their applications in several domains including network architecture or parallel machines. Nevertheless, the regularity of Cayley graphs is also a limit as they are always vertex-transitive and therefore not relevant to generate semi-regular networks. This observation motivated the definition, in 2005, of a new family of graphs defined from a group, called G-graphs. They also have many regular properties but are less restrictive. These graphs are in particular semi-regular k-partite, with a chromatic number k directly given in the group representation and they can be either transitive or not.This thesis proposes a new insight into this class of graphs using an approach based on operational research while most of previous studies have been so far dominated by algebraic approaches. Then, the thesis addresses different kind of questions:— Characterizing G-graphs: we propose improvements of previous results.— Identifying some classes of graphs as G-graphs through isomorphism or using the characterization theorem.— Studying the structure and properties of these graphs, in particular for possible applications to networks: semi-regular coloring, symmetries and robustness.— Algorithmic approach for recognizing this class with a first example of polynomial case when the group is abelian.

http://www.theses.fr/2014AGUY0787/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
As climate change continues to impact socio-ecological systems, tools that assist conservation managers to understand vulnerability and target adaptations are essential. Quantitative assessments of vulnerability are rare because available frameworks are complex and lack guidance for dealing with data limitations and integrating across scales and disciplines. This paper describes a semi-quantitative method for assessing vulnerability to climate change that integrates socio-ecological factors to address management objectives and support decision-making. The method applies a framework first adopted by the Intergovernmental Panel on Climate Change and uses a structured 10-step process. The scores for each framework element are normalized and multiplied to produce a vulnerability score and then the assessed components are ranked from high to low vulnerability. Sensitivity analyses determine which indicators most influence the analysis and the resultant decision-making process so data quality for these indicators can be reviewed to increase robustness. Prioritisation of components for conservation considers other economic, social and cultural values with vulnerability rankings to target actions that reduce vulnerability to climate change by decreasing exposure or sensitivity and/or increasing adaptive capacity. This framework provides practical decision-support and has been applied to marine ecosystems and fisheries, with two case applications provided as examples: (1) food security in Pacific Island nations under climate-driven fish declines, and (2) fisheries in the Gulf of Carpentaria, northern Australia. The step-wise process outlined here is broadly applicable and can be undertaken with minimal resources using existing data, thereby having great potential to inform adaptive natural resource management in diverse locations.
ISSN: 0308-597X

hal-01380403
https://hal-univ-perp.archives-ouvertes.fr/hal-01380403
DOI : 10.1016/j.marpol.2016.09.024

Éditeur(s) : Elsevier Science Bv
Résumé : The timing, routing and processes of sediment transfer from the continents to the oceans at millennial time-scale are still largely unknown. The potential of turbidite systems (dominantly deposited during sea-level lowstands) to record global or regional environmental fluctuations is usually under-exploited because of the difficulty to obtain robust chronostratigraphic constraints in turbiditic deposits, and therefore to tie changes in sedimentary processes to environmental fluctuations. We were able to obtain a millennial-scale chronostratigraphy based on oxygen isotopes of the scarce foraminifera preserved in turbiditic deposits of the Rhone Turbidite System within the Western Mediterranean. Our results show that 1) objective criteria can be defined for the selection of foraminifera preserved within the pelagic intervals between the turbiditic sequences, in order to obtain a reliable isotope stratigraphy; 2) Turbidites triggered by hyperpycnal currents are described for the first time within the Rhone Turbidite System. They are related to the periods of direct fluvial connection with the canyon head (during the sea-level lowstand and early rise), and to a period of high sediment flux in relation with the massive recession of the Rhone glaciers in the Alps; 3) The lithofacies change passing from hyperpycnal to “Bouma-type” is dated at ca 19 cal. ka BP, which might correspond to an acceleration of sea-level rise (19-ka Meltwater Pulse,).
Sedimentary Geology (0037-0738) (Elsevier Science Bv), 2015-06 , Vol. 323 , P. 148-166

Droits : 2015 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00266/37712/35730.pdf
DOI:10.1016/j.sedgeo.2015.04.009
http://archimer.ifremer.fr/doc/00266/37712/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
We study the convergence of the Mann Iteration applied to the partial complement of a firmly nonexpansive operator with respect to a linear subspace of a Hilbert space. A new concept considered here. A regularized version is also proposed. Furthermore, to motivate this concept, some applications to robust regression procedures and location problems are proposed.
ISSN: 1862-4472

hal-00776655
https://hal.univ-antilles.fr/hal-00776655
DOI : 10.1007/s11590-009-0172-3

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l’Oyapock (French Guiana). Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l’Oyapock. The final cross-validated model integrated two landscape variables—dense forest surface and built surface—together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner.
ISSN: 1932-6203

hal-01383486
https://hal.archives-ouvertes.fr/hal-01383486
https://hal.archives-ouvertes.fr/hal-01383486/document
https://hal.archives-ouvertes.fr/hal-01383486/file/Adde_et_al_PlosONE_2016.pdf
DOI : 10.1371/journal.pone.0164685