Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
A relevant and accurate description of three-dimensional (3D) protein structures can be achieved by characterizing recurrent local structures. In a previous study, we developed a library of 120 3D structural prototypes encompassing all known 11-residues long local protein structures and ensuring a good quality of structural approximation. A local structure prediction method was also proposed. Here, overlapping properties of local protein structures in global ones are taken into account to characterize frequent local networks. At the same time, we propose a new long local structure prediction strategy which involves the use of evolutionary information coupled with Support Vector Machines (SVMs). Our prediction is evaluated by a stringent geometrical assessment. Every local structure prediction with a Calpha RMSD less than 2.5 A from the true local structure is considered as correct. A global prediction rate of 63.1% is then reached, corresponding to an improvement of 7.7 points compared with the previous strategy. In the same way, the prediction of 88.33% of the 120 structural classes is improved with 8.65% mean gain. 85.33% of proteins have better prediction results with a 9.43% average gain. An analysis of prediction rate per local network also supports the global improvement and gives insights into the potential of our method for predicting super local structures. Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions. Proteins 2009. (c) 2009 Wiley-Liss, Inc.
ISSN: 0887-3585

inserm-00348740
http://www.hal.inserm.fr/inserm-00348740
http://www.hal.inserm.fr/inserm-00348740/document
http://www.hal.inserm.fr/inserm-00348740/file/Bornot_Proteins_2009_preprint_version.pdf
http://www.hal.inserm.fr/inserm-00348740/file/inserm-00348740_edited.pdf

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Giant earthquake (moment magnitude M-w >= 8.5) forecasts for subduction zones have been empirically related to both tectonic stresses and geometrical irregularities along the subduction interface. Both of these controls have been suggested as able to tune the ability of rupture to propagate laterally and, in turn, exert an important control on giant earthquake generation. Here we test these hypotheses, and their combined influence, by compiling a dataset of trench fill thickness (a proxy for smoothing of subducting plate relief by sediment input into the subduction channel) and upper plate strain (a proxy for the tectonic stresses applied to the subduction interface) for 44 segments of the global subduction network. We statistically compare relationships between upper plate strain, trench sediment thickness and maximal earthquake magnitude. We find that the combination of both large trench fill (>= 1 km) and neutral upper plate strain explains spatial patterns of giant earthquake occurrence to a statistically significant degree. In fact, the concert of these two factors is more highly correlated with giant earthquake occurrence than either factor on its own. Less frequent giant earthquakes of lower magnitude are also possible at subduction zones with thinner trench fill and compressive upper plate strain. Extensional upper plate strain and trench fill < 0.5 km appear to be unfavorable conditions, as giant earthquakes have not been observed in these geodynamical environments during the last 111 years. Citation: Heuret, A., C. P. Conrad, F. Funiciello, S. Lallemand, and L. Sandri (2012), Relation between subduction megathrust earthquakes, trench sediment thickness and upper plate strain, Geophys. Res. Lett., 39, L05304, doi: 10.1029/2011GL050712.
ISSN: 0094-8276

hal-00745636
https://hal.archives-ouvertes.fr/hal-00745636
https://hal.archives-ouvertes.fr/hal-00745636/document
https://hal.archives-ouvertes.fr/hal-00745636/file/heuretGRL2012.pdf
DOI : 10.1029/2011GL050712

Éditeur(s) : HAL CCSD
Résumé : International audience
The aim of this study is to perform a simulation of large scale Wireless Sensor Networks (WSN) working on medical diagnosis. The main feature of this WSN is its density and the fact that all sensors are in the same radio range. Our approach helps medical staff to diagnose diseases in an automatic way. In this context, each patient is equipped to a set of sensors. Each sensor is connected to a transducer dedicated to measure a specific health parameter . This WSN will perform some computations and run an alarm when some diseases are suspected. This technique is based on the population protocol to handle data exchanged between sensors. This approach is in fact an efficient distributed algorithm which implies that the diagnose may be done by any sensor dealing with the disease detection. The main result of this paper is: the method supports large scalability which proves its practicability for real cases.
Computers and Communications (ISCC), 2010 IEEE Symposium on Computers and Communications.
Riccione, Italy

