Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Joint inversions are now commonly used in the earth sciences. They have been developed to better understand the structure of the earth, since they provide more constraints on the inverted parameters. We propose a new process to simultaneously invert several data sets in order to better image 3D crustal and upper mantle structures. Our inversion uses three kinds of data that present good complementarity: (1) P-wave receiver functions to provide Moho depth variations, (2) teleseismic delay times of P-waves to retrieve velocity anomalies in the crust and the upper mantle, and (3) gravity anomalies to image density variations at the lithospheric scale. We use a stochastic scheme, where receiver functions are first inverted. The interpolated resulting Moho depths are incorporated as a priori information into the joint inversion of teleseismic delay times and gravity anomalies process. Moreover, velocity and density can be linked by empirical relationships, which justifies the joint inversion of those parameters. In our stochastic approach, we perform a model space search for Moho variations, P-velocity, and density structure to find an acceptable fit to the three data sets. In order to preferentially sample the good data fit regions, we chose the neighborhood algorithm of Sambridge to optimistically survey the model space. We model the delay times with 3D raytracing using evenly spaced velocity-density nodes. We present here the first results given by this method on synthetic tests. (C) 2011 Elsevier Ltd. All rights reserved.
ISSN: 0098-3004

hal-00643158
https://hal.archives-ouvertes.fr/hal-00643158
DOI : 10.1016/j.cageo.2010.11.017

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The thermal evolution of sediments in the shallowest part of sedimentary basins is challenging to investigate as most of the geothermometers are at their application limits. This is typically the case of the Callovian-Oxfordian claystones at the eastern border of the Paris Basin. A recent 2000 m deep well penetrated the entire Jurassic and Triassic sedimentary series and permitted coring of sediments never reached by previous drilling in this part of the basin. Thanks to the use of several independent geothermometers (apatite fission track thermochronology, fluid inclusion microthermometry, clay mineralogy and sedimentary organic matter evolution) the burial history of the Mesozoic series has been reconstructed, modeled and calibrated using kinetic algorithms relevant to the various paleothermometers used. In addition to these conventional methods, an innovative approach was developed using the temperature-dependence of the magnetic mineral assemblage within clay-rich sediments ("MagEval"). Thermal modeling indicates that the Callovian-Oxfordian and the Lower Triassic experienced maximum burial temperatures of 50 +/- 5 C-circle and 90 +/- 10 C-circle respectively, i.e., about 25 C higher than present-day. This temperature offset implies the erosion of several hundred meters of sediments which, depending on the thermal flux and conductivity considered, most likely constituted Upper Cretaceous chalk deposits. Falling sea level resulted in the exposure and subsequent dismantling of the chalk cover at the beginning of Cenozoic times. The eastern border of the basin was then subjected to slow erosion and discrete tectonic deformation.
ISSN: 0264-8172

hal-01313142
https://hal.archives-ouvertes.fr/hal-01313142
DOI : 10.1016/j.marpetgeo.2013.08.019

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Recently Auslender & Crouzeix introduced a well-behaved asymptotical notion for convex functions. The aim of this work is to extend this notion to the saddle case
ISSN: 0163-0563

hal-00773195
https://hal.univ-antilles.fr/hal-00773195
DOI : 10.1080/01630569708816806

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228

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
Résumé : International audience
We propose using a distributed algorithm to count individuals in a population and to collect abiotic factors in order to characterize habitat. The first phase consists of detecting the presence of individuals from mapping ecotopes, the second allows counting the number of individuals and the last aggregates the numbers of individuals over several paths. We propose an approach that uses a wireless sensor network built on a linear architecture based on the concept of green tunnel. Here, each mote has a successor and a predecessor.
à venir

hal-00857694
https://hal.archives-ouvertes.fr/hal-00857694

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper proposes a new knowledge discovery method called FLMin to discover frequent patterns in a social network. The algorithm works without previous knowledge on the network and exploits both the structure and the attributes of nodes to extract regularities called Frequent Links. Unlike traditional works in this area that solely exploit structural regularities of the network, the originality of FLMin is its ability to gather these two kinds of information in the search for patterns. In this paper, we detail the method proposed for extracting frequent links and discuss its complexity and its flexibility. The efficiency of our solution is evaluated by conducting qualitative and quantitative studies for understanding how behaves FLMin according to different parameters.
Networked Digital Technologies
Dubai, United Arab Emirates

hal-00768431
https://hal.archives-ouvertes.fr/hal-00768431
DOI : 10.1007/978-3-642-30567-2_38

