Éditeur(s) : HAL CCSD
Résumé : LPSC14037
Scientific data collected with modern sensors or dedicated detectors exceed very often the perimeter of the initial scientific design. These data are obtained more and more frequently with large material and human efforts. A large class of scientific experiments are in fact unique because of their large scale, with very small chances to be repeated and to superseded by new experiments in the same domain: for instance high energy physics and astrophysics experiments involve multi-annual developments and a simple duplication of efforts in order to reproduce old data is simply not affordable. Other scientific experiments are in fact unique by nature: earth science, medical sciences etc. since the collected data is "time-stamped" and thereby non-reproducible by new experiments or observations. In addition, scientific data collection increased dramatically in the recent years, participating to the so-called "data deluge" and inviting for common reflection in the context of "big data" investigations. The new knowledge obtained using these data should be preserved long term such that the access and the re-use are made possible and lead to an enhancement of the initial investment. Data observatories, based on open access policies and coupled with multi-disciplinary techniques for indexing and mining may lead to truly new paradigms in science. It is therefore of outmost importance to pursue a coherent and vigorous approach to preserve the scientific data at long term. The preservation remains nevertheless a challenge due to the complexity of the data structure, the fragility of the custom-made software environments as well as the lack of rigorous approaches in workflows and algorithms. To address this challenge, the PREDON project has been initiated in France in 2012 within the MASTODONS program: a Big Data scientific challenge, initiated and supported by the Interdisciplinary Mission of the National Centre for Scientific Research (CNRS). PREDON is a study group formed by researchers from different disciplines and institutes. Several meetings and workshops lead to a rich exchange in ideas, paradigms and methods. The present document includes contributions of the participants to the PREDON Study Group, as well as invited papers, related to the scientific case, methodology and technology. This document should be read as a "facts finding" resource pointing to a concrete and significant scientific interest for long term research data preservation, as well as to cutting edge methods and technologies to achieve this goal. A sustained, coherent and long term action in the area of scientific data preservation would be highly beneficial.
http://hal.in2p3.fr/in2p3-00959072

in2p3-00959072
http://hal.in2p3.fr/in2p3-00959072
http://hal.in2p3.fr/in2p3-00959072/document
http://hal.in2p3.fr/in2p3-00959072/file/PREDON_Scientific_Data_Preservation_2014.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : Nominally anhydrous minerals (NAMs) of Earth's mantle can contain hydrogen as atomic impurity in their crystal structures. This hydrogen substantially modifies many physical properties of Earth's mantle rocks. Also, the Earth's deep interior is made of rocks where minerals are separated by nanometer-scale interfaces call grain boundaries and interphase boundaries. These grain boundaries should carefully be considered as a potential hydrogen reservoir as well. I report here an experimental investigation of hydrogen diffusion through grain boundaries in olivine polycrystalline aggregates. Hot-press and diffusion experiments were performed using a gas-medium high-pressure vessel at a confining pressure of 300 MPa, over a temperature range of 1000-1200 degrees C. The diffusion assembly consisted of a dense polycrystalline cylinder of natural olivine from San Carlos (Arizona) mixed with olivine singles crystals of millimeter size. This mixture was couple with a talc cylinder. Ni capsule were used to buffer the oxygen fugacity at Ni-NiO level. Experiment durations varied from 3 min to 4 h. The presence of hydrogen in the sample was quantified using Fourier transform infrared spectroscopy. The calculation of the diffusion coefficients was based on the estimation of the length of polycrystalline solid affected by the diffusion of hydrogen. The absence or presence of hydrogen was recorded by the large olivines behaving here as "hydrogen sensor", which are implanted in the aggregate. The results indicate that effective hydrogen diffusivity which includes grain boundaries effect in olivine aggregate is barely one order of magnitude faster than hydrogen diffusion in an olivine single crystal with a diffusivity similar to 8.5x 10(-10) m(2) s(-1) 1000 degrees C and only twice faster similar to 2.1 x10(-9) m(2) s(-1) 1200 degrees C. Calculations of the diffusion data in relation to the Arrhenius Law, yield an activation energy of similar to 70 +/- 10 kJ mol(-l) . From these effective diffusivities and combined with published diffusion data for olivine single crystals, hydrogen diffusion in grain boundaries is extracted and yield diffusivities almost three order of magnitude faster (similar to 5 x 10(-6) m(2) s(-1) at 1200 degrees C) than in an olivine single crystal at the equivalent high temperature. On geological scales and for coarse-grain rocks, hydrogen diffusivity in grain boundaries is not fast enough to compete with lattice diffusion. The relative large grain size of mantle rocks will ensure a very limited hydrogen transport by effective diffusion, and a good conservation of water-rich zones in the Earth's mantle.
ISSN: 0012-821X