hal-00519595
https://hal.archives-ouvertes.fr/hal-00519595

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
Résumé : International audience
We present a study on the optimasation of the number of messages for medical diagnosis over wireless sensors networks (WSNs). We suggest distributed algorithms to diagnosis some diseases while monitoring a patient. Then, we compare the number of messages needed to make a decision between the algorithms. In our approach, each sensor will make some computations in order to participate to the decision. Indeed, some computation and collaboration tasks are performed over the sensors and the final diagnosis is performed in a distributed way. During the experimentation of our algorithms, we used a real data flow extracted from hospital monitoring.
Proceedings of the 14th IEEE Symposium on Computers and Communications (ISCC 2009), July 5-8, Sousse, Tunisia
Sousse, Tunisia

hal-00519593
https://hal.archives-ouvertes.fr/hal-00519593

Éditeur(s) : EDP Sciences
Résumé : Lessons for the future from two development projects in aquaculture in the French overseas territories. Numerous research and development projects have been launched since the seventies in the French overseas territories. Their aim was to foster new activities in agriculture based on local productions for local markets, notably in the French West Indies (FWI). In this paper we analyze two development projects on the rearing of giant freshwater prawn, one in the FWI and the other in French Guyana, over twenty years after their launching. The purpose of these compared studies is twofold: first to try to understand why a set of relevant technical innovations ended in failure 15 years later; second to identify recommendations in terms of methodology in order to diminish risks of mistakes or failure for future projects. To reach this goal we followed two approaches. A first analysis is based on a set of three criteria: social acceptability, legitimacy and time planning. The second analysis, justified by the subjective need for an explanatory tool, is based on the actor-network theory. The results show that beyond the levels of political support and financial investment and support the three key criteria for success are: (i) reactivity of the decision-makers, notably when markets change, (ii) quality of leadership transfer between the launching phase and the stabilized phase, and (iii) capacity of the decision-makers to take into account the concrete consequences of the various scenarios. Regarding this third criterion, our analysis suggests that the scenario of full technical success needs to be explored, notably in terms of economic sustainability. The integration of these two types of analyses into an ex-ante frame should contribute to reducing risks of failure in similar development projects.
De nombreux projets d’aquaculture ont été menés depuis les années 1970 dans les territoires et départements français d’outre-mer. L’objectif était de diversifier l’agriculture avec des productions destinées au marché local comme aux Antilles, ou à l’exportation comme en Guyane. L’étude s’intéresse au bilan de deux projets d’élevage de la crevette tropicale d’eau douce aux Antilles et en Guyane, plus de vingt ans après leur lancement. L’objectif est de comprendre comment des innovations technologiques pertinentes ont conduit à deux échecs sur le moyen terme et de tirer des recommandations de méthode afin de réduire les risques d’erreurs ultérieures. Pour cela, deux cadres d’analyse sont mobilisés : le premier s’appuie sur les concepts de temporalité, légitimité et acceptabilité ; le second, motivé par la recherche subjective de cadres explicatifs, emprunte la vision de la théorie de l’acteur-réseau. Les trois déterminants majeurs du succès ou de l’échec se révèlent être la réactivité des responsables face aux problèmes d’adaptation à l’évolution des marchés, la qualité du transfert du leadership lors du passage de la phase de lancement à la phase de croisière et enfin la capacité de prendre en compte dès le départ les conséquences des scénarios d’évolution du projet, y compris la réussite technique. Une capacité d’intégration de ces types d’analyse, dans un cadre ex ante, devrait permettre de réduire les risques d’échec dans des projets de développement similaires à venir.
Natures Sciences et Sociétés (1240-1307) (EDP Sciences), 2013-12 , Vol. 21 , N. 4 , P. 400-415

Droits : NSS-Dialogues, EDP Sciences 2014
http://archimer.ifremer.fr/doc/00187/29784/28242.pdf
DOI:10.1051/nss/2014004
http://archimer.ifremer.fr/doc/00187/29784/