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection in immunocompromised patients. Quantitative real-time PCR (qPCR) is more sensitive than microscopic examination for the detection of P. jirovecii but also detects colonized patients. Hence, its positive predictive value (PPV) needs evaluation. In this 4-year prospective observational study, all immunocompromised patients with acute respiratory symptoms who were investigated for PCP were included, totaling 659 patients (814 bronchoalveolar lavage fluid samples). Patients with negative microscopy but positive qPCR were classified through medical chart review as having retained PCP, possible PCP, or colonization, and their clinical outcomes were compared to those of patients with microscopically proven PCP. Overall, 119 patients were included for analysis, of whom 35, 41, and 43 were classified as having retained PCP, possible PCP, and colonization, respectively. The 35 patients with retained PCP had clinical findings similar to those with microscopically proven PCP but lower fungal loads (P extless 0.001) and were mainly non-HIV-infected patients (P extless 0.05). Although the mean amplification threshold was higher in colonized patients, it was not possible to determine a discriminant qPCR cutoff. The PPV of qPCR in patients with negative microscopy were 29.4% and 63.8% when considering retained PCP and retained plus possible PCP, respectively. Patients with possible PCP had a higher mortality rate than patients with retained PCP or colonization (63% versus 3% and 16%, respectively); patients who died had not received co-trimoxazole. In conclusion, qPCR is a useful tool to diagnose PCP in non-HIV patients, and treatment might be better targeted through a multicomponent algorithm including both clinical/radiological parameters and qPCR results.
ISSN: 0095-1137

hal-01063906
https://hal.archives-ouvertes.fr/hal-01063906
DOI : 10.1128/JCM.01480-14
PUBMED : 25009050

Éditeur(s) : HAL CCSD Springer Berlin / Heidelberg
Résumé : International audience
In distributed collaborative systems, replicated objects, shared by users, are subject to concurrency constraints. All methods [4, 13, 18, 15, 16, 19, 22] proposed to serialize concurrent operations and achieve copies convergence of replicated objects are based on the use of Operational Transformations. In this context, giving the user the ability to undo an operation has been recognized as a difficult problem [1, 2, 3, 12, 14, 20, 21]. The few general propositions to solve the problem sometimes compromise copies convergence and/or users' intention, insofar as the Operational Transformations used are unsuitable for undo. This paper has a twofold objective. Firstly, it aims to highlight two general conditions (named C3 and C4) that need to be satisfied by any transformation adapted to undo. Secondly, it presents a general undo algorithm based on the definition of a generic undo-fitted transformation, which automatically verifies these conditions. The interest of the proposed method is that the undoing of an operation obeys to the same processing as the one used for regular operations in collaborative systems such as [15,19].
12th International Conference on Cooperative Informations Systems
Agia Napa, Cyprus

hal-00684656
https://hal.archives-ouvertes.fr/hal-00684656
DOI : 10.1007/978-3-540-30468-5_12

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
Objectifs Aucun consensus n’existe concernant la prise en charge des pneumothorax spontanés de grande abondance. Les recommandations actuelles proposent soit une exsufflation à l’aiguille, soit un drainage thoracique, la plupart des patients étant hospitalisés. Nous avons voulu tester l’efficacité d’une prise en charge ambulatoire des pneumothorax par cathéters de petit calibre dit en « queue de cochon ». Méthodes De février 2007 à janvier 2011, tous les pneumothorax spontanés primaires et secondaires de grande abondance reçus à l’hôpital de Lorient ont été pris en charge par drainage via un cathéter de petit calibre associé à une valve anti-retour. Les patients rentraient immédiatement à domicile et étaient par la suite évalués tous les deux jours selon un algorithme précis. Résultats Sur 132 pneumothorax consécutifs (110 spontanés primaires, 22 secondaires), 103 ont été exclusivement traités en ambulatoire avec un retour complet à la paroi thoracique à j2 ou j4, ce qui représente un succès de l’ambulatoire à 78 %. La durée moyenne de drainage était de 3,4 jours. Sept patients ont été initialement hospitalisés, mais sont rapidement rentrés à domicile et ont été totalement guéris à j2 ou j4, ramenant le taux de succès à 83 %. L’usage d’antalgique était faible. Le taux de récidive à un an était de 26 %. En cas de succès, cette prise en charge est potentiellement économique avec un coût moyen estimé à 926 comprenant 2 consultations et une radiographie thoracique, en comparaison aux 4276 estimés si le patient était hospitalisé avec mise en place d’un drain thoracique pendant 4 jours. Conclusion La prise en charge ambulatoire des pneumothorax spontanés de grande abondance par cathéters de type « queue de cochon » associés à une valve anti-retour peut être considérée comme un traitement de première intention raisonnable. En comparaison avec d’autres études, notre protocole ne nécessite pas d’hospitalisation et est économique
ISSN: 0761-8425

hal-01163246
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163246
DOI : 10.1016/j.rmr.2015.04.019