hal-00512821
https://hal.archives-ouvertes.fr/hal-00512821
DOI : 10.1016/j.epsl.2010.04.019

Éditeur(s) : HAL CCSD
Résumé : International audience
Optimizing the resource extraction and limiting the environmental constraint motivate to accurately characterize reservoirs. The extraction of resources induces volume change of the reservoir causing displacements in the surrounding medium up to the surface. The resulting surface deformation is usually significant enough to be measurable by geodetic instruments (GPS, satellites, tiltmeters, strainmeters). However, the data needs to be associated to a reservoir model using an inverse scheme to allow the estimation of physical properties of the reservoir. Complete geodetic data including InSAR, GPS, tilt, strain and gravimetric data are uncommon for conventional, unconventional or mining exploitations. In this study, we work on the one site that gathers a wide range of geodetic data: the salt exploitation of Vauvert, France, operated by KemOne. Our approach aims at estimating the volume changes of the cavities created by the extraction combining all the available geodetic data. To do so, we minimize a global functional including weighting factors for each data type. The weighting factors are optimally estimated for our study and can be adapted depending on the issue. Hence, an optimal distribution of data can be suggested for a specific reservoir characterization.
79th EAGE Conference
Paris, France

Droits : http://hal.archives-ouvertes.fr/licences/copyright/
hal-01575426
https://hal.archives-ouvertes.fr/hal-01575426
https://hal.archives-ouvertes.fr/hal-01575426/document
https://hal.archives-ouvertes.fr/hal-01575426/file/reservoir-characterization-inversion.pdf
DOI : 10.3997/2214-4609.201700987

Éditeur(s) : HAL CCSD
Résumé : International audience
Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757

lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757/document

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
The present study is a contribution to the "neXt50 challenge", a coordinated effort across C-HPP teams to identify the SO most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 healthy donors. A targeted mass spectrometry-based strategy consisting of the development of LC-PRM assays (with heavy labeled synthetic peptides) targeting 92 proteotypic peptides of the 38 selected MPs was used. Out of the 38 selected MPs, 12 were identified with two or more peptides and 3 with one peptide after extensive SDS-PAGE fractionation of the two samples and with overall low-intensity signals. The PRM data are available via ProteomeXchange in PASSEL (PASS01013). Further validation by immunohistochemistry on human testes sections and cytochemistry on sperm smears was performed for eight MPs with antibodies available from the Human Protein Atlas. Deep analysis of human sperm still allows the validation of MPs and therefore contributes to the C-HPP worldwide effort. We anticipate that our results will be of interest to the reproductive biology community because an in-depth analysis of these MPs may identify potential new candidates in the context of human idiopathic infertilities.
ISSN: 1535-3893

hal-01681656
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01681656
DOI : 10.1021/acs.jproteome.7b00374

Éditeur(s) : HAL CCSD
Résumé : International audience
Dans ce travail, nous analysons les données concernant les articles publiés à la conférence EGC. Notre objectif est d’identifier et de comprendre les tendances en matière de collaborations. Pour ce faire, nous adoptons une modélisation descriptive, à travers une approche réseau qui consiste à générer tout d’abord le réseau de collaborations des auteurs à partir des données. Nous enrichissons ensuite les noeuds de ce réseau d’une dizaine d’attributs individuels extraits à partir des données. Enfin, nous recherchons des vues conceptuelles, une approche récente de clustering de liens, qui permet de synthétiser des réseaux en mettant en évidence les ensembles d’attributs retrouvés fréquemment liés dans le réseau. Les résultats obtenus montrent les tendances existantes dans les comportements de collaborations. Dans ce papier, nous présentons ces tendances et montrons comment elles évoluent selon différents seuils d’extraction.
Extraction et gestion des connaissances
Reims, France

