Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study constitutes one of the few works conducted on the colonization of recent lava flows by fish communities in coral reef environment. It attempted to describe the mechanisms of colonization and environmental variables infuencing the structure of communities on the lava flows of the Piton de la Fournaise volcano at Reunion Island. It also proposed some hypotheses on the mechanisms of selection and speciation of endemic species of thesouthwestern Indian Ocean region, particularly diversified on the most recent lava flows of the Piton de la Fournaise, and provided a model of distribution of environmental and fish assemblage variables in four homogeneous patterns of colonization (landscapes) retained within the study area. The results showed fish community structure strongly related to measured environmental variables, of which depth, width of the island shelf, age of the lava flow and distance to the most recent lava flow were the most influential. It also appeared that the maximum endemic species richness was measured on the shallower stations, with narrow insular shelf, located on recent lava flows, near the lava flow from the eruption of 2007 (latest volcanic event). These characteristics define a harsh environment, to which endemic species seem well-adapted due in particular to their strong demographic and dietary flexibility. Finally, the patterns of colonization were characterized by significantly different environmental variables. The four homogeneous areas, defined by two geomorphological features, basalt blocks and drop-offs, nested within two locations, inside and outside the volcanic enclosure (current caldera), hosted fish communities whose dominant diets mainly depend on the nature, the abundance and the accessibility of available food resources. Overall, the study highlights that during early stages of ecological succession, site selection by fish communities is highly dependent on environmental constraints, specially of volcanic origin, but the physical habitat selection (geomorphology, substrate rugosity, percentage of soft substrate) seems to have littleimportance, while at least on the trophic structure and the distribution of endemic species.
ISSN: 0022-0981

hal-01253768
https://hal.archives-ouvertes.fr/hal-01253768
https://hal.archives-ouvertes.fr/hal-01253768/document
https://hal.archives-ouvertes.fr/hal-01253768/file/Pinault%20et%20al.%20-%202014%20-%20Fish%20community%20structure%20in%20relation%20to%20environmen_hal.pdf
DOI : 10.1016/j.jembe.2014.06.005

Éditeur(s) : HAL CCSD IEEE
Résumé : Object classification is a challenging task in computer vision. Many approaches have been proposed to extract meaningful descriptors from images and classifying them in a supervised learning framework. In this paper, we revisit the classic k-nearest neighbors (k-NN) classification rule, which has shown to be very effective when dealing with local image descriptors. However, k-NN still features some major drawbacks, mainly due to the uniform voting among the nearest prototypes in the feature space. In this paper, we propose a generalization of the classic k-NN rule in a supervised learning (boosting) framework. Namely, we redefine the voting rule as a strong classifier that linearly combines predictions from the k closest prototypes. To induce this classifier, we propose a novel learning algorithm, MLNN (Multiclass Leveraged Nearest Neighbors), which gives a simple procedure for performing prototype selection very efficiently. We tested our method on 12 categories of objects, and observed significant improvement over classic k-NN in terms of classification performances.
International Workshop on Image Analysis for Multimedia Interactive Services
Desenzano del Garda, Italy

hal-00481725
https://hal.archives-ouvertes.fr/hal-00481725
https://hal.archives-ouvertes.fr/hal-00481725/document
https://hal.archives-ouvertes.fr/hal-00481725/file/pbnn_wiamis_10.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
“Affective Computing is computing that relates to, arises from, or deliberately influences emotions” (R.W. Picard, MIT Press, 1997). Specifically, psychosocial equilibrium is now considered as a major issue for both individual and public health. Predicting human emotions via non-intrusive methods is a great challenge triggered by the rise of intelligent assisting systems. In order to determine the emotional state of a subject having a potential psychosocial disorder, it is required to process both neutral and expressive emotions. A computer-engineered method aiming to provide emotional information from videos is proposed. An original approach for affect classification and its interpretation is presented.The database is part of the HUMAINE database, and consists of a large volume of video clips, each displaying individuals, depressed or not, talking with a conversational agent. Both the high-dimensionality of data and its temporal aspect require a pre-training that consists of cleaning, sorting and feature selection, in order to make relevant information usable for further processing by MachineLearning methods. Next step consists in classifying the affective state of subjects according to their positivity or negativity (Russell's model, 1980). By means of six independent classifiers, each running a Support Vector Machine algorithm, separate performances are obtained for each class of emotions. The results reveal an interesting “neutral area phenomenon”, where emotions tend to be harder to be detected.Though more frequent, neutral emotions seem to carry less discriminant information than expressive ones. This issue will be a key for designing a tuning step in further research.
Caribbean Academy Of Science
Deshaies, France

hal-01408029
https://hal.univ-antilles.fr/hal-01408029

Éditeur(s) : HAL CCSD
Résumé : International audience
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation
Journal of Chemical Physics

hal-01263103
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01263103
DOI : 10.1063/1.4940149
PUBMED : 26801045

