Éditeur(s) : HAL CCSD
Résumé : International audience
18th International Conference on Software Engineering and Data Engineering (SEDE'09)

hal-00406165
https://hal.archives-ouvertes.fr/hal-00406165

Éditeur(s) : HAL CCSD ACM
Résumé : International audience
Applications over wireless sensor networks are growing quickly. Traditional software development tools are not well adapted to this technology. In particular, adequate testing methodologies are required. Many issues have not been formally addressed as energy-conservation, congestion control, reliability data dissemination, security. In this paper, we present a pragmatic approach to detect some kind of anomalies based on defined scenarios on wireless sensor networks. A scenario is considered as a set of events which should happen on the network in an ordered way. We discuss a formal architecture able to perform these scenarios over the wireless sensor networks and to raise alarms if necessary. This methodology has been implemented on a prototype and has been experimented with various examples. This contribution is a first attempt for a formal testing methodology for wireless sensor networks.
Proceedings of the 6th ACM workshop on QoS and security for wireless and mobile networks

Droits : info:eu-repo/semantics/OpenAccess
hal-00596118
https://hal.archives-ouvertes.fr/hal-00596118
https://hal.archives-ouvertes.fr/hal-00596118/document
https://hal.archives-ouvertes.fr/hal-00596118/file/Q2sWinet_10.pdf
DOI : 10.1145/1868630.1868641

Résumé : This study is inserted within the research project Risco, which aims at understanding the causes of oysters mortalities in the bay of Quiberon, since 2006. The objective was to test the feasability of an automatic segmentation of sonar images devoted to the distinction of molluscs (oysters and crepidulas) and sedimentary substrate. The method tested was of the type "segmentation dirigée basée région", implemented on the software SonarScope. It could be applied successfully only on muddy sediment where it succeeded to identify the shellfish sectors with negligeable error. However the distinction between oysters and crepidulas proved to be very delicate. A generalization to other sectors of the bay will be attempted.
Dans le cadre du projet RISCO sur la compréhension des facteurs de mortalité d'huîtres en Baie de Quiberon (France), l'objectif du stage était de tester la possibilité d'une segmentation automatique d'imagerie sonar en vue de distinguer les faciès coquilliers (huîtres et crépidules) du substrat sédimentaire. La méthode testée était de type « segmentation dirigée basée région » implémentée sous le logiciel SonarScope. Cette approche testée uniquement en secteur vaseux s'est montrée capable de détecter sans confusion les secteurs coquilliers. La distinction entre crépidules et huîtres s'est par contre avérée pour le moment très délicate. Une généralisation a d'autres secteurs sédimentaires de la Baie reste à menée.

Droits : 2011 Ifremer, UBS
http://archimer.ifremer.fr/doc/00128/23946/21911.pdf
http://archimer.ifremer.fr/doc/00128/23946/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
AimBiological invasions are major contributors to global change and native biodiversity decline. However, they are overlooked in marine conservation plans. Here, we examine for the first time the extent to which marine conservation planning research has addressed (or ignored) biological invasions. Furthermore, we explore the change of spatial priorities in conservation plans when different approaches are used to incorporate the presence and impacts of invasive species.LocationGlobal analysis with a focus on the Mediterranean Sea region.MethodsWe conducted a systematic literature review consisting of three steps: (1) article selection using a search engine, (2) abstract screening and (3) review of pertinent articles, which were identified in the second step. The information extracted included the scale and geographical location of each case study as well as the approach followed regarding invasive species. We also applied the software Marxan to produce and compare conservation plans for the Mediterranean Sea that either protect, or avoid areas impacted by invasives, or ignore the issue. One case study focused on the protection of critical habitats, and the other on endemic fish species.ResultsWe found that of 119 papers on marine spatial plans in specific biogeographic regions, only three (2.5%) explicitly took into account invasive species. When comparing the different conservation plans for each case study, we found that the majority of selected sites for protection (ca. 80%) changed in the critical habitat case study, while this proportion was lower but substantial (27%) in the endemic fish species case study.Main conclusionsBiological invasions are being widely disregarded when planning for conservation in the marine environment across local to global scales. More explicit consideration of biological invasions can significantly alter spatial conservation priorities. Future conservation plans should explicitly account for biological invasions to optimize the selection of marine protected areas.
ISSN: 1366-9516

hal-01431351
https://hal-univ-perp.archives-ouvertes.fr/hal-01431351
DOI : 10.1111/ddi.12491

