Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
ISSN: 1476-9271

hal-01401685
https://hal.inria.fr/hal-01401685
DOI : 10.1016/j.compbiolchem.2016.01.012
PUBMED : 26878129

Éditeur(s) : HAL CCSD
Résumé : International audience
In this paper, we introduce the Intuidoc-Loustic Gestures DataBase (ILGDB), a new publicly available database of realistic pen-based gestures for evaluation of recognition systems in pen-enabled interfaces. ILGDB was collected in a real world context and in an immersive environment. As it contains a large number of unconstrained user-defined gestures, ILGDB offers a unique diversity of content that is likely to serve as a precious tool for benchmarking of gesture recognition systems. We report first baseline experimental results on the task of Writer-Dependent gesture recognition.
ICPR2012 - 21st International Conference on Pattern Recognition
Tsukuba, Japan

hal-00802340
https://hal.inria.fr/hal-00802340
https://hal.inria.fr/hal-00802340/document

Éditeur(s) : HAL CCSD
Résumé : Cell signaling contains the whole biological mecanisms allowing the response of a cell to its microenvironnement in an adapted way. Many extremely intertwinned biological reactions are involved in a network that behaves as a complex system. The understanding of cell response requires the development of data acquisition technics and methods to formalize data into models. This point is the main drive of this thesis. We present here two approaches in order to analyse different granularities of cell signaling. In the first one, we used differential model to study the role of a new component of TGF-β canonical pathway. In the second one, we explored the combinatorial complexity of cell signaling, developing a discrete formalism based on guarded transitions. In this approach, we interpreted the whole database Pathway Interaction Database into a single unified model of signal transduction. Simulation and analysis methods, such as reachability and invariance research, have been developed. The interests are presented through an application on cell cycle regulation by cell signaling, and a global analysis on the regulation of genes compared to experimental data.
La signalisation cellulaire regroupe l'ensemble des mécanismes biologiques permettant à une cellule de répondre de façon adaptée à son microenvironnement. Pour ce faire, de nombreuses réactions biologiques entrent en jeux avec un important enchevêtrement, créant ainsi un réseau dont le comportement s'apparente à un système complexe. Le compréhension de la réponse cellulaire à une stimulation passe par le développement conjoint des techniques d'acquisition de données, et des méthodes permettant de formaliser ces données dans un modèle. C'est sur ce dernier point que s'inscrivent les travaux exposés dans cette thèse. Nous présentons ici deux approches visant à répondre à des questions de natures différentes sur la signalisation cellulaire. Dans la première nous utilisons un modèle différentiel pour étudier le rôle d'un nouvel interactant dans la voie canonique du TGF-beta. Dans la seconde nous avons exploré la combinatoire de la signalisation cellulaire en développant un formalisme discret basé sur les transitions gardées. Cette approche regroupe l'interprétation de la base de données Pathway Interaction Database dans un unique modèle dynamique de propagation du signal. Des méthodes de simulations et d'analyses inspirées des techniques de vérification de modèles telles que l'atteignabilité et l'invariance ont été développées. En outre, nous avons étudié la régulation du cycle cellulaire en réponse à la signalisation, ainsi que la régulation des gènes de notre modèle en comparaison avec des données d'expressions.
https://tel.archives-ouvertes.fr/tel-00926487

Droits : info:eu-repo/semantics/OpenAccess
tel-00926487
https://tel.archives-ouvertes.fr/tel-00926487
https://tel.archives-ouvertes.fr/tel-00926487/document
https://tel.archives-ouvertes.fr/tel-00926487/file/AndrieuxThese.pdf

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
This paper presents our response to the first interna- tional challenge on Facial Emotion Recognition and Analysis. We propose to combine different types of features to automatically detect Action Units in facial images. We use one multi-kernel SVM for each Action Unit we want to detect. The first kernel matrix is computed using Local Gabor Binary Pattern histograms and a histogram intersection kernel. The second kernel matrix is computed from AAM coefficients and an RBF kernel. During the training step, we combine these two types of features using the recently proposed SimpleMKL algorithm. SVM outputs are then averaged to exploit temporal information in the sequence. To eval- uate our system, we perform deep experimentations on several key issues: influence of features and kernel function in histogram- based SVM approaches, influence of spatially-independent in- formation versus geometric local appearance information and benefits of combining both, sensitivity to training data and interest of temporal context adaptation. We also compare our results to those of the other participants and try to explain why our method had the best performance during the FERA challenge.
ISSN: 1083-4419

hal-00731864
http://hal.upmc.fr/hal-00731864
http://hal.upmc.fr/hal-00731864/document
http://hal.upmc.fr/hal-00731864/file/senechal12tsmc_preprint.pdf
DOI : 10.1109/TSMCB.2012.2193567

