RDF Knowledge Graph Visualization From a Knowledge Extraction System

In this paper, we present a system to visualize RDF knowledge graphs. These graphs are obtained from a knowledge extraction system designed by GEOLSemantics. This extraction is performed using natural language processing and trigger detection. The user can visualize subgraphs by selecting some ontology features like concepts or individuals. The system is also multilingual, with the use of the annotated ontology in English, French, Arabic and Chinese

Gestion de l'incertitude dans le processus d'extraction de connaissances à partir de textes

The increase of textual sources over the Web offers an opportunity for knowledge extraction and knowledge base creation. Recently, several research works on this topic have appeared or intensified. They generally highlight that to extract relevant and precise information from text, it is necessary to define a collaboration between linguistic approaches, e.g., to extract certain concepts regarding named entities, temporal and spatial aspects, and methods originating from the field of semantics' processing. Moreover, successful approaches also need to qualify and quantify the uncertainty present in the text. Finally, in order to be relevant in the context of the Web, the linguistic processing need to be consider several sources in different languages. This PhD thesis tackles this problematic in its entirety since our contributions cover the extraction, representation of uncertain knowledge as well as the visualization of generated graphs and their querying. This research work has been conducted within a CIFRE funding involving the Laboratoire d'Informatique Gaspard Monge (LIGM) of the Université Paris-Est Marne la Vallée and the GEOLSemantics start-up. It was leveraging from years of accumulated experience in natural language processing (GeolSemantics) and semantics processing (LIGM).In this context, our contributions are the following:- the integration of a qualifation of different forms of uncertainty, based on ontology processing, within the knowledge extraction processing,- the quantification of uncertainties based on a set of heuristics,- a representation, using RDF graphs, of the extracted knowledge and their uncertainties,- an evaluation and an analysis of the results obtained using our approachLa multiplication de sources textuelles sur le Web offre un champ pour l'extraction de connaissances depuis des textes et à la création de bases de connaissances. Dernièrement, de nombreux travaux dans ce domaine sont apparus ou se sont intensifiés. De ce fait, il est nécessaire de faire collaborer des approches linguistiques, pour extraire certains concepts relatifs aux entités nommées, aspects temporels et spatiaux, à des méthodes issues des traitements sémantiques afin de faire ressortir la pertinence et la précision de l'information véhiculée. Cependant, les imperfections liées au langage naturel doivent être gérées de manière efficace. Pour ce faire, nous proposons une méthode pour qualifier et quantifier l'incertitude des différentes portions des textes analysés. Enfin, pour présenter un intérêt à l'échelle du Web, les traitements linguistiques doivent être multisources et interlingue. Cette thèse s'inscrit dans la globalité de cette problématique, c'est-à-dire que nos contributions couvrent aussi bien les aspects extraction et représentation de connaissances incertaines que la visualisation des graphes générés et leur interrogation. Les travaux de recherche se sont déroulés dans le cadre d'une bourse CIFRE impliquant le Laboratoire d'Informatique Gaspard Monge (LIGM) de l'Université Paris-Est Marne la Vallée et la société GEOLSemantics. Nous nous appuyons sur une expérience cumulée de plusieurs années dans le monde de la linguistique (GEOLSemantics) et de la sémantique (LIGM).Dans ce contexte, nos contributions sont les suivantes :- participation au développement du système d'extraction de connaissances de GEOLSemantics, en particulier : (1) le développement d'une ontologie expressive pour la représentation des connaissances, (2) le développement d'un module de mise en cohérence, (3) le développement d'un outil visualisation graphique.- l'intégration de la qualification de différentes formes d'incertitude, au sein du processus d'extraction de connaissances à partir d'un texte,- la quantification des différentes formes d'incertitude identifiées ;- une représentation, à l'aide de graphes RDF, des connaissances et des incertitudes associées ;- une méthode d'interrogation SPARQL intégrant les différentes formes d'incertitude ;- une évaluation et une analyse des résultats obtenus avec notre approch

Treatment of autoimmune encephalomyelitis with a histone deacetylase inhibitor: Analyzing the role of immune-response genes

We have previously shown that treatment of female NOD mice with a potent nonselective histone deacetylase inhibitor attenuated experimental autoimmune encephalomyelitis, a model for progressive multiple sclerosis. Herein we show that immunization with the MOG35-55 peptide induced prolonged upregulation of genes encoding interleukin 17A (IL-17A), aryl hydrocarbon receptor, and histone deacetylase 11 in the spinal cord whereas the subunits of IL-27, IL-27p28 and IL-27ebi3 were significantly increased in secondary lymphoid organs after a lag period. Interestingly, the nitric oxide synthase gene was prominently expressed in both of these anatomic compartments following immunization. Treatment with the histone modifier repressed the transcription of all of these genes induced by immunization. Moreover, the drug suppressed the steady-state levels of the migration inhibitory factor and CD274 genes in both the spinal cord and peripheral lymphoid tissues. At the same time, the CD39 gene was downregulated only in secondary lymphoid organs. Paradoxically, the epigenetic drug enhanced the expression of Declin-1 in the spinal cord, suggesting a protective role in neuronal disease. Immunization profoundly enhanced transcription of the chemokine CCL2 in the secondary lymphoid tissues without a corresponding increase in the translation of CCL2 protein. Histone hyperacetylation neither altered the transcription of CCL2 nor its cognate receptor CCR2 in the central nervous system and peripheral lymphoid tissues. Surprisingly, the drug did not exert modulatory influence on most other immune response-related genes previously implicated in encephalomyelitis. Nevertheless, our data uncover several potential molecular targets for the intervention of experimental autoimmune encephalomyelitis that have implications for the treatment of progressive multiple sclerosis

