Détection des contradictions dans les annotations sémantiques

L'annotation sémantique a pour objectif d'apporter au texte une représentation explicite de son interprétation sémantique. Dans un précédent article, nous avons proposé d'étendre les ontologies par des règles d'annotation sémantique. Ces règles sont utilisées pour l'annotation sémantique d'un texte au regard d'une ontologie dans le cadre d'une plate-forme d'annotation linguistique automatique. Nous présentons dans cet article une mesure, basée sur la valeur de Shapley, permettant d'identifier les règles qui sont sources de contradiction dans l'annotation sémantique. Par rapport aux classiques mesures de précision et de rappel, l'intérêt de cette me- sure est de ne pas nécessiter de corpus manuellement annoté, d'être entièrement automatisable et de permettre l'identification des règles qui posent problème

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces

Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational efficiency based on the assumption that errors are negligible for reasonable cutoffs or compensated for by adjusting other interaction parameters. Arising from a metadynamics study of the wetting transition of water on a solid substrate, we find that the influence of the cutoff is unexpectedly strong and can change the character of the wetting transition from continuous to first order by creating artificial metastable wetting states. Common cutoff corrections such as the use of a force switching function, a shifted potential, or a shifted force do not avoid this. Such a qualitative difference urges caution and suggests that using truncated non-bonded potentials can induce unphysical behavior that cannot be fully accounted for by adjusting other interaction parameters

Ontologies étendues pour l'annotation sé́mantique

National audienceThis article tries to formalize the process of semantically annotating a text with respect to an ontology. The semantic annotation puts fragments of a text in correspondence with the elements of an ontology, but all the difficulties consist in identifying fragments to be annotated and labels to be associated with them. We propose in this paper to extend ontologies by semantic annotation rules instead of by additional meta-lexical properties. This solution allows reusing best NLP tools which produce linguistic annotations at each of their levels. It also has the merit to distinguish clearly the process of linguistic analysis and the ontological interpretation

gem-Dibromocyclopropanes and enzymatically derived cis-1,2-dihydrocatechols as building blocks in alkaloid synthesis

The application of the title building blocks, the 6,6-dibromobicyclo[3.1.0]hexanes and the cis-1,2-dihydrocatechols, to the total synthesis of crinine and lycorinine alkaloids is described.We thank the Australian Research Council and the Institute of Advanced Studies for generous financial support

A Bayesian Generative Model for Surface Template Estimation

3D surfaces are important geometric models for many objects of interest in image analysis and Computational Anatomy. In this paper, we describe a Bayesian inference scheme for estimating a template surface from a set of observed surface data. In order to achieve this, we use the geodesic shooting approach to construct a statistical model for the generation and the observations of random surfaces. We develop a mode approximation EM algorithm to infer the maximum a posteriori estimation of initial momentum μ, which determines the template surface. Experimental results of caudate, thalamus, and hippocampus data are presented

Ligation of protease-activated receptor 1 enhances alpha(v)beta(6) integrin-dependent TGF-beta activation and promotes acute lung injury

Activation of latent TGF-beta by the alpha(v)beta(6) integrin is a critical step in the development of acute lung injury. However, the mechanism by which a alpha(v)beta(6)-mediated TGF-beta activation is regulated has not been identified. We show that thrombin, and other agonists of protease-activated receptor 1(PAR1), activate TGF-beta in an alpha(v)beta(6) integrin-specific manner. This effect is PART specific and is mediated by RhoA and Rho kinase. Intratracheal instillation of the PART-specific peptide TFLLRN increases lung edema during high-tidal-volume ventilation, and this effect is completely inhibited by a blocking antibody against the alpha(v)beta(6) integrin. Instillation of TFLLRN during high-tidal-volume ventilation is associated with increased pulmonary TGF-beta activation; however, this is not observed in Itgb6(-/-) mice. Furthermore, Itgb6(-/-) mice are also protected from ventilator-induced lung edema. We also demonstrate that pulmonary edema and TGF-beta activity are similarly reduced in Par1(-/-) mice following bleomycin-induced lung injury. These results suggest that PART-mediated enhancement of a alpha(v)beta(6)-dependent TGF-beta activation could be one mechanism by which activation of the coagulation cascade contributes to the development of acute lung injury, and they identify PART and the alpha(v)beta(6) integrin as potential therapeutic targets in this condition