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Radiofrequency radiations constitute a new form of environmental pollution. Among them, millimeter waves (MMW) will be widely used in the near future for high speed communication systems. This study aimed therefore to evaluate the biocompatibility of MMW at 60 GHz. For this purpose, we used a whole gene expression approach to assess the effect of acute 60 GHz exposure on primary cultures of human keratinocytes. Controls were performed to dissociate the electromagnetic from the thermal effect of MMW. Microarray data were validated by RT-PCR, in order to ensure the reproducibility of the results. MMW exposure at 20 mW/cm2, corresponding to the maximum incident power density authorized for public use (local exposure averaged over 1 cm2), led to an increase of temperature and to a strong modification of keratinocyte gene expression (665 genes differentially expressed). Nevertheless, when temperature is artificially maintained constant, no modification in gene expression was observed after MMW exposure. However, a heat shock control did not mimic exactly the MMW effect, suggesting a slight but specific electromagnetic effect under hyperthermia conditions (34 genes differentially expressed). By RT-PCR, we analyzed the time course of the transcriptomic response and 7 genes have been validated as differentially expressed: ADAMTS6, NOG, IL7R, FADD, JUNB, SNAI2 and HIST1H1A. Our data evidenced a specific electromagnetic effect of MMW, which is associated to the cellular response to hyperthermia. This study raises the question of co-exposures associating radiofrequencies and other environmental sources of cellular stress.
ISSN: 1932-6203

hal-01118066
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118066
PUBMED : 25302706
DOI : 10.1371/journal.pone.0109435
PUBMEDCENTRAL : PMC4193780

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A novel antimicrobial peptide, named Bicarinalin, has been isolated from the venom of the ant Tetramorium bicarinatum. Its amino acid sequence has been determined by de novo sequencing using mass spectrometry and by Edman degradation. Bicarinalin contained 20 amino acid residues and was C-terminally amidated as the majority of antimicrobial peptides isolated to date from insect venoms. Interestingly, this peptide had a linear structure and exhibited no meaningful similarity with any known peptides. Antibacterial activities against Staphylococcus aureus and S. xylosus strains were evaluated using a synthetic replicate. Bicarinalin had a potent and broad antibacterial activity of the same magnitude as Melittin and other hymenopteran antimicrobial peptides such as Pilosulin or Defensin. Moreover, this antimicrobial peptide has a weak hemolytic activity compared to Melittin on erythrocytes, suggesting potential for development into an anti-infective agent for use against emerging antibiotic-resistant pathogens.
ISSN: 0196-9781

hal-00996401
https://hal.archives-ouvertes.fr/hal-00996401
DOI : 10.1016/j.peptides.2012.08.018
PUBMED : 22960382

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
Polycyclic aromatic hydrocarbons (PAHs) such as benzo(a)pyrene (B(a)P) are widely distributed environmental contaminants, known as potent ligands of the aryl hydrocarbon receptor (AhR). These chemicals trigger an early and transient increase of intracellular calcium concentration ([Ca(2+)](i)), required for AhR-related effects of PAHs. The mechanisms involved in this calcium mobilization were investigated in the present study. We demonstrated that B(a)P-mediated [Ca(2+)](i) induction was prevented in endothelial HMEC-1 cells by counteracting β2-adrenoreceptor (β2ADR) activity using pharmacological antagonists, anti-β2ADR antibodies, or siRNA-mediated knockdown of β2ADR expression; by contrast, it was strongly potentiated by β2ADR overexpression in human kidney HEK293 cells. B(a)P was shown, moreover, to directly bind to β2ADR, as assessed by in vitro binding assays and molecular modeling. Pharmacological inhibition and/or siRNA-mediated silencing of various signaling actors acting downstream of β2ADR in a sequential manner, such as G protein, adenylyl cyclase, Epac-1 protein, and inositol 1,4,5-trisphosphate (IP(3))/IP(3) receptor, were next demonstrated to prevent B(a)P-induced calcium signal. Inhibition or knockdown of these signaling elements, as well as the use of chemical β-blockers, were finally shown to counteract B(a)P-mediated induction of cytochrome P-450 1B1, a prototypical AhR target gene. Taken together, our results show that B(a)P binds directly to β2ADR and consequently utilizes β2ADR machinery to mobilize [Ca(2+)](i), through activation of a G protein/adenylyl cyclase/cAMP/Epac-1/IP(3) pathway. This β2ADR-dependent signaling pathway activated by PAHs may likely be crucial for PAH-mediated up-regulation of AhR target genes, thus suggesting a contribution of β2ADR to the health-threatening effects of these environmental pollutants.
ISSN: 0021-9258