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is much slower compared to the rest of the phase space. These metastable regimes depend on the network topology and on the orders of magnitude of the kinetic parameters. Benchmarking of the method on a computational biology model repository suggests that the number of metastable regimes is sub-exponential in the number of variables and equations. The dynamics of the network can be described as a sequence of jumps from one metastable regime to another. We show that a geometrically computed con-nectivity graph restricts the set of possible jumps. We also provide finite state machine (Markov chain) models for such dynamic changes. Applied to signal transduction models, our approach unravels dynamical and functional * corresponding author capacities of signalling pathways, as well as parameters responsible for speci-ficity of the pathway response. In particular, for a model of TGFβ signalling, we find that the ratio of TGFBR2 to TGFBR1 receptors concentrations can be used to discriminate between metastable regimes. Using expression data from the NCI60 panel of human tumor cell lines, we show that aggressive and non-aggressive tumour cell lines function in different metastable regimes and can be distinguished by measuring the relative concentrations of receptors of the two types.
ISSN: 0303-2647

hal-01379033
https://hal.inria.fr/hal-01379033
https://hal.inria.fr/hal-01379033/document
https://hal.inria.fr/hal-01379033/file/Samal_et_al_Biosystems_final.pdf
DOI : 10.1016/j.biosystems.2016.07.004

Éditeur(s) : HAL CCSD
Résumé : 6 pages, 4 figures. In ICML 2013 Workshop on Machine Learning for Bioacoustics
International audience
The work presented in this paper is part of a global framework which long term goal is to design a wireless sensor network able to support the observation of a population of endangered birds. We present the first stage for which we have conducted a knowledge discovery approach on a sample of acoustical data. We use MFCC features extracted from bird songs and we exploit two knowledge discovery techniques. One that relies on clustering-based approaches, that highlights the homogeneity in the songs of the species. The other, based on predictive modeling, that demonstrates the good performances of various machine learning techniques for the identification process. The knowledge elicited provides promising results to consider a widespread study and to elicit guidelines for designing a first version of the automatic approach for data collection based on acoustic sensors.
ICML 2013 Workshop on Machine Learning for Bioacoustics
Atlanta, United States

hal-00840741
https://hal.archives-ouvertes.fr/hal-00840741
ARXIV : 1306.5349

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : The paper focuses on investigation of the importance of nature and development of tourism in protected areas. Therefore, in this context a new challenge is emerging: the need to conserve and protect bio and geo diversity, as well as the economic valorisation of these areas based mainly on tourism and leisure. At EU level, Natura 2000 protected areas have developed, implemented and cultivated the need to practice sport and recreational activities in these areas both for spending leisure time and also as stress antidote. The recreational and sporting practices that can be undertaken within the ecological network Natura 2000 sites adapted to the specificity of each protected area, in close connection with the environmental conditions. For the preservation of the natural environment should develop and maintain a close collaboration with tourism and sports associations that organize such activities in those areas.
La réflexion est centrée sur l’importance de la nature et des enjeux du développement de tourisme dans les aires protégées. Un nouveau défi émerge dans le contexte actuel où il s'agit de concilier le besoin de conserver et de protéger la géodiversité et la biodiversité avec la valorisation économique de ces espaces naturels investis par les pratiques touristiques et récréatives. Au niveau de l'Union européenne, les espaces protégés Natura 2000 ont mis en œuvre des programmes permettant de répondre à l’accueil des activités sportives et de loisirs dans ces zones, tant pour passer du temps libre que comme antidote au stress. Ces pratiques entreprises dans le réseau écologique Natura 2000 sites sont adaptés à la spécificité de chaque secteur protégé, en relation avec les conditions environnementales. Pour favoriser la conservation du cadre naturel, il est important de maintenir une étroite collaboration avec les associations touristiques et sportives qui organisent des activités dans ces zones.
Bihor
Roumanie

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.11262
http://journals.openedition.org/etudescaribeennes/11262