Éditeur(s) : HAL CCSD
Résumé : National audience
1ère Journée de l’IREM des Antilles
Pointe-à-Pitre, France

hal-01278559
https://hal.archives-ouvertes.fr/hal-01278559

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We introduce the Convex Circuit-Free coloration and Convex Circuit-Free chromatic numberView the MathML source of an oriented graph View the MathML source and establish various basic results. We show that the problem of deciding if an oriented graph verifies View the MathML source is NP-complete if k≥3, and polynomial if k≤2. We introduce an algorithm which finds the optimal convex circuit-free coloration for tournaments, and characterize the tournaments that are vertex-critical for the convex circuit-free coloration.
ISSN: 0195-6698

hal-00716574
https://hal.archives-ouvertes.fr/hal-00716574
DOI : 10.1016/j.ejc.2008.02.012

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper deals with texture classification using a multifractal approach. More precisely we analyse the singularity/regularity exponent that compose the textures because they theoretically carry most of the information. The analysis is made using the Legendre spectrum. Then a parameter vector is computed to describe this spectrum in order to classify the textures with an unsupervised k-means classifier. The resulting algorithm is evaluated against a classification directly based on the textures.
ICSP Proceedings
Beijing, China

hal-00602270
https://hal.archives-ouvertes.fr/hal-00602270

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
BACKGROUND: Dengue and malaria are two major public health concerns in tropical settings. Although the pathogeneses of these two arthropod-borne diseases differ, their clinical and biological presentations are unspecific. During dengue epidemics, several hundred patients with fever and diffuse pain are weekly admitted at the emergency room. It is difficult to discriminate them from patients presenting malaria attacks. Furthermore, it may be impossible to provide a parasitological microscopic examination for all patients. This study aimed to establish a diagnostic algorithm for communities where dengue fever and malaria occur at some frequency in adults. METHODOLOGY/PRINCIPAL FINDINGS: A sub-study using the control groups of a case-control study in French Guiana - originally designed to compare dengue and malaria co-infected cases to single infected cases - was performed between 2004 and 2010. In brief, 208 patients with malaria matched to 208 patients with dengue fever were compared in the present study. A predictive score of malaria versus dengue was established using .632 bootstrap procedures. Multivariate analysis showed that male gender, age, tachycardia, anemia, thrombocytopenia, and CRP>5 mg/l were independently associated with malaria. The predictive score using those variables had an AUC of 0.86 (95%CI: 0.82-0.89), and the CRP was the preponderant predictive factor. The sensitivity and specificity of CRP>5 mg/L to discriminate malaria from dengue were of 0.995 (95%CI: 0.991-1) and 0.35 (95%CI 0.32-0.39), respectively. CONCLUSIONS/SIGNIFICANCE: The clinical and biological score performed relatively well for discriminating cases of dengue versus malaria. Moreover, using only the CRP level turned to be a useful biomarker to discriminate feverish patients at low risk of malaria in an area where both infections exist. It would avoid more than 33% of unnecessary parasitological examinations with a very low risk of missing a malaria attack.
ISSN: 1935-2727

inserm-00872353
http://www.hal.inserm.fr/inserm-00872353
http://www.hal.inserm.fr/inserm-00872353/document
http://www.hal.inserm.fr/inserm-00872353/file/journal.pntd.0002420.pdf
DOI : 10.1371/journal.pntd.0002420

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
This article is concerned with a generalization of the hybrid steepest descent method from variational inequalities to the multivalued case. This will be reached by replacing the multivalued operator by its Yosida approximate, which is always Lipschitz continuous. It is worth mentioning that the hybrid steepest descent method is an algorithmic solution to variational inequality problems over the fixed point set of certain nonexpansive mappings and has remarkable applicability to the constrained nonlinear inverse problems like image recovery and MIMO communication systems
ISSN: 0163-0563

hal-00776641
https://hal.univ-antilles.fr/hal-00776641
DOI : 10.1080/01630563.2011.619676