Éditeur(s) : HAL CCSD
Résumé : International audience
proceedings of 13th International Conference on Intelligent and Adaptive Systems and Software Engineering (IASSE-2004)
Nice, France

hal-00354653
https://hal.archives-ouvertes.fr/hal-00354653

Éditeur(s) : HAL CCSD
Résumé : International audience
Pen-based interfaces allow users to interact with the help of a stylus and/or fingers. Thanks to a recognition system, users can execute commands by drawing gestures. Because of the complexity of the software, the set of gesture commands can be very large. Consequently, it becomes difficult for the users to remember all the commands. In this paper we introduce "Semicustomizable gestural commands". The idea is to take into account the commands usage frequency: to facilitate the memorization of the most used commands we leave users the freedom/liberty to define their associated gestures (by) themselves. The remaining gesture commands will be automatically generated on the base of the defined gestures according to their hierarchical categorization. Several comparative tests demonstrate that this new approach improved the progressive memorization of the gestural commands.
ICFHR 2012 - International Conference on Frontiers in Handwriting Recognition
Bari, Italy

hal-00708750
https://hal.inria.fr/hal-00708750
https://hal.inria.fr/hal-00708750/document
https://hal.inria.fr/hal-00708750/file/ICFHR_LI_IEEE.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Various types of genome and gene similarity networks along with their characteristics have been increasingly used for retracing different kinds of evolutionary and ecological relationships. Here, we present a new polynomial time algorithm and the corresponding software (BRIDES) to provide characterization of different types of paths existing in evolving (or augmented) similarity networks under the constraint that such paths contain at least one node that was not present in the original network. These different paths are denoted as Breakthroughs , Roadblocks, Impasses, Detours, Equal paths, and Shortcuts. The analysis of their distribution can allow discriminating among different evolutionary hypotheses concerning genomes or genes at hand. Our approach is based on an original application of the popular shortest path Dijkstra's and Yen's algorithms.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01361753
http://hal.upmc.fr/hal-01361753
http://hal.upmc.fr/hal-01361753/document
http://hal.upmc.fr/hal-01361753/file/journal.pone.0161474.PDF
DOI : 10.1371/journal.pone.0161474

Éditeur(s) : HAL CCSD
Résumé : International audience
Background In life sciences, there is a growing need for new informatics tools designed to provide automated solutions in order to analyze big amounts of images obtained from high-throughput imaging systems. Among the most widely used assays in neurotoxicity, endocrinology and brain diseases, the neurite outgrowth assay is popular. New method Cell-to-cell quantification of the main morphological features of neurite outgrowth assays remains very challenging. Here, we provide a new pipeline developed on Fiji software for analysis of series of two-dimensional images. It allows the automated analysis of most of these features. Results We tested the accuracy and usefulness of the software by confirming the effects of estradiol and hypoxia on in vitro neuronal differentiation, previously published by different authors with manual analysis methods. With this new method, we highlighted original interesting data. Comparison with existing method(s) The innovation brought by this plugin lies in the fact that it can process multiple images at the same time, in order to obtain: the number of nuclei, the number of neurites, the length of neurites, the number of neurites junctions, the number of neurites branches, the length of each branch, the position of the branch in the image, the angle of each branch, but also the area of each cell and the number of neurites per cell. Conclusions This plugin is easy to use, highly sensitive, and allows the experimenter to acquire ready-to-use data coming from a vast amount of images. © 2016 Elsevier B.V.
Journal of Neuroscience Methods

hal-01367152
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367152
DOI : 10.1016/j.jneumeth.2016.07.011
PUBMED : 27450924

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
UNLABELLED: ABSTRACT: BACKGROUND: Genomics, transcriptomics and proteomics of glioblastoma multiforme (GBM) have recently emerged as possible tools to discover therapeutic targets and biomarkers for new therapies including immunotherapy. It is well known that macroscopically complete surgical excision, radiotherapy and chemotherapy have therapeutic limitations to improve survival in these patients. In this study, we used a differential proteomic-based technique (2D-Difference Gel Electrophoresis) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to identify proteins that may serve as brain tumor antigens in new therapeutic assays. Five samples of patients presenting a GBM and five samples of microscopically normal brain tissues derived from brain epileptic surgery specimen were labeled and run in 2D-PAGE (Two-Dimensional Polyacrylamide Gel Electrophoresis) with an internal pool sample on each gel. Five gels were matched and compared with DIA (Difference In-gel Analysis) software. Differential spots were picked, in-gel digested and peptide mass fingerprints were obtained. RESULTS: From 51 protein-spots significantly up-regulated in GBM samples, mass spectrometry (MS) identified twenty-two proteins. The differential expression of a selected protein set was first validated by western-blotting, then tested on large cohorts of GBM specimens and non-tumor tissues, using immunohistochemistry and real-time RT-PCR. CONCLUSIONS: Our results confirmed the importance of previously described proteins in glioma pathology and their potential usefulness as biological markers but also revealed some new interesting targets for future therapies.
ISSN: 1477-5956