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Introduction: The selection of patients with metastatic clear cell renal cell carcinoma (ccRCC) who may benefit from targeted tyrosine kinase inhibitors has been a challenge, even more so now with the advent of new therapies. Hilar fat infiltration (HFI) is a validated prognostic factor in nonmetastatic ccRCC (TNM 2009 staging system) but has never been studied in metastatic patients. We aimed to assess its phenotype and prognostic effect in patients with metastatic ccRCC treated with first-line sunitinib.Materials and methods: In a multicentric study, we retrospectively included 90 patients and studied the corresponding ccRCC at the pathological, immunohistochemical, and molecular levels. Patient and tumor characteristics were compared using univariate and multivariate analysis. All the features were then studied by Cox models for prognostic effect.Results: HFI was found in 42 patients (46.7%), who had worse prognosis (Heng criteria) (P = 0.003), liver metastases (P = 0.036), and progressive diseases at first radiological evaluation (P = 0.024). The corresponding ccRCC was associated with poor pathological prognostic factors that are well known in nonmetastatic ccRCC. For these patients, median progression-free survival was 4 months vs. 13 months (P = 0.02), and median overall survival was 14 months vs. 29 months (P = 0.006). In a multivariate Cox model integrating all the variables, only poor prognosis, according to the Heng criteria and HFI, remained independently associated with both progression-free survival and overall survival.Conclusion: HFI was demonstrated for the first time to be an independent poor prognostic factor. Its potential role in predicting resistance to antiangiogenic therapy warrants further investigation.
ISSN: 1078-1439

hal-01632553
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01632553
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01632553/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01632553/file/Hilar%20fat%20infiltration_accepted.pdf
DOI : 10.1016/j.urolonc.2017.05.015

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Geomorphic landscape features have been suggested as indicators of forest diversity. However, their explanatory power has not yet been explicitly tested at a regional scale in tropical rainforest. We used forest inventories conducted according to a stratified sampling design (3,132 plots in 111 transects at 33 sites) and holistic multi-scale geomorphological mapping derived from a Shuttle Radar Topography Mission digital elevation model to describe and explain spatial patterns in floristic composition across French Guiana (80,000 km2). We measured and identified 123,906 trees with DBH C20 cm and used constrained and unconstrained ordinations to analyze variations in the abundance of 221 taxa and 51 families. Variance partitioning and variograms were used to detect spatial patterns in species composition, compare the explanatory power of spatial and environmentalfactors, and select the variables that best explain forest composition. Strong floristic patterns corresponded to a major latitudinal gradient and significant sub-regional floristic structure. Geomorphological landscapes shaped by historic climate fluctuations and major geological events successfully captured these patterns and explained the variation in abundance of 80 taxa, corresponding to 65 % of the inventoried trees. Our findings suggest that long-term forest dynamics are under substantial ‘‘geomorphographic control’’. A geomorphological perspective on landscapes that incorporates current and past environmental filters and historical biogeographical processes could thus be used more systematically in tropical regions for regional planning and forest conservation
ISSN: 0960-3115

hal-01204224
https://hal.archives-ouvertes.fr/hal-01204224
DOI : 10.1007/s10531-014-0854-8
PRODINRA : 295767

