Éditeur(s) : HAL CCSD
Résumé : International audience
The study of complex biological processes requires to forgo simplified models for extensive ones. Yet, these models' size and complexity place them beyond understanding. Their analysis requires new methods for identifying general patterns. The Transforming Growth Factor TGF-β is a multifunctional cytokine that regulates mammalian cell development , differentiation, and homeostasis. Depending on the context, it can play the antagonistic roles of growth inhibitor or of tumor promoter. Its context-dependent pleiotropic nature is associated with complex sig-naling pathways. The most comprehensive model of TGF-β-dependent signaling is composed of 15,934 chains of reactions (trajectories) linking TGF-β to at least one of its 159 target genes. Identifying functional patterns in such a network requires new automated methods. This article presents a framework for identifying groups of similar trajec-tories composed of the same molecules using an exhaustive and without prior assumptions approach. First, the trajectories were clustered using the Relevant Set Correlation model, a shared nearest-neighbors clustering method. Five groups of trajectories were identified. Second, for each cluster the over-represented molecules were determined by scoring the frequency of each molecule implicated in trajectories. Third, Gene set enrichment analysis on the clusters of trajectories revealed some specific TGF-β-dependent biological processes, with different clusters associated to the antagonists roles of TGF-β. This confirms that our approach yields biologically-relevant results. We developed a web interface that facilitates graph visualization and analysis. Our clustering-based method is suitable for identifying families of functionally-similar trajectories in the TGF-β signaling network. It can be generalized to explore any large-scale biological pathways.
CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology
Darmstadt, France

hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249/document
https://hal.archives-ouvertes.fr/hal-01559249/file/JeanCoquet_CMSB.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
La recherche de liens conceptuels fréquents (FCL) est une nouvelle approche de clustering de réseaux, qui exploite à la fois la structure et les attributs des noeuds. Bien que les travaux récents se soient déjà intéressés à l’optimisation des algorithmes de recherche des FCL, peu de travaux sont aujourd’hui menés sur la complémentarité qui existe entre les liens conceptuels et l’approche classique de clustering qui consiste en l’extraction de communautés. Ainsi dans ce papier, nous nous intéressons à ces deux approches. Notre objectif est d’évaluer les relations potentiellement existantes entre les communautés et les FCL pour comprendre la façon dont les motifs obtenus par chacune des méthodes peuvent correspondre ou s’intersecter ainsi que la connaissance utile résultant de la prise en compte de ces deux types de connaissance. Nous proposons pour cela un ensemble de mesures originales, basées sur la notion d’homogénéité, visant à évaluer le niveau d’intersection des FCL et des communautés lorsqu’ils sont extraits d’un même jeu de données. Notre approche est appliquée à deux réseaux et démontre l’importance de considérer simultanément plusieurs types de connaissance et leur intersection.
Extraction et gestion des connaissances
Rennes, France