hal-00682497
https://hal.archives-ouvertes.fr/hal-00682497
DOI : 10.1074/jbc.M111.319970
PUBMED : 22167199

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
TIF1γ (Transcriptional Intermediary Factor 1 γ) has been implicated in Smad-dependent signaling by Transforming Growth Factor beta (TGF-β). Paradoxically, TIF1γ functions both as a transcriptional repressor or as an alternative transcription factor that promotes TGF-β signaling. Using ordinary differential-equation models, we have investigated the effect of TIF1γ on the dynamics of TGF-β signaling. An integrative model that includes the formation of transient TIF1γ-Smad2-Smad4 ternary complexes is the only one that can account for TGF-β signaling compatible with the different observations reported for TIF1γ. In addition, our model predicts that varying TIF1γ/Smad4 ratios play a critical role in the modulation of the transcriptional signal induced by TGF-β, especially for short stimulation times that mediate higher threshold responses. Chromatin immunoprecipitation analyses and quantification of the expression of TGF-β target genes as a function TIF1γ/Smad4 ratios fully validate this hypothesis. Our integrative model, which successfully unifies the seemingly opposite roles of TIF1γ, also reveals how changing TIF1γ/Smad4 ratios affect the cellular response to stimulation by TGF-β, accounting for a highly graded determination of cell fate.
ISSN: 1932-6203

hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483/document
https://hal.archives-ouvertes.fr/hal-00851483/file/pone.0033761.pdf
DOI : 10.1371/journal.pone.0033761

Éditeur(s) : HAL CCSD
Résumé : International audience
Two fluorescent galactofuranosides were synthesized and their biological activities evaluated on non-infected and Leishmania infected macrophages. Both tagged scaffolds were able to penetrate macrophages. Compared to the activity of the parent octyl galactofuranoside used as a reference, the fluorescein-conjugate showed altered biological properties while the rhodamine 6G one synergistically acted with the lipid chain to significantly increase antiparasitic activity.
Bioorganic & Medicinal Chemistry Letters

hal-01446721
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01446721
PUBMED : 27956346
DOI : 10.1016/j.bmcl.2016.11.090

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper presents the early work, done in the context of the IntuiScript project, on handwriting quality analysis. This IntuiScript project aims at developing a digital workbook to help with teaching children how to handwrite. To do so, we must be able to analyse their handwriting, to evaluate if the letters are correctly written, and to detail what aspects of the child symbols – letters, numbers, and geometric forms-do not correspond to the teacher models. We use an online fuzzy model to easily build target models, and to automatically evaluate the adequacy of children letters to these reference models, with respect to different aspects: symbol shape, drawing direction and stroke order for example.
17th Biennial Conference of the International Graphonomics Society
Pointe-à-Pitre, Guadeloupe

Droits : info:eu-repo/semantics/OpenAccess
hal-01165765
https://hal.univ-antilles.fr/hal-01165765
https://hal.univ-antilles.fr/hal-01165765/document
https://hal.univ-antilles.fr/hal-01165765/file/IGS_2015_submission_4.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the 'omics' data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation.
DATABASE

hal-01342472
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01342472
DOI : 10.1093/database/baw070
PUBMED : 27173522