Résumé : Cette thèse traite de la problématique de l'analyse automatique de tracés manuscrits réalisés à mains levée, à caractère géométrique et acquis en ligne. Lorsque l'on analyse un tracé en ligne, on peut le faire selon plusieurs angles. Comme pour les tracés hors ligne, on peu s'atteler à reconnaitre la forme produite. Mais le caractère en ligne de l'acquisition permet également d'autres niveaux d'analyse, comme l'analyse de la procédure utilisée par le dessinateur lors de la production de son dessin. Nous avons dans le cadre de ce travail élaboré des outils permettant de telles analyses de la production de tracé. Dans une première partie nous traitons des pré traitements à effectuer sur le tracé afin de pouvoir procéder aux analyses spatio-graphique et procédurale. Ces pré traitements sont le filtrage, la segmentation mixte à base d'arcs de cercles et de segments de droite, la sélection des points d'intérêt ainsi que l'identification de la nature de ces points. La seconde partie concerne l'analyse visuo-spatiale. Nous abordons alors deux aspects: la question de la reconnaissance des formes et celle de l'évaluation automatique de leur qualité. Notre contribution consiste en une méthode de reconnaissance basée sur l'apparence utilisant des descripteurs locaux. La dernière partie traite de l'analyse procédurale. Nous proposons une méthode d'extraction et de modélisation de la procédure mise en œuvre lors du dessin d'une forme. Nous montrons comment en utilisant cette modélisation, nous pouvons non seulement déterminer la procédure favorite d'un utilisateur mais également reconnaitre un dessinateur par l'analyse de sa procédure.
This thesis handles the problem of the automatic analysis of online hand drawn geometric sketches. An online sketch can be analysed according to several points of view. As for offline sketching, we can try to recognize the produced shape. However, online sketching allows other levels of analysis. For example the analysis of the behavior of the drawer during the production of the sketch. In this thesis, we have tried to develop tools allowing a multi level analysis, including both shape and behavior analysis. The first part of our work deals with the pre treatments that must be performed on the sketch in order to allow upper level analysis. Those pre treatments are filtering, mixed segmentation and feature points detection and labelisation. In the second part, we approach shape analysis in two aspects: shape recognition and evaluation. We have developed a appearance based method which use local descriptors to allows both recognition and evaluation of the quality of a produced shape compared to the model . in the last part we propose a method for drawer's behavior extraction and modeling. Then we show how we can not only determine the favorite procedure of a drawer but also recognize the drawer by analyzing his behavior.

http://www.theses.fr/2010AGUY0394/document

Éditeur(s) : HAL CCSD
Résumé : International audience
Clear cell renal cell carcinoma (ccRCC) has a poor prognosis with a 50% risk of metastases. Little is known about the phenotypic and molecular profiles of metastases regarding their corresponding primary tumors. This study aimed to screen phenotypic and genotypic differences between metastases and their corresponding primary tumors. We selected four cases with available frozen material. The histological, immunohistochemical (VEGFA, CD31, SMA, Ki67, p53, PAR-3), FISH (VHL gene), next-generation sequencing (VHL and c-MET genes), multiplex ligation-dependent probe amplification, and array-(comparative genomic hybridization) CGH analyses were realized. Metastases were nodal, hepatic (synchronous), adrenal, and pulmonary (metachronous). High-grade tumor cells were significantly more frequent in metastases (p = 0.019). Metastases and high-grade zones of primary tumors shared similar characteristics compared to low-grade zones: a lower microscopic vascular density (43.5 vs 382.5 vessels/mm(2); p = 0.0027), a higher expression of VEGF (73 vs 10%, p = 0.045), Ki67 (37.6 vs 8.3%; p = 0.011), and p53 (54 vs 10.6%; p = 0.081), and a cytoplasmic and membranous PAR-3 staining. Metastases exhibited more chromosomal imbalances than primary tumors in total (18.75 ± 6.8; p = 0.044) with more genomic gains (13.5 ± 7; p = 0.013). The loss of chromosome 9 and gain of Xq were found in both primary tumors and metastases but gains of loci or chromosomes 2p, 3q, 5, 8q, 12, and 20 were only found in metastases. The VHL gene status was similar in each tumor couple. Although metastases and primary tumors share common histological features, this study highlights chromosomal differences specific to metastases which could be involved in ccRCC metastatic evolution.
Virchows Archiv

hal-01560281
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560281
DOI : 10.1007/s00428-017-2124-0
PUBMED : 28488172