Éditeur(s) : HAL CCSD INRIA
Résumé : International audience
Markov chain Monte Carlo (MCMC) methods together with hidden Markov models are extensively used in the Bayesian inference for many scientific fields like environment and ecology. Through simulated examples we show that the speed of convergence of these methods can be very low. In order to improve the convergence properties, we propose a method to make parallel chains interact. We apply this method to a biomass evolution model for fisheries.
Les méthodes de Monte Carlo par chaînes de Markov (MCMC) couplées à des modèles de Markov cachés sont utilisées dans de nombreux domaines, notamment en environnement et en écologie. Sur des exemples simples, nous montrons que la vitesse de convergence de ces méthodes peut être très faible. Nous proposons de mettre en interaction plusieurs algorithmes MCMC pour accélérer cette convergence. Nous appliquons ces méthodes à un modèle d'évolution de la biomasse d'une pêcherie.
ISSN: 1638-5713

inria-00506386
https://hal.inria.fr/inria-00506386
https://hal.inria.fr/inria-00506386/document
https://hal.inria.fr/inria-00506386/file/campillo2008d.pdf

Éditeur(s) : HAL CCSD
Résumé : 32 pages
Wind energy production is very sensitive to instantaneous wind speed fluctuations. Thus rapid variation of wind speed due to changes in the local meteorological conditions can lead to electrical power variations of the order of the nominal power output. In small grids, as they exist for example on some islands in the French West Indies, such fluctuations can cause instabilities in case of intermediate power shortages. To palliate these difficulties, it is essential to identify and characterize the wind speed distributions. This allows to anticipate the eventuality of power shortage or power surge. Therefore, it is of interest to categorize wind speed fluctuations into distinct classes and to estimate the probability of a distribution to belong to a class. This paper presents a method for classifying wind speed histograms by estimating a finite mixture of Dirichlet distributions. The SAEM algorithm that we use provides a fine distinction between wind speed distribution classes. It's a new nonparametric method for wind speed sequences classification. However, we show that the wind speed distributions in each class correspond to specific Gram- Charlier densities.
https://hal.archives-ouvertes.fr/hal-00319608

hal-00319608
https://hal.archives-ouvertes.fr/hal-00319608
https://hal.archives-ouvertes.fr/hal-00319608v2/document
https://hal.archives-ouvertes.fr/hal-00319608/file/Article_dirichlet.pdf
ARXIV : 0810.4422

Éditeur(s) : HAL CCSD
Résumé : International audience
Half away between edge detection and object recognition this study aim to characterize singularities in order to guide this two phases. The caracterization is obtained with a generalization of the Lipschitz exponents .for complex structures. This new characterization is called " maxima chain " and integrates the notion of value and spatial repartition of the maxima. The maxima chains are obtained with a multiscale decomposition using a Diadic Discrete Wavelet Transform (DDWT). We use the maxima of the gradient image computed with the wavelet details. The local maxima detect the position of irregular structures (edges) in the image (Canny algorithm). Then we characterize each maxima using their evolution across the different scales. A classification is made using the maxima chains. We integrate the classification to eliminate unwanted maxima (from noise or other objects) to drive the search of closed contours. In fact, there is a totally different signature from one maxima to another depending on the parameters of the objects : nature, shape, size, gray scale, texture, ...
RFIA Proceedings
Toulouse, France

hal-00602265
https://hal.archives-ouvertes.fr/hal-00602265

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND: Surveillance of HIV-1 drug resistance in treated patients with plasma viral load (VL) >50 copies/mL. METHODS: The protease and reverse transcriptase (RT) genes were systematically sequenced in samples from 756 patients with VL >50 copies/mL in 2009. The genotyping results were interpreted for each antiretroviral drug (ARV) by using the ANRS algorithm v21. Weighted analyses were used to derive representative estimates of percentages of patients. Prevalence rates were compared with those obtained in 2004 among patients with VL >1000 copies/mL. RESULTS: Sequences were obtained for 506 patients. Sequencing was successful in 45%, 80% and 96% of samples with VL of 51-500, 501-1000 and >1000 copies/mL, respectively. Resistance or possible resistance to at least one ARV was observed in 59% of samples. Overall, 0.9% of samples contained viruses resistant to all drugs belonging to at least three drug classes. All resistance prevalence rates were significantly lower in 2009 than in 2004. CONCLUSION: In France, where 86% of patients were receiving combination antiretroviral therapy in 2009, only 15.0% of patients had a VL >50 copies/mL, suggesting that only 8.9% of treated patients could potentially transmit resistant viruses. Only 0.08% of patients harboured viruses fully resistant to at least three antiretroviral drug classes. Further studies are needed to determine whether resistance continues to decline over time.
ISSN: 0305-7453

hal-00875092
https://hal.archives-ouvertes.fr/hal-00875092
DOI : 10.1093/jac/dkt033
PUBMED : 23404192