hal-01312560
https://hal.archives-ouvertes.fr/hal-01312560

Éditeur(s) : HAL CCSD
Résumé : Integrating ecological connectivity into marine ecosystem management and planning is important, especially in a global context of severe fish stocks depletion and growing habitat degradation. Environmental tools such as Marine Protected Areas have been proposed to protect biodiversity, restore damaged ecosystems, sustain fisheries, and rebuild overexploited stocks. The effectiveness of marine protected areas depends in part on the maintenance of connectivity between marine populations, linked by ecological processes such as larval dispersal. In this thesis, we applied a biophysical model driven by ocean currents derived from satellite altimetry to evaluate connectivity between Western Indian Ocean reefs and across the current MPA system in the Mediterranean Sea. We applied different methods of analysis such as graph-theoretic and clustering. In the Western Indian Ocean, marine connectivity analyses show that the number of connections between reefs increases with fish pelagic larval duration. It also highlights a low connectivity across the region and a high interconnectivity within several regions (Mozambique Channel, Mascarene archipelago). In the Mediterranean Sea, connectance is globally low at the regional scale. This connectance is more important in Western than Eastern Mediterranean. Moreover, the marine connectivity analyses revealed high domestic connectivity rates. Depending on the study area, priority reefs or sites for MPA implementation are proposed. Finally, implications for transboundary marine policies and regional cooperation are discussed.
Intégrer les connaissances sur la connectivité écologique dans la gestion des écosystèmes marins est essentiel, surtout dans un contexte d'appauvrissement des ressources marines et de dégradation des habitats côtiers à l'échelle mondiale. Des outils environnementaux, tels que les Aires Marines Protégées ont été mises en œuvre pour protéger la biodiversité, restaurer les écosystèmes endommagés, soutenir les pêcheries et reconstituer les stocks surexploités. Leur efficacité dépend en partie du maintien de la connectivité entre les populations marines, assurée à travers divers processus écologiques dont la dispersion larvaire. Dans le cadre de ce travail de thèse, un modèle biophysique intégrant des données de courants, issues de mesures d'altimétrie par satellite, a été utilisé pour évaluer la connectivité entre les récifs de l'océan Indien d'une part, et à travers le réseau d'AMP de Méditerranée d'autre part. Différentes méthodes d'analyse ont été utilisées, telles que la théorie des graphes et le clustering. Dans l'océan Indien occidental, l'analyse des connectivités marines montre que le nombre de connexions entre les récifs augmente avec la durée de vie larvaire des poissons. Elle met également en évidence une faible connectivité à l'échelle de la région, mais une forte inter-connectivité au sein de plusieurs sous-régions (Canal du Mozambique, Mascareignes). En Méditerranée, la connectance est globalement faible à l'échelle régionale, bien que plus importante dans le bassin occidental que le bassin oriental. L'analyse des connectivités marines montre également un taux de connectivité élevé à l'échelle d'un même pays. Selon le cas d'étude, une liste de récifs ou de sites prioritaires dans la mise en œuvre des AMP a été proposée. Enfin, les implications de ces résultats en termes de politiques transfrontalières et de coopération régionale sont discutées.
https://tel.archives-ouvertes.fr/tel-01269631

NNT : 2015LARE0003
tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631
https://tel.archives-ouvertes.fr/tel-01269631/document
https://tel.archives-ouvertes.fr/tel-01269631/file/2015lare0003_ECrochelet.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
The extraction of knowledge from social networks is an area that has experienced significant growth in recent years. Indeed, thanks to the improvement of storage and calculation capacities, and the heterogeneity of data that can currently be extracted, much effort has been made to go beyond traditional knowledge, by proposing new kinds of patterns that take into account the context. However, while many works were interested in designing new patterns of knowledge or in optimizing existing approaches, few studies have been focused in merging patterns and on the useful knowledge emerging from such fusions. In this work, we focus on two network clustering approaches, able to extract two distinct kinds of patterns, and we seek to understand both the intersections that can exist between them and the knowledge that emerges from their fusion. The first is the classical nodes clustering approach that consists in searching for communities into a network. The second is the search for frequent conceptual links, a new link clustering approach that aims identifying frequent links between groups of nodes sharing common attributes. We propose a set of original measures that aim to evaluate the amount of shared information between these patterns when they are extracted from a same network. These measures are applied to three datasets and demonstrate the interest in simultaneously considering several sources of knowledge.
Advances in Knowledge Discovery and Management (AKDM)

hal-01514227
https://hal.archives-ouvertes.fr/hal-01514227
DOI : 10.1007/978-3-319-45763-5_13

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Numerous methods have been proposed in order to perform clustering from social networks. While significant works have been carried out on the design of new approaches, able to search for various kinds of clusters, a major challenge concerns the scalability of these approaches. Indeed, given the mass of data that can now be collected from online social networks, particularly from social platforms, it is important to have efficient methods for exploring and analyzing these very large amount of data. One of the recent social network clustering approaches is the extraction of conceptual links, a new approach that performs link clustering by exploiting both the structure of the network and attributes of nodes to identify strong links between groups of nodes in which nodes share common attributes. In this paper, we focus on the optimization of the search for conceptual links. In particular, we propose PALM, a parallel algorithm that aims to improve the efficiency of the extraction by simultaneously exploring several areas of the search space. For this purpose, we begin by demonstrating that the solution space forms a concept lattice. Then, we propose an approach that explores in parallel the branches of the lattice while reducing the search space based on various properties of conceptual links. We demonstrate the efficiency of the algorithm by comparing the performances with the original extraction approach. The results obtained show a significant gain on the computation time.
28th International Conference on Database and Expert Systems Applications (DEXA)
Lyon, France

hal-01637554
https://hal.archives-ouvertes.fr/hal-01637554
DOI : 10.1007/978-3-319-64471-4_21