Éditeur(s) : HAL CCSD
Résumé : International audience
The aim of this study is to suggest an automated technique for distributed decision. It is based on protocol population deployed on Wireless Sensor Networks (WSN). This approach is able to help medical staff to detect earlier than usual some diseases on patients. It could be easily adapted for many other fields (fire monitoring, environment supervising, ...) In this context, a patient is equipped with health parameter transducers which are connected to a WSN. This WSN will perform some computations and raise an alarm when some diseases are suspected. The algorithm is distributed, i.e., the decision may be done by any mote dealing with the disease detection. The experimentations show promising results.
a venir
Denver, Colorado, United States

hal-00519597
https://hal.archives-ouvertes.fr/hal-00519597

Résumé : Le concept de réseau offre un modèle de représentation pour une grande variété d'objets et de systèmes, aussi bien naturels que sociaux, dans lesquels un ensemble d'entités homogènes ou hétérogènes interagissent entre elles. Il est aujourd'hui employé couramment pour désigner divers types de structures relationnelles. Pourtant, si chacun a une idée plus ou moins précise de ce qu'est un réseau, nous ignorons encore souvent les implications qu'ont ces structures dans de nombreux phénomènes du monde qui nous entoure. C'est par exemple le cas de processus tels que la diffusion d'une rumeur, la transmission d'une maladie, ou même l'émergence de sujets d'intérêt commun à un groupe d'individus, dans lesquels les relations que maintiennent les individus entre eux et leur nature s'avèrent souvent être les principaux facteurs déterminants l'évolution du phénomène. C'est ainsi que l'étude des réseaux est devenue l'un des domaines émergents du 21e siècle appelé la "Science des réseaux". Dans ce mémoire, nous abordons trois problèmes de la science des réseaux: le problème de la diffusion dans les réseaux sociaux, où nous nous sommes intéressés plus particulièrement à l'impact de la dynamique du réseau sur le processus de diffusion, le problème de l'analyse des réseaux sociaux, dans lequel nous avons proposé une solution pour tirer parti de l'ensemble des informations disponibles en combinant les informations sur la structure du réseau et les attributs des noeuds et le problème central de la collecte de données sociales, où nous nous sommes intéressés au cas particulier de la collecte de données en milieux sauvages
The concept of network provides a model for representing a wide variety of objects and systems, both natural and social, in which a set of homogeneous or heterogeneous entities interact. It is now widely used to describe various kinds of relational structures. However, if everyone has an idea of the concept of network, we often ignore the implications that these structures have in real world phenomena. This is for example the case of processes such as the spread of a rumor, the disease transmission, or even the emergence of subjects of common interest for a group of individuals, in which the relations maintained between individuals, and their nature, often prove to be the main factors determining the evolution of the phenomenon. This is the reason why the study of networks has become one of the emerging areas in the 21st century called the "Science of networks." ln this thesis, we address three issues of the domain of the science of networks: the problem of diffusion in social networks, where we have addressed more particularly the impact of the network dynamics on the diffusion process, the problem of the analysis of social networks, in which we have proposed a solution to take full advantage of all information available on the network by combining information on both structure and node attributes and the central problem of the social data collection, for which we have focused on the particular case of the data collection in a wild environment.

http://www.theses.fr/2012AGUY0569/document

Éditeur(s) : HAL CCSD
Résumé : International audience
A key issue for any project that aims to study endangered animals is the counting process. In this work, we propose an algorithm for automatic counting of singing birds in their habitat by using wireless sensors fitted with microphone. Sensors are used to record audio samples of bird songs and samples are analyzed to extract fingerprints that permit to recognize bird species. This paper details the counting algorithm that uses graph theory and audio inputs comparison. Finally, we demonstrate our scheme efficiency through experimentations.
International Symposium on a World of Wireless, Mobile and Multimedia Networks
Lucca, Italy

hal-00618563
https://hal.archives-ouvertes.fr/hal-00618563
DOI : 10.1109/WoWMoM.2011.5986215