Enzyme prodrug therapy achieves site-specific, personalized physiological responses to the locally produced nitric oxide

Nitric oxide (NO) is a highly potent but short-lived endogenous radical with a wide spectrum of physiological activities. In this work, we developed an enzymatic approach to the site-specific synthesis of NO mediated by biocatalytic surface coatings. Multilayered polyelectrolyte films were optimized as host compartments for the immobilized β-galactosidase (β-Gal) enzyme through a screen of eight polycations and eight polyanions. The lead composition was used to achieve localized production of NO through the addition of β-Gal–NONOate, a prodrug that releases NO following enzymatic bioconversion. The resulting coatings afforded physiologically relevant flux of NO matching that of the healthy human endothelium. The antiproliferative effect due to the synthesized NO in cell culture was site-specific: within a multiwell dish with freely shared media and nutrients, a 10-fold inhibition of cell growth was achieved on top of the biocatalytic coatings compared to the immediately adjacent enzyme-free microwells. The physiological effect of NO produced via the enzyme prodrug therapy was validated ex vivo in isolated arteries through the measurement of vasodilation. Biocatalytic coatings were deposited on wires produced using alloys used in clinical practice and successfully mediated a NONOate concentration-dependent vasodilation in the small arteries of rats. The results of this study present an exciting opportunity to manufacture implantable biomaterials with physiological responses controlled to the desired level for personalized treatment

Small Vessel Replacement by Human Umbilical Arteries With Polyelectrolyte Film-Treated Arteries In Vivo Behavior

ObjectiveThe aim of this study was to evaluate the patency of human umbilical arteries treated with polyelectrolyte multilayers (PEMs) after rabbit implantation.BackgroundThe development of small-caliber vascular substitutes with high patency after implantation remains a real challenge for vascular tissue engineering.MethodsCryopreserved human umbilical arteries were enzymatically de-endothelialized and the luminal surfaces were coated with poly(styrene sulfonate)/poly(allylamine hydrochloride) (PSS/PAH) multilayers. The PEM-untreated arteries and PEM-treated rabbit carotids were used as graft control. The native rabbit carotids were bypassed by grafts.ResultsThe Doppler ultrasound evaluation, performed in vivo, showed that all PEM-treated grafts remained patent during the full experimental period, whereas after only 1 week, no blood circulation was detected in untreated arteries. Scanning electron microscopy and histological graft examination showed pervasive thrombus formation on the luminal surface of untreated arteries after 1 week and clean luminal surface for treated arteries for at least up to 12 weeks. The arterial wall cells were identified through alpha-smooth muscle actin αυδ platelet endothelial cell adhesion molecule-1 expression. The smooth muscle cells positive to alpha-smooth muscle actin were identified in adventitia and media and the endothelial cells positive to platelet endothelial cell adhesion molecule in intima. Von Kossa reaction didn't reveal any calcium salt deposits on the wall arteries, suggesting a good wall remodelling with no sign of graft rejection.ConclusionsThe in vivo evaluation of human umbilical arteries treated with PSS/PAH multilayers demonstrated a high graft patency after 3 months of implantation. Such modified arteries could constitute a useful option for small vascular replacement

Chemically Detachable Polyelectrolyte Multilayer Platform for Cell Sheet Engineering

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Modulation of Cellular Colonization of Porous Polyurethane Scaffolds via the Control of Pore Interconnection Size and Nanoscale Surface Modifications.

Full-scale cell penetration within porous scaffolds is required to obtain functional connective tissue components in tissue engineering applications. For this aim, we produced porous polyurethane structures with well-controlled pore and interconnection sizes. Although the influence of the pore size on cellular behavior is widely studied, we focused on the impact of the size of the interconnections on the colonization by NIH 3T3 fibroblasts and Wharton's jelly-derived mesenchymal stem cells (WJMSCs). To render the material hydrophilic and allow good material wettability, we treated the material either by plasma or by polydopamine (PDA) coating. We show that cells weakly adhere on these surfaces. Keeping the average pore diameter constant at 133 μm, we compare two structures, one with LARGE (52 μm) and one with SMALL (27 μm) interconnection diameters. DNA quantification and extracellular matrix (ECM) production reveal that larger interconnections is more suitable for cells to move across the scaffold and form a three-dimensional cellular network. We argue that LARGE interconnections favor cell communication between different pores, which then favors the production of the ECM. Moreover, PDA treatment shows a truly beneficial effect on fibroblast viability and on matrix production, whereas plasma treatment shows the same effect for WJMSCs. We, therefore, claim that both pore interconnection size and surface treatment play a significant role to improve the quality of integration of tissue engineering scaffolds.journal article2019 Jun 052019 05 24importe