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

Éditeur(s) : Wiley-blackwell
Résumé : Aim The aims of this study were: (1) to identify global communities of tuna and billfish species through quantitative statistical analyses of global fisheries data; (2) to describe the spatial distribution, main environmental drivers and species composition of each community detected; and (3) to determine whether the spatial distribution of each community could be linked to the environmental conditions that affect lower trophic levels by comparing the partitions identified in this study with Longhursts biogeochemical provinces. Location The global ocean from 60 degrees S to 65 degrees N. Methods We implemented a new numerical procedure based on a hierarchical clustering method and a nonparametric probabilistic test to divide the oceanic biosphere into biomes and ecoregions. This procedure was applied to a database that comprised standardized data on commercial longline catches for 15 different species of tuna and billfish over a period of more than 50 years (i.e. 1953-2007). For each ecoregion identified (i.e. characteristic tuna and billfish community), we analysed the relationships between species composition and environmental factors. Finally, we compared the biogeochemical provinces of Longhurst with the ecoregions that we identified. Results Tuna and billfish species form nine well-defined communities across the global ocean. Each community occurs in regions with specific environmental conditions and shows a distinctive species composition. High similarity (68.8% homogeneity) between the spatial distribution of the communities of tuna and billfish and the biogeochemical provinces suggests a strong relationship between these species and the physical and chemical characteristics of the global ocean. Main conclusions Despite their high tolerance for a wide range of environmental conditions, these highly migratory species are partitioned into clear geographical communities in the ocean at a global scale. The similarity between biogeochemical and biotic divisions in the ocean suggests that the global ocean is a mosaic of large biogeographical ecosystems, each characterized by specific environmental conditions that have a strong effect on the composition of the trophic web.
Journal Of Biogeography (0305-0270) (Wiley-blackwell), 2012-01 , Vol. 39 , N. 1 , P. 114-129

Droits : 2011 Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00060/17141/14716.pdf
DOI:10.1111/j.1365-2699.2011.02582.x
http://archimer.ifremer.fr/doc/00060/17141/

Éditeur(s) : HAL CCSD
Résumé : International audience
In this article, we analyse a collaborative network to understand the underlying patterns that structure the co-writing process of scientific articles. Our goal is to identify and understand the collaboration tendencies from authors publishing activities. For this purpose, we adopt a descriptive modelling through a network approach that consists first in generating the collaborative network from data on publications. Nodes of the network are then enriched with a set of individual attributes extracted from the publishing activity of each author. Finally, we search for conceptual views, a recent link clustering approach, which allows to summarize any kind of networks by highlighting the sets of attributes found frequently linked. Results show that it exists strong tendencies that unconsciously structure the collaboration behaviours. In this paper, we present these tendencies and show how they evolve according to different extraction thresholds.
EEE/ACM International Conference on Advances in Social Networks Analysis and Mining
Sydney, Australia

hal-01637563
https://hal.archives-ouvertes.fr/hal-01637563
DOI : 10.1145/3110025.3110146

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
ABSTRACT: BACKGROUND: Climate change poses unprecedented challenges, ranging from global and local policy challenges to personal and social action. Heat-related deaths are largely preventable, but interventions for the most vulnerable populations need improvement. Therefore, the prior identification of high risk areas at the community level is required to better inform planning and prevention. We aimed to demonstrate a simple and flexible conceptual framework relying upon satellite thermal data and other digital data with the goal of easily reproducing this framework in a variety of urban configurations. RESULTS: The study area encompasses Rennes, a medium-sized French city. A Landsat ETM + image (60 m resolution) acquired during a localized heatwave (June 2001) was used to estimate land surface temperature (LST) and derive a hazard index. A land-use regression model was performed to predict the LST. Vulnerability was assessed through census data describing four dimensions (socio-economic status, extreme age, population density and building obsolescence). Then, hazard and vulnerability indices were combined to deliver a heatwave health risk index. The LST patterns were quite heterogeneous, reflecting the land cover mosaic inside the city boundary, with hotspots of elevated temperature mainly observed in the city center. A spatial error regression model was highly predictive of the spatial variation in the LST (R2 = 0.87) and was parsimonious. Three land cover descriptors (NDVI, vegetation and water fractions) were negatively linked with the LST. A sensitivity analysis (based on an image acquired on July 2000) yielded similar results. Southern areas exhibited the most vulnerability, although some pockets of higher vulnerability were observed northeast and west of the city. The heatwave health risk map showed evidence of infra-city spatial clustering, with the highest risks observed in a north--south central band. Another sensitivity analysis gave a very high correlation between 2000 and 2001 risk indices (r = 0.98, p < 10-12). CONCLUSIONS: Building on previous work, we developed a reproducible method that can provide guidance for local planners in developing more efficient climate impact adaptations. We recommend, however, using the health risk index together with hazard and vulnerability indices to implement tailored programs because exposure to heat and vulnerability do not require the same prevention strategies.
ISSN: 1476-072X

inserm-00762303
http://www.hal.inserm.fr/inserm-00762303
http://www.hal.inserm.fr/inserm-00762303/document
http://www.hal.inserm.fr/inserm-00762303/file/1476-072X-11-38.pdf
DOI : 10.1186/1476-072X-11-38