inserm-00585020
http://www.hal.inserm.fr/inserm-00585020
http://www.hal.inserm.fr/inserm-00585020/document
http://www.hal.inserm.fr/inserm-00585020/file/1477-5956-9-16.pdf
DOI : 10.1186/1477-5956-9-16

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches. Results: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts. Conclusion: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.
ISSN: 1471-2148

hal-01544799
https://hal.archives-ouvertes.fr/hal-01544799
DOI : 10.1186/1471-2148-13-146

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : Absolute Mα and Mβ X-ray intensities were measured for the elements Pt, Au, Pb, U, and Th by electron impact for energies ranging from 6 to 38 keV. Experimental data were obtained by measuring the X-ray intensity emitted from bulk samples with an electron microprobe using high-resolution wavelength-dispersive spectrometers. Recorded X-ray intensities were converted into absolute X-ray yields by evaluation of the detector efficiency and then compared with X-ray intensities calculated by means of Monte Carlo simulations. Simulated Mα and Mβ X-ray intensities were found to be in good agreement with the measurements, allowing their use in standardless quantification methods. A procedure and a software program were developed to accurately obtain virtual standard values. Standardless quantifications of Pb and U were tested on standards of PbS, PbTe, PbCl2, vanadinite, and UO2.
ISSN: 0003-2700

hal-01217495
https://hal.archives-ouvertes.fr/hal-01217495
DOI : 10.1021/acs.analchem.5b01443

Éditeur(s) : HAL CCSD University of California, Los Angeles
Résumé : International audience
The dbmss package for R provides an easy-to-use toolbox to characterize the spatial structure of point patterns. Our contribution presents the state of the art of distance-based methods employed in economic geography and which are also used in ecology. Topographic functions such as Ripley’s K, absolute functions such as Duranton and Overman’s Kd and relative functions such as Marcon and Puech’s M are implemented. Their confidence envelopes (including global ones) and tests against counterfactuals are included in the package
ISSN: 1548-7660

hal-01498361
https://hal-agroparistech.archives-ouvertes.fr/hal-01498361
DOI : 10.18637/jss.v067.c03

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 Wiley
Résumé : International audience
Two genome-wide association studies (GWASs) recently highlighted the HLA-DRA and HLA-DRB5 genes as associated with Parkinson disease (PD). However, because HLA-DRA displays a low level of polymorphisms and HLA-DRB5 is only present in approximately 20% of the population, these findings are difficult to interpret. Our aims were: (1) to replicate and investigate in greater detail the association between PD and the HLA-DR region; (2) to identify PD-associated HLA alleles; and (3) to perform a meta-analysis of our top finding. As part of 2 French population-based case-control studies of PD including highly ethnically homogeneous participants, we investigated the association between PD and 51 Single-nucleotide polymorphisms (SNPs) in the HLA-DR region. HLA-DRB1 alleles were imputed using the HLA(*) IMP software. HLA typing was performed in a subsample of the participants. We performed a meta-analysis of our top finding based on 4 GWAS data sets. Among 499 cases and 1123 controls, after correction for multiple testing, we found an association with rs660895 (OR/minor allele, 0.70; 95% CI, 0.57-0.87) within the HLA-DRB1 gene, which encodes the most polymorphic HLA-DR chain (DRβ). A meta-analysis (7996 cases, 36455 controls) confirmed this association (OR, 0.86; 95% CI, 0.82-0.91; P < .0001). SNP-based imputation of HLA alleles showed an inverse association between PD and the HLA-DRB1(*) 04 allele. We replicated an association between PD and the HLA-DR region and provided further insight into the loci and alleles involved. The highly polymorphic HLA-DRB1 locus contains rs660895, which represents a more legitimate candidate than previous ones. Our finding is in agreement with the hypothesis of an immune component in PD pathophysiology. © 2012 Movement Disorder Society.
ISSN: 0885-3185

inserm-00721562
http://www.hal.inserm.fr/inserm-00721562
http://www.hal.inserm.fr/inserm-00721562/document
http://www.hal.inserm.fr/inserm-00721562/file/Table1.pdf
http://www.hal.inserm.fr/inserm-00721562/file/Table2.pdf