hal-01312559
https://hal.archives-ouvertes.fr/hal-01312559

Éditeur(s) : HAL CCSD
Résumé : International audience
Modelling techniques for river hydrologic forecasting systems have taken advantage of machine learning methods especially for flood prediction. But current solutions, mostly based on artificial neural networks do not always meet end users requirements on the readability and the understandability of predictive models. In this paper, we present a new version of our original solution based on the concept of aggregate variables in order to predict flash flood events from observed water level and/or rain measurements, particularly in the context of caribbean watersheds in which flash flood are much uncertain. We combine aggregate variables in juries. Juries of aggregate variables are trained and tested using a typical 10-fold cross validation scheme. Best juries are searched through an evolutionary approach that is optimized. Different parameters are set up like aggregation periods and jury sizes to prove the efficiency of the proposed approach compared to classical solutions.
Congress on Evolutionary Computation (CEC) 2013
Cancun, Mexico

hal-00847582
https://hal.archives-ouvertes.fr/hal-00847582
DOI : 10.1109/CEC.2013.6557656

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
We report the development of the ReproGenomics Viewer (RGV), a multi-and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
ISSN: 0305-1048

hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/file/nar.gkv345.full.pdf
PUBMED : 25883147

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The Mediterranean hydrometeorological observatory Cévennes-Vivarais (OHM-CV) coordinates hydrometeorological observations (radars, rain gauges, water level stations) on a regional scale in southeastern France. In the framework of OHM-CV, temporary GPS measurements have been carried out for 2 months in autumn 2002, when the heaviest rainfall are expected. These measurements increase the spatial density of the existing permanent GPS network, by adding three more receivers between the Mediterranean coast and the Cévennes-Vivarais range to monitor maritime source of water vapour flow feeding the precipitating systems over the Cévennes-Vivarais region. In addition, a local network of 18 receivers covered an area of 30 by 30 km within the field of view of the meteorological radar. These regional and local networks of permanent and temporary stations are used to monitor the precipitable water vapour (PWV) with high temporal resolution (15 min). Also, the dense local network provided data which have been inverted using tomographic techniques to obtain the 3-D field of tropospheric water vapour content. This study presents methodological tests for retrieving GPS tropospheric observations from dense networks, with the aim of assessing the uncertainties of GPS retrievals. Using optimal tropospheric GPS retrieval methods, high resolution measurements of PWV on a local scale (a few kilometres) are discussed for rain events. Finally, the results of 3-D fields of water vapour densities from GPS tomography are analysed with respect to precipitation fields derived from a meteorological radar, showing a good correlation between precipitation and water vapour depletion areas.
ISSN: 1867-1381

hal-01022833
https://hal.archives-ouvertes.fr/hal-01022833
https://hal.archives-ouvertes.fr/hal-01022833/document
https://hal.archives-ouvertes.fr/hal-01022833/file/amt-7-553-2014.pdf
DOI : 10.5194/amt-7-553-2014

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A data stream is a potentially uninterrupted flow of data. Mining this flow makes it necessary to cope with uncertainty, as only a part of the stream can be stored. In this paper, we evaluate a statistical technique which biases the estimation of the support of patterns, so as to maximize either the precision or the recall, as chosen by the user, and limit the degradation of the other criterion. Theoretical results show that the technique is not far from the optimum, from the statistical standpoint. Experiments performed tend to demonstrate its potential, as it remains robust even under significant distribution drifts.
ISSN: 0031-3203

lirmm-00365474
https://hal-lirmm.ccsd.cnrs.fr/lirmm-00365474

Éditeur(s) : HAL CCSD Lavoisier
Résumé : International audience
In this paper, we present an heuristic based approach for feature selection in the context of flood prediction. Features are complex variables that represent aggregate values. We apply a preprocessing method on data in order to elicit relevant information that could not be easily accessible initially because it is split through several lines of a dataset. A genetic algorithm is used in order to search for the features that may prove the best performances for flood prediction.
ISSN: 1633-1311

hal-00840738
https://hal.archives-ouvertes.fr/hal-00840738
DOI : 10.3166/isi.16.3.113-139