Éditeur(s) : HAL CCSD
Résumé : National audience
Traditional network generation models attempt to replicate global structural properties (degree distribution, average distance, clustering coefficient, communities, etc.) through synthetic link formation mechanisms such as triadic closure or preferential attachment. In this work, we study the evolution of a very big communication network coming from mobile telephony and we analyse the link formation process. A first study conducted on the standard mechanisms allows observing that several mechanisms are responsible for the properties observed in this network. In a second study, we characterize more precisely the link formation process by searching for correlations between the probability of creating a new link and some individual properties such as the degree, the clustering coefficient and the age of the nodes.
Conférence sur les modèles et l'analyse des réseaux : Approches mathématiques et informatiques
Saint-Etienne, France

hal-00873990
https://hal.archives-ouvertes.fr/hal-00873990

Éditeur(s) : HAL CCSD American Physiological Society
Résumé : Full text: http://jn.physiology.org/content/88/3/1475
International audience
The contribution of voltage-gated calcium channels (VGCC) to the development of cultured embryonic cockroach brain neurons was assessed using pharmacological agents. VGCC currents were recorded using the patch-clamp technique and were found to be blocked dose-dependently by micromolar concentrations of mibefradil. The activation and inactivation properties of the calcium channels enable a sizeable calcium current to flow at rest (about -30 and -20 mV in high-potassium culture media). As expected, the cytoplasmic-free calcium concentration was found to rise when the extracellular potassium concentration was raised from 3 to 15 and 30 mM. The effects of VGCC blockers and calcium chelators were different in fresh and in mature cultures in which the neurons were connected to each other to form a defined network. In fresh cultures, the two non-selective VGCC blockers (verapamil and mibefradil) induced a dose-dependent cell death that was proportional to their blocking effect on I(Ba). This effect could not be prevented by addition of fetal calf serum to the culture medium. A similar effect was obtained using intra- or extracellular calcium chelating agents (10 microM BAPTA-AM or 10 mM EGTA). Quite unexpectedly, blockade of the P/Q-like (omega-Aga WA-sensitive) component of the calcium current by 500 nM of omega-AgaTx IVA had no lethal effect, suggesting that the corresponding channels are not involved in the survival mechanism. As expected from their lack of effect on I(Ba), isradipine, nifedipine, and omega-CgTx GVIA did not induce cell death. When the neurons started growing neurites, their sensitivity to calcium channel blockade by mibefradil decreased, indicating a correlation between neurite outgrowth and resistance to calcium depletion. In mature cultures, the neurons became resistant to mibefradil, verapamil, and BAPTA-AM. However, these agents, as well as omega-AgaTx IVA, had a significant inhibitory effect on the increase in diameter of the connectives that linked adjacent clusters of neurons. This effect has been shown to result, in the case of mibefradil, from an inhibition of neurite outgrowth characterized by a significant reduction of the number of primary neurites and secondary branchings but not to a significant modification of the diameter of individual neurites. These results support the view that, as in vertebrates, calcium influx through VGCC plays an important role in survival and neurite outgrowth of cultured embryonic insect neurons. The differential contribution of the P/Q-like and R-like (omega-Aga WA-sensitive) calcium channels in these processes is discussed.
ISSN: 0022-3077

hal-00982287
https://hal.archives-ouvertes.fr/hal-00982287
DOI : 10.1152/jn.00749.2001
PUBMED : 12205168