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: The TGF-β transforming growth factor is the most pleiotropic cytokine controlling a broad range of cellular responses that include proliferation, differentiation and apoptosis. The context-dependent multifunctional nature of TGF-β is associated with complex signaling pathways. Differential models describe the dynamics of the TGF-β canonical pathway, but modeling the non-canonical networks constitutes a major challenge. Here, we propose a qualitative approach to explore all TGF-β-dependent signaling pathways. RESULTS: Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating the 137 human signaling maps from the Pathway Interaction Database into a single unified dynamic model. Temporal property-checking analyses of 15934 trajectories that regulate 145 TGF-β target genes reveal the association of specific pathways with distinct biological processes. We identify 31 different combinations of TGF-β with other extracellular stimuli involved in non-canonical TGF-β pathways that regulate specific gene networks. Extensive analysis of gene expression data further demonstrates that genes sharing CADBIOM trajectories tend to be co-regulated. CONCLUSIONS: As applied here to TGF-β signaling, CADBIOM allows, for the first time, a full integration of highly complex signaling pathways into dynamic models that permit to explore cell responses to complex microenvironment stimuli.
ISSN: 1752-0509

inserm-00978313
http://www.hal.inserm.fr/inserm-00978313
http://www.hal.inserm.fr/inserm-00978313/document
http://www.hal.inserm.fr/inserm-00978313/file/1752-0509-8-30.pdf
DOI : 10.1186/1752-0509-8-30

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Tilt fluctuations can potentially reflect the response of hydrosystems to important rainfall. In this context, long baseline tiltmeters have been installed in an underground tunnel penetrating the Fontaine de Vaucluse karst to study the medium deformation related to solicitations exerted by water infiltrating the hydrosystem. The instruments monitor the tilt as well as its spatial variation. Northward tilts reaching a 1 μrad amplitude are observed consecutively to rainfalls. The tilt amplitude is highly correlated with the Fontaine de Vaucluse outlet flow fluctuations. The measured tilt signal is also relatively homogeneous over a 150 m length. Different types of structure likely to produce such observations are tested in order to identify their location with respect to the tiltmeters, their dimension as well as the amount of water level variation in the structure. Following rainfalls, the infiltration of water modifies the pore pressure, inducing a medium deformation. The hypothesis of an homogeneous surface loading on the Vaucluse plateau is first refuted since the related tilt is much lower than the one measured. The water supplied by rainfalls has to accumulate in discontinuities in order to generate a higher tilt. So, the deformation related to a pressure exerted on a fracture filled by water is assessed. A first study reveals the interest of the tilt homogeneity information that constrains strongly the fracture properties. Thus, the fracture must be located at a distance more than a few hundreds metres from the tiltmeters in order to produce a tilt homogeneous in space. If the fracture is initially dry, it must also be filled on a height higher than 150 m consecutive to a rainfall in order to generate a tilt amplitude in the same magnitude as the one measured. Then, we explore the influence of water level variations on the tilt produced by a fracture located at the interface between the saturated and unsaturated zones, which are thereby permanently flooded. Since several parameters of that model satisfactorily explain the field observations, we discuss how simultaneous geodetical observations could provide complementary information that would further constrain the geometry of the structure at the origin of the medium deformation.
ISSN: 0956-540X

insu-01408482
https://hal-insu.archives-ouvertes.fr/insu-01408482
https://hal-insu.archives-ouvertes.fr/insu-01408482/document
https://hal-insu.archives-ouvertes.fr/insu-01408482/file/Lesparre-2017.pdf
DOI : 10.1093/gji/ggw446

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
This study demonstrates that 20-100 GHz range can be used for spatially-accurate focusing of heating inside the skin achieved by varying frequency and exposure beam size, as well as by enforcing air convection. The latter is also used to reduce overheating of skin surface. Heating at different skin depths depending on these parameters is investigated in detail using the hybrid bio-heat equation. In particular, it is shown that decreasing frequency and/or increasing exposure beam size at forced airflow result in elevation of heating of deeper layers of tissue and decrease of skin surface temperature. Changes of water content within 15%, which exceed those due to aging and presence of tumors, only slightly affect heating. Exposure intensity necessary to reach a target temperature significantly increases in different areas of body with elevated blood flow. Dependence on exposure intensity and hyperthermia treatment duration is also investigated and discussed. Results of this study suggest that the lower part of the millimeter-wave range is an attractive alternative for non-invasive thermal treatment of skin cancer with a high spatial resolution. Bioelectromagnetics. 36:464-475, 2015. © 2015 Wiley Periodicals, Inc
ISSN: 0197-8462

hal-01187403
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187403
DOI : 10.1002/bem.21929
PUBMED : 26179286