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In oblique collision settings, parallel and perpendicular components of the relative plate motion can be partitioned into different structures of deformation and may be localized close to the plate boundary, or distributed on a wider region. In the Southern Alps of New Zealand, it has been proposed that one-third of the regional convergence is distributed in a broad area along the Southern Alps orogenic wedge. To better document and understand the regional dynamics of such systems, reliable markers of the horizontal tectonic motion over geological time scales are needed. River networks are able to record a large amount of distributed strain and they can thus be used to reconstruct the mode and rate of distribution away from major active structures. To explore the controls on river resilience to deformation, we develop an experimental model to investigate river pattern evolution over a doubly-vergent orogenic wedge growing in a context of oblique convergence. We use a rainfall system to activate erosion, sediment transport and river development on the model surface. At the end of the experiment, the drainage network is statistically rotated clockwise, confirming that rivers can record the distribution of motion along the wedge. Image analysis of channel time-space evolution shows how the fault-parallel and fault-perpendicular components of motion decrease toward the fault and impose rotation to the main trunk valleys. However, rivers do not record the whole imposed rotation rate, which suggest that the natural lateral channel dynamics can alter the capacity of rivers to act as passive markers of deformation.
ISSN: 0040-1951

hal-01467564
https://hal.archives-ouvertes.fr/hal-01467564
DOI : 10.1016/j.tecto.2016.04.016

Éditeur(s) : HAL CCSD
Résumé : poster
International audience
Locations for earthquake recorded in the Lesser Antilles subduction zone are processed separately by regional observatories, NEIC and ISC. There is no earthquake location catalog available compiling all available phase arrival data. We propose a new best complete earthquake catalog by merging all available phase arrival data for better constrains on earthquake locations. ISC provides the phase arrival data of 29243 earthquakes (magnitude range from 1.4 to 6.4) recorded by PRSN (Porto Rico), SRC (British West Indies), and from FUNVISIS (Venezuela). We add phases data from IPGP observatories for 68718 earthquakes from magnitudes 0.1 to 7.5 (OVSG, Guadeloupe, recorded 53226 earthquakes since 1981, and OVSM, Martinique, recorded 29931 earthquakes since 1972). IPGP also provides the accelerometer waveform data of the GIS-RAP network. We achieved automatic picking on the GIS-RAP data using the Component Energy Correlation Method. The CECM provides high precision phase detection, a realistic estimation of picking error and realistic weights that can be used with manual pick weights. The CECM add an average of 3 P-waves and 2 S-waves arrivals to 3846 earthquakes recorded by the GIS-RAP network since 2002. The final catalog contains 84979 earthquakes between 1972 and 2013, 24528 of which we compiled additional data. We achieve earthquake location using NonLinLoc, regional P and S waves data and a set of one dimensional velocity models. We produce improved locations for 22974 earthquakes (better residuals, on equal or larger arrival dataset) and improved duration magnitudes for 6258 earthquakes (using duration data and improved locations). A subset of best constrained 15626 hypocenters (with more than 8 phases and an average RMS of 0.48_0.77s) could be used for structural analysis and earthquake local tomography. Relative locations are to be applied in order to image active faulting. We aim to understand coupling in the seismogenic zone as well as triggering mechanisms of intermediate depth seismicity like fluid migration beneath the volcanic arc.
Geophysical Research Abstracts
Vienne, Austria

hal-01059207
https://hal-brgm.archives-ouvertes.fr/hal-01059207

Éditeur(s) : HAL CCSD
Résumé : International audience
EmailPrintRequest PermissionsThe emergence of new communication means such as online newspapers and exchange and sharing websites allow us to go further in the understanding of diffusion phenomena. Indeed, these public discussion areas are now firmly established in our societies and are known to be strong sensors of both human behaviors and collective feelings. In this paper we focus on diffusion phenomena that occur on Twitter and we propose a set of measures that aims to characterize globally and locally the processes. Our objective is to identify what are the conditions in which a person decides to forward the information. Our measures have been used to study two events occurred in January 2015: the presentation of Microsoft HoloLens, a new augmented reality headset, and the political election in Greece. The results obtained show a strong heterogeneity in the individual behaviours involved in the diffusion process. Our approach has been implemented into a graphical tool which is able to conduct real time analysis on any kind of topics occurring on Twitter.
IEEE International Conference on Research Challenges in Information Science (RCIS)
Athens, Greece

hal-01312382
https://hal.univ-antilles.fr/hal-01312382
DOI : 10.1109/RCIS.2015.7128894