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Few studies have explored how noise might contribute to social health inequalities, and even fewer have considered infant mortality or its risk factors as the health event of interest.In this paper, we investigate the impact of neighbourhood characteristics - both socio-economic status and ambient noise levels - on the spatial distribution of infant mortality in the Lyon metropolitan area, in France. METHODS: All infant deaths (n = 715) occurring between 2000 and 2009 were geocoded at census block level. Each census block was assigned multi-component socio-economic characteristics and Lden levels, which measure exposure to noise. Using a spatial-scan statistic, we examined whether there were significant clusters of high risk of infant mortality according to neighbourhood characteristics. RESULTS: Our results highlight the fact that infant mortality is non-randomly distributed spatially, with clusters of high risk in the south-east of the Lyon metropolitan area (RR = 1.44; p = 0.09). After adjustments for socio-economic characteristics and noise levels, this cluster disappears or shifts according to in line with different scenarios, suggesting that noise and socio-economic characteristics can partially explain the spatial distribution of infant mortality. CONCLUSION: Our findings show that noise does have an impact on the spatial distribution of mortality after adjustments for socio-economic characteristics. A link between noise and infant mortality seems plausible in view of the three hypothetical, non-exclusive, pathways we propose in our conceptual framework: (i) a psychological pathway, (ii) a physiological disruption process and (iii) an unhealthy behaviours pathway. The lack of studies makes it is difficult to compare our findings with others. They require further research for confirmation and interpretation.
ISSN: 1476-069X

Droits : info:eu-repo/semantics/OpenAccess
inserm-00924503
http://www.hal.inserm.fr/inserm-00924503
http://www.hal.inserm.fr/inserm-00924503/document
http://www.hal.inserm.fr/inserm-00924503/file/1476-069X-12-109.pdf
PUBMED : 24341620

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper deals with data structures within GIS. Continuous phenomenons are usually represented by raster structures for simplicity reasons. With such structures spatial repartitions of the data is not easily interpretable. Moreover, in an overlapping clustering context these structures remove the links between the data and the algorithms. We propose a vector representation of such data based on non-regular multi-rings polygons. The structure requires multipart nested polygons and new set operations. We present the formalism based on belief theory and uncertainty reasoning. We also detail the implementation of the structures and the set operations. The structures and the set operations are illustrated in the context of forest classification having diffuse transitions.
IF&GIS
Shangai, China

hal-01514239
https://hal.archives-ouvertes.fr/hal-01514239

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Vibrioses are the predominant bacterial infections in marine shrimp farms. Vibrio nigripulchritudo is an emerging pathogen of the cultured shrimp Litopenaeus stylirostris in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have revealed that recent pathogenic V. nigripulchritudo isolates from New Caledonia all cluster into a monophyletic clade and contain a small plasmid, pB1067. Here, we report that a large plasmid, pA1066 (247 kb), can also serve as a marker for virulent V. nigripulchritudo, and that an ancestral version of this plasmid was likely acquired prior to other virulence-linked markers. Additionally, we demonstrate that pA1066 is critical for the full virulence of V. nigripulchritudo in several newly developed experimental models of infection. Plasmid pB1067 also contributes to virulence; only strains containing both plasmids induced the highest level of shrimp mortality. Thus, it appears that these plasmids, which are absent from non-pathogenic isolates, may be driving forces, as well as markers, for the emergence of a pathogenic lineage of V. nigripulchritudo.
Environmental Microbiology (1462-2912) (Wiley-blackwell Publishing, Inc), 2011-02 , Vol. 13 , N. 2 , P. 296-306

Droits : 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
http://archimer.ifremer.fr/doc/00031/14196/11469.pdf
DOI:10.1111/j.1462-2920.2010.02329.x
http://archimer.ifremer.fr/doc/00031/14196/

Éditeur(s) : HAL CCSD IRD
Résumé : International audience
Malaria remains a major health problem in French Guiana despite the decrease in the number of cases since 2010. A previous study in Camopi, an Amerindian village on the Oyapock River, revealed that Plasmodium falciparum malaria incidence was significantly related to landscape features and that its spatial distribution exhibited some obvious patterns. In the present study, we first identified the spatial patterns that exhibit a significant Moran's index of spatial auto-correlation and that significantly explain P. falciparum malaria incidence within the multiple linear regression framework. Secondly, we linked these patterns with remotely sensed environmental features. The selected model is composed of five spatial components: three patterns, representing 50.7% of the total variance, are associated with large scale variations of the incidence, and the remaining patterns are associated with local scale variations and represent 28.7% of the total variance. Different hamlet clusters that have specificities in terms of P. falciparum malaria incidence rate, environmental characteristics and mosquito control strategies have been identified. The methodology proposed in the present study can provide useful knowledge on the spatial distribution of the P. falciparum malaria incidence in Camopi at different scales and on possible explanation of such distribution, as a function of the scale.
Symposium of the Latin American Society for Remote Sensing and Spatial Information Systems (SELPER)
Cayenne, French Guiana

ird-00797353
http://hal.ird.fr/ird-00797353
http://hal.ird.fr/ird-00797353/document
http://hal.ird.fr/ird-00797353/file/Roux_et_al_SELPER_2012.pdf
IRD : fdi:010058342