Éditeur(s) : HAL CCSD
Résumé : National audience
Congrès de la SPTC - Société de Pharmaco-Toxicologie Cellulaire
Paris, France

hal-01122677
https://hal.archives-ouvertes.fr/hal-01122677

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
Constitutive activation of the PI3K/mTOR signaling pathway contributes to carcinogenesis and metastasis in most, if not all, breast cancers. From a chromene backbone reported to inhibit class I PI3K catalytic subunits, several rounds of chemical syntheses led to the generation of a new collection of chromologues that showed enhanced ability to kill PI3K-addicted cancer cells and to inhibit Akt phosphorylation at serine 473, a hallmark of PI3K/mTOR activation. This initial screen uncovered a chromene designated DHM25 that exerted potent antitumor activity against breast tumor cell lines. Strikingly, DHM25 was shown to be a selective and covalent inhibitor of mTOR using biochemical and cellular analyses, modeling, and a large panel of kinase activity assays spanning the human kinome (243 kinases). Finally, in vivo, this novel drug was an efficient inhibitor of growth and metastasis of triple-negative breast cancer cells, paving the way for its clinical application in oncology
ISSN: 0022-2623

hal-01187307
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01187307
DOI : 10.1021/acs.jmedchem.5b00991
PUBMED : 26237138

Éditeur(s) : HAL CCSD
Résumé : International audience
Millimeter waves (MMW) will be increasingly used for future wireless telecommunications. Previous studies on skin keratinocytes showed that MMW could impact the mRNA expression of Transient Receptor Potential cation channel subfamily Vanilloid, member 2 (TRPV2). Here, we investigated the effect of MMW exposure on this marker, as well as on other membrane receptors such as Transient Receptor Potential cation channel subfamily Vanilloid, member 1 (TRPV1) and purinergic receptor P2X, ligand-gated ion channel, 3 (P2 × 3). We exposed the Neuroscreen-1 cell line (a PC12 subclone), in order to evaluate if acute MMW exposures could impact expression of these membrane receptors at the protein level. Proteotoxic stress-related chaperone protein Heat Shock Protein 70 (HSP70) expression level was also assessed. We used an original high-content screening approach, based on fluorescence microscopy, to allow cell-by-cell analysis and to detect any cell sub-population responding to exposure. Immunocytochemistry was done after 24 h MMW exposure of cells at 60.4 GHz, with an incident power density of 10 mW/cm2. Our results showed no impact of MMW exposure on protein expressions of HSP70, TRPV1, TRPV2, and P2 × 3. Moreover, no specific cell sub-populations were found to express one of the studied markers at a different level, compared to the rest of the cell populations. However, a slight insignificant increase in HSP70 expression and an increase in protein expression variability within cell population were observed in exposed cells, but controls showed that this was related to thermal effect. Bioelectromagnetics. 37:444–454, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Bioelectromagnetics

hal-01371963
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01371963
DOI : 10.1002/bem.21995
PUBMED : 27483046

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
: A new set-up for exposure of human cells in vitro at 37°C to pulse-modulated 300 MHz and 500 MHz signals of future magnetic resonance imaging (MRI) systems is designed, built up, and characterized. Two dipole antennas, specifically designed for ultra high field MRI, are used as radiating structures. The electromagnetic (EM) field distribution inside the incubator containing the cells is computed, and it is shown to be in a good agreement with measurements. The electric field at the cell level is quantified numerically. Local, 1g average, and averaged over the culture medium volume SAR are provided along with the standard deviation values for each well. Temperature increments are measured inside the culture medium during the exposure using an optical fiber thermometer. Then we identify the pulse parameters corresponding to the thermal threshold of 1°C, usually considered as a threshold for thermally-induced biological effects. For these parameters, the induction of heat shock proteins is assessed to biologically verify a potential thermal response of cells. The data demonstrate that, under the considered experimental conditions, exposure to pulsemodulated radiations emulating typical ultra high field MRI signals, corresponding to temperature increments below 1°C, does not trigger any heat shock response in human brain cells.
ISSN: 0018-9294

hal-00874329
https://hal.archives-ouvertes.fr/hal-00874329
DOI : 10.1109/TBME.2013.2270371
PUBMED : 23799680

Éditeur(s) : HAL CCSD
Résumé : International audience
BioEM 2015
Monterey, United States

hal-01164074
https://hal.archives-ouvertes.fr/hal-01164074