Résumé : Face aux difficultés d’identification des arbres de la famille des Lauracées et dans un but d’établissement d’une production durable et certifiée d’huiles essentielles, l’entreprise KLR a voulu mettre en place un nouvel outil d’identification multi-critères qui consiste à croiser plusieurs types de caractères afin d’obtenir une détermination taxonomique fiable.Trois méthodes d’identification ont été utilisées : la chimie (analyse de l’odeur de l’écorce), le code barre génétique et l’anatomie du bois. Une analyse par positionnement multidimensionnel non-métrique a permis de faire un tri des critères anatomiques du bois pertinents dans l’identification des Lauracées étudiées, au final 14 critères ont été retenus. D’après les données anatomiques dont nous disposons, nous proposons une clé de détermination au genre. En génétique, la technique de code barres de la région chloroplastique intergénique trnH-psbA a été appliquée aux individus récoltés. En comparant les séquences de tous les individus, 40% des individus peuvent être identifiés au genre car ils présentent des haplotypes uniques. Des haplotypes au sein des genres ont été déterminés et permettent d’identifier l’espèce pour 40 à 100 % des individus selon le genre. L’analyse SPME de l’odeur des écorces a permis de définir pour chaque espèce une carte d’identité chimique à partir des molécules majoritaires. Des chémotypes ont été définis au sein des espèces Licaria cannella, Ocotea indirectinervia et Sextonia rubra. Ces trois domaines d’observation ont permis de constituer une base de type Xper2 pour l’identification.Un criblage des essences intéressantes de par leur rendement en huile essentielle a été effectué. En ce qui concerne la partie extraction de l’huile essentielle, trois espèces montrent un rendement en huile essentielle de l’écorce supérieur à 0,3% et 5 espèces montrent un rendement en huile essentielle du bois supérieur à 0,3%. Les évaluations olfactives menées par un expert ont permis de séparer les huiles distillées en 5 différentes notes. Nous avons jugé intéressant de savoir si l’outil d’identification multicritère pouvait prédire les compositions et rendements en huile essentielle de l’espèce identifiée avant l’abattage de l’arbre. Des études complémentaires ont donc été menées. Pour plus de la moitié des arbres, la signature de l’écorce, la composition de l’huile essentielle de l’écorce et la composition de l’huile essentielle du bois sont similaires. La tentative d’établir un lien entre les caractéristiques des cellules à huile et le rendement s’est avérée infructueuse.
In order to develop a sustainable production of certified essential oils extracts, the compangy KLR has struggled with the identification of the trees from the family of Lauraceae. This is the main reason that led to the project of creating an identification tool for this family.This tool would be based on three approaches: chemistry (chemical signature of the dark), wood anatomy and genetic barcoding. By means of a non-metric multidimensional scaling analysis, we selected a list of 14 relevant wood anatomical features that can identify the trees to the genera. For the genetics, the barcoding of trnH-psbA an intergenic region of the DNA has been used. When comparing all the sequences from all the individuals, 40% of the individuals can be identified to the genera because of their specific haplotype. Haplotypes within the genera have also been established. Chemical identity cards have been set with the SPME analysis technique and chemotypes have been defined inside the species Licaria cannella, Ocotea indirectinervia and Sextonia rubra. These three identification approaches allowed us to construct an identification tool on Xper².During the study, we aimed to screen what species would be interesting for its essential oil yield. Three species showed an essential oil bark yield above 0.3%. five species showed an essential oil wood yield above 0.3%. An expert held an olfactory evaluation on the oils and divided the essential oils in five olfactory groups. We found it relevant to improve the identification tool by trying to predict the compositions of the oils before the three was cut down. In the case of the half of trees studied by SPME analyses, the composition of the wood and the bark essential oils were similar. On the other hand, no link was found between the oil cells dimensions and the essential oil yield.

http://www.theses.fr/2012AGUY0516/document

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Grain deviations and high extractives content are common features of many tropical woods. We aimed at clarifying their respective impact on vibrational properties, referring to African Padauk (Pterocarpus soyauxii Taub.), a species selected for its interlocked grain, high extractives content, and uses in xylophones. Specimens were cut parallel to the trunk axis (L), and local variations in grain angle (GA), microfibril angle (MFA), specific Young's modulus (E'L/ρ, where r stands for specific gravity) and damping coefficient (tanδL), were measured. GA dependence was analyzed by a mechanical model which allowed to identify the specific Young's modulus (E'3/ρ) and shear modulus (G'/ρ) along the grain (3), as well as their corresponding damping coefficients (tanδ3, tanδG). This analysis was done for native and then for extracted wood. Interlocked grain resulted in 0-25° GA and in variations of a factor 2 in E'L/ρ and tanδL. Along the grain, Padauk wood was characterized, as compared to typical hardwoods, by a somewhat lower E'3/ρ and elastic anisotropy (E'/G'), due to a wide microfibril angle plus a small weight effect of extracts; and a very low tanδ3 and moderate damping anisotropy (tanδG/tanδ3). Extraction affected mechanical parameters in the order: tanδ3 ≈ tanδG > G'/ρ >> E'3/ρ. That is, extractives' effects were nearly isotropic on damping but clearly anisotropic on storage moduli.
ISSN: 0043-7719

hal-00544382
https://hal.archives-ouvertes.fr/hal-00544382
https://hal.archives-ouvertes.fr/hal-00544382/document
https://hal.archives-ouvertes.fr/hal-00544382/file/Identification_anisotropic_vibrational_properties_Bremaud_al.pdf
DOI : 10.1007/s00226-010-0348-0