Éditeur(s) : Amer Soc Microbiology
Résumé : A molecular typing study on Vibrio strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian V. penaeicida isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of Vibrio spp. and their implication in shrimp disease in aquaculture.
Applied And Environmental Microbiology (0099-2240) (Amer Soc Microbiology), 1999-03 , Vol. 65 , N. 3 , P. 1145-1151

Droits : American society for microbiology
http://archimer.ifremer.fr/doc/1999/publication-2734.pdf
http://archimer.ifremer.fr/doc/00000/2734/

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
he search for frequent conceptual links (FCL) is a new network clustering approach that exploits both the network structure and the node properties. While recent works have been focused on the optimisation of the FCL extraction, no study has been conducted on the matching or the intersections between the conceptual links and the classical clustering approach which consists in extracting communities. In this paper, we focus on these two approaches. Our objective is to evaluate the possible relationships existing between FCL and communities to understand how the patterns obtained by each kind of methods may match as well as the useful knowledge resulting from the intersections of these two kinds of knowledge. For this purpose, we propose a set of original measures, based on the notion of homogeneity, assessing the level of shared information between these patterns when they are extracted from the same dataset. The measures are applied on three datasets and demonstrate the importance of considering simultaneously various kinds of knowledge and their intersections.
ISSN: 1869-5450

hal-01312313
https://hal.archives-ouvertes.fr/hal-01312313
DOI : 10.1007/s13278-014-0197-1

Éditeur(s) : HAL CCSD
Résumé : International audience
Numerous social network mining methods have been proposed until now for addressing social mining tasks and specially searching for communities or frequent social patterns. However, the degree of complementarity of these methods has been very little studied. In this paper, we focus on two knowledge extraction processes in social networks: a link-based clustering that may extract social communities and a recent approach that searches for frequent conceptual link involving both clustering and search for frequent social patterns. We explore how the models extracted by each method may match and which potential useful knowledge they may provide. Our objective is to evaluate the potential relationships between communities and frequent conceptual links. For this purpose, we propose a set of measures for evaluating the degree to which these patterns extracted from the same dataset are matching. Our approach is applied on two datasets and demonstrates the importance of considering simultaneously various kinds of knowledge and their complementarity.
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining
Niagara falls, Canada

hal-00874351
https://hal.archives-ouvertes.fr/hal-00874351

Éditeur(s) : HAL CCSD
Résumé : International audience
We focus on some French BTS (Brevet de Technicien Supérieur / Advanced Technician Certificate), namely tourism and assistant manager, which are two important diplomas for the local development and in which microeconomic and management sciences plays a great part. The French BTS is a short Vocational Diploma prepared in two years after the “baccalauréat”, with national programs and evaluation criteria.The successful candidates are supposed to be immediately employable, especially in their local geographical environment. Thus, there exists a paradox between the national definition of the diploma and the local contexts of teaching and (supposed) professional integration. However, the professional traineeship plays a great part in this diploma. For this reason, it seems interesting to investigate how the conception of students evolve, with respect to the aforementioned paradox, during and after professional traineeship. For this purpose, questionnaire surveys have been carried out at various moment of the scholar during two years (two cohorts).The main results can be summarized as follows. The professional traineeship is positively perceived by the students at the beginning of the training. They consider it as very important for the development of professional skills. Over time, this positive representation progresses homogeneously. The students are convinced ofthe efficiency of professional traineeship: their professional project strengthened but, they also realize that their professional future will not necessarily be in Guadeloupe. This is probably linked with a better representation of the economic situation of Guadeloupe and shows, as excepted, that the context of the professional traineeship modifies the representation of students. For the BTS assistant manager, we specially note a degradation of the representation of the profession of assistant manager, whereas this training’s choice was realized with conviction.
20th GENERAL ASSEMBLY AND BIENNAL MEETING “ Biodiversity, Energy, Risks and Health from scientific knowledge to the emergence of innovative development strategies in the Caribbean”
Deshaies, Guadeloupe

hal-01535042
https://hal.univ-antilles.fr/hal-01535042