Éditeur(s) : HAL CCSD Lavoisier
Résumé : National audience
Dans cette étude, nous présentons, une méthode permettant de découvrir, par le biais de variables agrégées et d’un algorithme génétique, des informations non connues a priori et utiles pour la prédiction de crues. Cette méthode se prête particulièrement bien aux données dans lesquelles des informations à propos d’un même élément sont dispersées à travers plusieurs lignes du jeu de données initial.
In this paper, we present an heuristic based approach for feature selection in the context of flood prediction. Features are complex variables that represent aggregate values. We apply a preprocessing method on data in order to elicit relevant information that could not be easily accessible initially because it is split through several lines of a dataset. A genetic algorithm is used in order to search for the features that may prove the best performances for flood prediction.
ISSN: 1633-1311

hal-01184510
https://hal.archives-ouvertes.fr/hal-01184510

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an "integrative omics" strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this "integrative omics" strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
PLoS ONE

hal-01063901
https://hal.archives-ouvertes.fr/hal-01063901
DOI : 10.1371/journal.pone.0104418
PUBMED : 25111155

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
This study describes a laboratory experiment on rip current circulations over a moveable bed. Rip current characteristics over eight contrasting nature-like beach morphologies are investigated. The seabed varied from reasonably alongshore uniform to strongly alongshore nonuniform with crescentic patterns and bar-rip morphologies, representative of a full morphological down-state sequence. The same offshore shore-normal waves were generated by the wavemaker for the eight situations with the same mean water level to study the sensitivity of rip current characteristics as a function of the beach morphology only. In each case, a 30 to 60 min video run was used to track a large number of drifters released within the surf zone. Results show the presence of classic rip current patterns with counterrotating cells and a relatively narrow offshore-directed jet varying from shore-normal to strongly skewed. Wave-driven circulations were strongly unstable. Computed standard deviations of flow intensity and direction provide high-resolution information on the spatial variability of rip current instabilities. Highly pulsating and weakly directionally variable offshore-directed flow is observed in the rip neck for well-developed bar-rip morphologies that turns into a weakly pulsating and highly directional variable rip current flow with decreasing beach alongshore nonuniformity. Proposing a definition of rip current intensity based on the rip current circulation geometry, rip current intensity was found to linearly increase with increasing measure of beach alongshore nonuniformity within both the low-energy and moderate-energy rip current regimes. To date, our laboratory experiment provides the first extensive quantitative rip current information during a full down-state sequence for a given wave condition.
ISSN: 0148-0227

hal-00602920
https://hal.archives-ouvertes.fr/hal-00602920
DOI : 10.1029/2010JC006343

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In this work we perform a statistical analysis of global solar radiation measured at two sites, Petit Canal and Pointe a Pitre, 38 km distant from, Guadeloupe, French West Indies. We have established a correlation model based on the coefficient of variation assuming a time scale separation. The coefficient of variation is calculated on 10 min interval with data measured at 1 Hz. This analysis highlights the dynamic correlation that can occur between measurements from two different sites with a time step of 1 s. From these results, knowing the coefficient of variation on a site, we have established a new correlation model on this parameter for another site. A diagram linking the standard deviation for the studied sites, for a given coefficient of variation is proposed for correlated and non-correlated cases. Moreover this analysis evidences the existence of a threshold time under which there is no significant correlation. The methodology and the model can be applied to any other sites to establish diagrams of the coefficient of variation.This model can be useful in choosing new sites of PV production in establishing correlation from on site to another
ISSN: 0960-1481

hal-01528078
https://hal.archives-ouvertes.fr/hal-01528078
DOI : 10.1016/j.renene.2015.10.049