Éditeur(s) : Actes de colloque Ifremer n°28, 2000. ISBN-13 978-2-84433-047-5 ISBN-10 978-2-84433-047-5
Résumé : The international symposium "Tuna Fishing and Fish Aggregating Devices " , October 1999, in Martinique, takes stock of the exploitation of large pelagic fish around FADs, based on regional synthesis for the three oceans and the Mediterranean Sea. Main themes include technology, fishing methods, impact on resources, biology of fish aggregation, anthropology and economic aspects of FAD exploitation. The meeting will gather and disseminate results from recent and ongoing studies on FADs in the different oceans of the world, enhance collaboration between scientists and managers involved in the development of FADs, promote the emergence of scientific and technical research, form a network for cooperation and enhance communications between researchers in the different locations concerned.
Le colloque international « Pêche thonière et dispositifs de concentration de poissons» organisé en octobre 1999, en Martinique, permet de dresser un bilan, sous forme de synthèses régionales, de l'exploitation des grands poissons pélagiques à l'aide de DCP dans les trois océans et en Méditerranée. La technologie, les méthodes de pêche, l'impact sur les ressources, le comportement agrégatif des poissons et les aspects socio-économiques de l'utilisation des DCP sont les principaux thèmes développés. Ces travaux permettront d'assurer une diffusion large des résultats à l'échelle de l'océan mondial, de favoriser les échanges entre les scientifiques et les gestionnaires impliqués dans le développement des systèmes DCP, de promouvoir l'émergence de thèmes et projets de recherche scientifique et technologique, de mettre en oeuvre un réseau de communication et d'échanges entre les sites et les régions concernées.

Droits : 2000 Ifremer
http://archimer.ifremer.fr/doc/00042/15326/12646.pdf
http://archimer.ifremer.fr/doc/00042/15326/

Éditeur(s) : Amer Geophysical Union
Résumé : Sea surface salinity (SSS) measured from space by the Soil Moisture and Ocean Salinity (SMOS) mission is validated in the subtropical North Atlantic Ocean. 39 transects of ships of opportunity equipped with thermosalinographs (TSG) crossed that region from 2010 to 2012, providing a large database of ground truth SSS. SMOS SSS is also compared to Aquarius SSS. Large seasonal biases remain in SMOS and Aquarius SSS. In order to look at the capability of satellite SSS to monitor spatial variability, especially at scales less than 300 km (not monitored with the Argo network), we first apply a monthly bias correction derived from satellite SSS and In Situ Analysis System (ISAS) SSS differences averaged over the studied region. Ship SSS averaged over 25 km is compared with satellite and ISAS SSS. Similar statistics are obtained for SMOS, Aquarius and ISAS products (root mean square error of about 0.15 and global correlation coefficient r of about 0.92). However, in the above statistics, SSS varies due to both large scale and mesoscale (here, for scales around 100 km) variability. In order to focus on mesoscale variability, we consider SSS anomalies with respect to a monthly climatology. SMOS SSS and Aquarius SSS anomalies are more significantly correlated (r > 0.5) to TSG SSS anomaly than ISAS. We show the effective gain of resolution and coverage provided by the satellite products over the interpolated in situ data. We also show the advantage of SMOS (r=0.57) over Aquarius (r=0.52) to reproduce SSS mesoscale features.
Journal Of Geophysical Research-oceans (0148-0027) (Amer Geophysical Union), 2014-12 , Vol. 119 , N. 12 , P. 8878-8896

Droits : 2014. American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00210/32150/34082.pdf
DOI:10.1002/2013JC009610
http://archimer.ifremer.fr/doc/00210/32150/