Proteomic and functional analyses of the virion transmembrane proteome of cyprinid herpesvirus 3

Virion transmembrane proteins (VTPs) mediate key functions in the herpesvirus infectious cycle. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses. The present study was devoted to CyHV-3 VTPs. Using mass spectrometry approaches, we identified 16 VTPs of the CyHV-3 FL strain. Mutagenesis experiments demonstrated that eight of these proteins are essential for viral growth in vitro (ORF32, ORF59, ORF81, ORF83, ORF99, ORF106, ORF115, and ORF131), and eight are non-essential (ORF25, ORF64, ORF65, ORF108, ORF132, ORF136, ORF148, and ORF149). Among the non-essential proteins, deletion of ORF25, ORF132, ORF136, ORF148, or ORF149 affects viral replication in vitro, and deletion of ORF25, ORF64, ORF108, ORF132, or ORF149 impacts plaque size. Lack of ORF148 or ORF25 causes attenuation in vivo to a minor or major extent, respectively. The safety and efficacy of a virus lacking ORF25 were compared to those of a previously described vaccine candidate deleted for ORF56 and ORF57 (Δ56-57). Using quantitative PCR, we demonstrated that the ORF25 deleted virus infects fish through skin infection and then spreads to internal organs as reported previously for the wild-type parental virus and the Δ56-57 virus. However, compared to the parental wild-type virus, the replication of the ORF25 deleted virus was reduced in intensity and duration to levels similar to those observed for the Δ56-57 virus. Vaccination of fish with a virus lacking ORF25 was safe but had low efficacy at the doses tested. This characterization of the virion transmembrane proteome of CyHV-3 provides a firm basis for further research on alloherpesvirus VTPs. IMPORTANCE Virion transmembrane proteins play key roles in the biology of herpesviruses. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses and the causative agent of major economic losses in common and koi carp worldwide. In this study of the virion transmembrane proteome of CyHV-3, the major findings were: (i) the FL strain encodes 16 virion transmembrane proteins; (ii) eight of these proteins are essential for viral growth in vitro; (iii) seven of the non-essential proteins affect viral growth in vitro, and two affect virulence in vivo; and (iv) a mutant lacking ORF25 is highly attenuated but induces moderate immune protection. This study represents a major breakthrough in understanding the biology of CyHV-3 and will contribute to the development of prophylactic methods. It also provides a firm basis for the further research on alloherpesvirus virion transmembrane proteins

Zeeman effect in centrosymmetric antiferromagnets controlled by an electric field

Centrosymmetric antiferromagnetic semiconductors, although abundant in nature, seem less promising than ferromagnets and ferroelectrics for practical applications in semiconductor spintronics. As a matter of fact, the lack of spontaneous polarization and magnetization hinders the efficient utilization of electronic spin in these materials. Here, we propose a paradigm to harness electronic spin in centrosymmetric antiferromagnets via Zeeman spin splittings of electronic energy levels -- termed as spin Zeeman effect -- which is controlled by electric field.By symmetry analysis, we identify twenty-one centrosymmetric antiferromagnetic point groups that accommodate such a spin Zeeman effect. We further predict by first-principles that two antiferromagnetic semiconductors, Fe$_2$TeO$_6$ and SrFe$_2$S$_2$O, are excellent candidates showcasing Zeeman splittings as large as $\sim$55 and $\sim$30 meV, respectively, induced by an electric field of 6 MV/cm. Moreover, the electronic spin magnetization associated to the splitting energy levels can be switched by reversing the electric field. Our work thus sheds light on the electric-field control of electronic spin in antiferromagnets, which broadens the scope of application of centrosymmetric antiferromagnetic semiconductors