Éditeur(s) : HAL CCSD Frontiers
Résumé : International audience
The generation of handwriting is a complex neuromotor skill requiring the interaction of many cognitive processes. It aims at producing a message to be imprinted as an ink trace left on a writing medium. The generated trajectory of the pen tip is made up of strokes superimposed over time. The Kinematic Theory of rapid human movements and its family of lognormal models provide analytical representations of these strokes, often considered as the basic unit of handwriting. This paradigm has not only been experimentally confirmed in numerous predictive and physiologically significant tests but it has also been shown to be the ideal mathematical description for the impulse response of a neuromuscular system. This latter demonstration suggests that the lognormality of the velocity patterns can be interpreted as reflecting the behavior of subjects who are in perfect control of their movements. To illustrate this interpretation, we present a short overview of the main concepts behind the Kinematic Theory and briefly describe how its models can be exploited, using various software tools, to investigate these ideal lognormal behaviors. We emphasize that the parameters extracted during various tasks can be used to analyze some underlying processes associated with their realization. To investigate the operational convergence hypothesis, we report on two original studies. First, we focus on the early steps of the motor learning process as seen as a converging behavior toward the production of more precise lognormal patterns as young children practicing handwriting start to become more fluent writers. Second, we illustrate how aging affects handwriting by pointing out the increasing departure from the ideal lognormal behavior as the control of the fine motricity begins to decline. Overall, the paper highlights this developmental process of merging toward a lognormal behavior with learning, mastering this behavior to succeed in performing a given task, and then gradually deviating from it with aging.
ISSN: 1664-1078

hal-01098124
https://hal.archives-ouvertes.fr/hal-01098124
DOI : 10.3389/fpsyg.2013.0094

Éditeur(s) : HAL CCSD
Résumé : International audience
Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports. Availability and Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www.outils.genomique.biologie.ens.fr/aozan/. Aozan source code is available on GitHub: https://github.com/GenomicParisCentre/aozan.
Bioinformatics

hal-01545317
https://hal.archives-ouvertes.fr/hal-01545317
DOI : 10.1093/bioinformatics/btx154

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 Oxford University Press (OUP)
Résumé : International audience
Ocean loading effects cause 3-D displacements large enough to affect space geodesy measurements either at the subdiurnal periods or at longer time scales by the means of spurious signals. GPS measurements, in turn, could provide local improvements of the models in coastal areas if their ability to precisely monitor such rapid displacements is assessed. In this paper, we use 105 days of continuous GPS measurements collected in 2004 in the French Brittany and Cotentin region to investigate: (1) the precision achieved by the GPS analysis on measuring 3-D subdiurnal displacements and amplitude and phase of the tidal constituents, (2) the quality of the most recent ocean tide model FES2004 in such a complex coastal context. Indeed, in this area, tide amplitudes are among the largest in the world (up to 16 cm of loading displacements on the vertical component) and are believed to show strong shallow-water tides. From a state of the art GPS analysis using the scientific GAMIT software over 2-h sessions, we test two independent strategies for the realization of the reference frame. The position time series are then compared with the displacements predicted by the FES2004 model applied on an elastic Earth model. The two sets of results are consistent with each other at the same level of agreement than with the predicted displacements, namely 3–5 mm on the horizontal components, 10 mm on the vertical. This assesses the capability of this technique for measuring 3-D ocean tide loading deformation. We validate the FES2004 model in the Brittany area, even though it slightly (2–7 mm) underestimates the three components amplitudes. With a harmonic analysis of the observed position time series, we obtain nevertheless an agreement at a submillimetre level for the M2, N2, O1, Q1 tidal constituents and at a millimetre level for the K1 and S2 tidal constituents. Moreover, we can extract a significant M4 load signal at the 95 per cent confidence level from the GPS time series at the stations located in the Mont St Michel area. The detection of other shallow-water constituents would be helpful to understand the amplitude deficit between the FES2004 predicted and GPS observed displacements.
ISSN: 0956-540X

insu-00335909
https://hal-insu.archives-ouvertes.fr/insu-00335909
https://hal-insu.archives-ouvertes.fr/insu-00335909/document
https://hal-insu.archives-ouvertes.fr/insu-00335909/file/Vergnolle_GJI_08_revised.pdf
DOI : 10.1111/j.1365-246X.2008.03734.x