Éditeur(s) : HAL CCSD
Résumé : The recent accumulation of genomic sequence data has shown that gene evolution is not strictly tree-Like. Many evolutionary processes, like exon shuffling, gene fusion or nonhomologous recombination remodel genes by creating composite structures that are made from parts with different evolutionary histories. The development of sequence similarity networks provides an analytical framework to study the impact of these processes on molecular evolution, by structuring the resemblance relationships between sequences and by formalizing, in terms of graph theory, the detection of composite genes (intransitive triplets) and gene families (clique minimal separators). The size of current data sets, typically several million sequences, has also required the development of new tools and methods: sequence comparison parallelization, large networks visualization with Louvain communities and large cycles identification. When applied to eukaryotic and viral genome data sets, these methods have shown that composite genes are found throughout cellular organisms and mobile genetic elements. Proportionally, composite genes are more numerous in eukaryotic genomes; in absolute number, they are more numerous in viruses. In the latter, composite genes functional distribution is biased (enrichment of genes families that are essential for the perpetuation of the viral cycle), and the various parts of composite genes sometimes even originate from the genetic material of different viral classes. More generally, the extent of combinatorial processes, by unravelling other evolutionary bonds than homology bonds in the strictest sense, legitimates a pluralistic study of similarity relationships between sequences.
L’accumulation récente de données de séquences génomiques a montré que l’évolution des gènes n’est pas strictement arborescente. De nombreux processus évolutifs, comme l’exon shuffling, la fusion de gènes ou la recombinaison illégitime remodèlent les gènes, créant des structures composites, formées de parties dont les histoires évolutives sont différentes. Le développement de réseaux de similarité de séquences fournit un cadre analytique permettant d’étudier l’impact de ces processus sur l’évolution moléculaire, en structurant les relations de ressemblance entre séquences et en formalisant en termes de graphes la détection de gènes (triplets intransitifs) et de familles de gènes (cliques minimales séparatrices) composites. La taille des jeux de données actuels, de l’ordre de plusieurs millions de séquences, a également requis le développement de nouveaux outils et méthodes : parallélisation des comparaisons de séquences, visualisation de très grands réseaux par simplification en communautés de Louvain et identification de grands cycles. Appliquées à des jeux de données de génomes eucaryotes et viraux, ces méthodes ont démontré la présence de gènes composites dans tout le vivant et les éléments génétiques mobiles. En proportion, les gènes composites sont plus nombreux dans les génomes eucaryotes ; en nombre absolu, ils sont plus nombreux à être portés par des virus. Chez ces derniers, la distribution fonctionnelle des gènes composites est biaisée (enrichissement dans les familles essentielles pour la perpétuation du cycle viral), et les éléments des gènes composites trouvent même parfois leurs origines dans le matériel génétique de classes virales différentes. Plus généralement, l’étendue des processus combinatoires, en révélant des liens évolutionnaires autres que les liens d’homologie au sens fort, justifie une étude pluraliste des relations de similarité entre séquences.
https://tel.archives-ouvertes.fr/tel-01127379

NNT : 2014PA066358
tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379/document
https://tel.archives-ouvertes.fr/tel-01127379/file/2014PA066358.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This paper describes an operational protocol for integrating conservation and restoration with land-use planning in islands. Conservation challenges are intensified in insular systems due to higher ecosystem vulnerability, limited spatial options, low data availability, rapid land-use change and, globally, short-term vision planning. Our operational planning protocol integrates ecological and socio-economic factors to identify the best spatial options for conserving and restoring biodiversity, inside and outside extant reserves, while minimising future land-use conflicts. Conservation and restoration targets are formulated for species, habitats and ecological processes that support biodiversity. An optimal network of priority sites is selected to achieve those targets across the landscape. The prioritisation process integrates a Conservation Costs Index to optimise conservation and restoration investments. We discuss the outcomes of the planning protocol in terms of site prioritisation, stakeholders' participation and general implications for spatial planning in insular systems. As with many islands, the study area of Réunion Island has experienced rapid urban and agricultural expansion, which threatens its unique biodiversity. Forty three per cent of the island is currently protected in a National Park but only half of this reserve network contributes to the achievement of targets. An additional 21% of land should be conserved mainly to ensure the persistence of ecological connections between the marine, terrestrial and freshwater realms. Finally we emphasize that our method doesn't substitute the land-use planning debate but is aimed to better prepare the conservation sector for negotiating future land-use allocation with other socio-economic sectors in islands
Landscape and Urban Planning

halsde-00676425
https://hal.archives-ouvertes.fr/halsde-00676425
DOI : 10.1016/j.landurbplan.2011.02.004