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Microbial-based indicators, such as C and N contents or microbial functions involved in C and N cycles, are currently used to describe the status of soils in disturbed areas. Microbial functions are more accurate indicators but their measurement for studies at the ecosystem level remains problematical because of the huge spatial variability of these processes and, consequently, of the large number of soil samples which must be analyzed. Our goal was to test the capacity of near-infrared reflectance spectroscopy (NIRS) to predict respiration and denitrification but also carbon and nitrogen contents of soils submitted to various procedures of restoration. To achieve this objective, we took advantage of an experiment conducted on a reforestation system established after open-cast gold mining in French Guiana. In this experimental station, plantations of various ages and various soil textures were at our disposal. Our results showed that both plantations and soil texture had a strong impact on the recovery of soil functioning: carbon and nitrogen contents, respiration and denitrification increased with age of plantation and clay content. Calibrations were performed between spectral data and microbial-based indicators using partial least squares regression (PLS). The results showed that C and N contents were accurately predicted. Microbial functions were less precisely predicted with results more accurate on clayey soils than on sandy soils. In clayey soils, perturbed or restored soils and the year of plantation were discriminated very efficiently through principal component analyses of spectral signatures (over 80% of variance explained on the first two axes). Near-infrared spectroscopy may thus be extended to the prediction of functional soil parameters, but the capacity of this method must be strengthened by expending the databases with other soils in other contexts. The possibility of using NIRS provides many opportunities for understanding both the temporal dynamics and the spatial variability of the recovery of key microbial functions during soil restoration.
ISSN: 0929-1393

hal-01032188
https://hal.archives-ouvertes.fr/hal-01032188
DOI : 10.1016/j.apsoil.2007.07.001

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The western margin of the Gulf of Mexico (Veracruz State, Mexico) displays an extensive Neogene gravitational system, whereby the Neogene siliciclastic sediments are detached from underlying Mesozoic carbonates along decollement surface in Oligocene underpressured clays. Rapidly subsiding half-grabens develop above the footwall associated with major listric faults, whereas mini-basins develop in the deepest parts of the slope, in conjunction with the growth of west-verging compressional features. Between the high-angle normal faults in the west and the thrust anticlines in the east, a wide roll-over structure has grown progressively, resulting in a major topographic break in the morphology of the slope profile. Coupled forward kinematic modelling (Thrustpack) and stratigraphic modelling (Dionisos), calibrated against seismic profiles and two key nearshore wells, have been applied to representative regional transects across the margin, in order to quantify the vertical (subsidence) and horizontal (gravitational) deformations, and to discuss the impact of various key parameters on the distribution of debris flow depositions. These simulations are compared with data from distant ODP wells and discussed in the scope of current exploration strategies in both the US and Mexican portions of the Gulf of Mexico basin.
ISSN: 0040-1951

hal-00424595
https://hal.archives-ouvertes.fr/hal-00424595
DOI : 10.1016/j.tecto.2008.06.017

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : Upper Carboniferous heating and melting of the middle orogenic crust associated with the emplacement of syntectonic granitoids are documented in the Upper Gneissic Unit of the Livradois area (central part of the French Massif Central). Crustal melting post-dates peak metamorphism conditions (800-625 degrees C, 10-8 kb) dated at 360 +/- 4 Ma (U-Th-Pb on monazite). The P-T evolution of the metamorphic series indicates that Barrovian metamorphism was followed by a decompression (from 10 +/- 1 kbar to 6 +/- 1 kbar) associated with either a decrease in temperature in the southern part of the series or with an increase in temperature (of about 150 degrees C) in the northern part of the series. This evolution records the first step of the exhumation of the series coeval with granitoids intrusion, of which the emplacements were dated at 315 +/- 4 and 311 +/- 18 Ma (U-Pb on zircon). The final stage of the exhumation is associated with an isobaric cooling of the whole series. Similarity of Ar-40/Ar-39 ages for biotite in the paragneisses (307-300 Ma) and K-feldspar in the granitoids (306-300 Ma) document rapid cooling for this stage. Moreover dextral reverse mylonites, at the border and the northern part of the metamorphic series indicate north-south compression coeval with the unroofing of the series. Youngest Ar-40-Ar-39 ages on K-feldspar (274.6 +/- 5 Ma) combined with normal shearing in mylonites limiting the Carboniferous Brassac-les-Mines basin document the late Carboniferous-early Permian stage of extension coeval with the upwelling of the Velay granitic dome.
EISSN: 1777-5817

hal-00617429
https://hal.archives-ouvertes.fr/hal-00617429
DOI : 10.2113/gssgfbull.182.1.5

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
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome. © 2016 American Chemical Society.
Journal of Proteome Research

hal-01406074
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01406074
DOI : 10.1021/acs.jproteome.6b00400
PUBMED : 27444420