Identification of Fertile Translations in Medical Comparable Corpora: a Morpho-Compositional Approach

This paper defines a method for lexicon in the biomedical domain from comparable corpora. The method is based on compositional translation and exploits morpheme-level translation equivalences. It can generate translations for a large variety of morphologically constructed words and can also generate 'fertile' translations. We show that fertile translations increase the overall quality of the extracted lexicon for English to French translation

Inverse problems in the mechanical characterization of elastic arteries

International audienceThis article presents an overview of diverse material models used to represent the mechanical behavior of arteries and of the inverse problems posed by the identification of their constitutive parameters. After a brief introduction about the definition of inverse problems and about the general features of arteries, the article addresses three main questions involving inverse problems and arterial wall characterization: (1) macroscopic identification of the parameters of sophisticated constitutive models from traditional uniaxial and biaxial experiments; (2) mesoscopic identification of regional variations in the material parameters of arteries, tracking the effects of functional adaptation or lesions; (3) how constitutive models and inverse problems allow to obtain information on the arterial microstructure and how the structural constituents interact in the mechanical response. Finally, the article shows that a significant effort has been made so far to relate the complex mechanical behavior of arteries to their microstructure but a new class of inverse problems has recently appeared. It is related to the identification of mechanobiological parameters which are the parameters involved in the numerical models of growth and remodeling

Mineralization-driven bone tissue evolution follows from fluid-to-solid phase transformations in closed thermodynamic systems

AbstractThe fundamental mechanisms that govern bone mineralization have been fairly well evidenced by means of experimental research. However, rules for the evolution of the volume and composition of the bone tissue compartments (such as the mineralized collagen fibrils and the extrafibrillar space in between) have not been provided yet. As an original contribution to this open question, we here test whether mineralizing bone tissue can be represented as a thermodynamically closed system, where crystals precipitate from an ionic solution, while the masses of the fibrillar and extrafibrillar bone tissue compartments are preserved. When translating, based on various experimental and theoretical findings, this mass conservation proposition into diffraction–mass density relations, the latter are remarkably well confirmed by independent experimental data from various sources. Resulting shrinkage and composition rules are deemed beneficial for further progress in bone materials science and biomedical engineering

Molécules anti-facteurs de virulence : étude de l’efficacité et de l’amélioration d’une molécule inhibitrice du système de sécrétion de type IV de Helicobacter pylori

Helicobacter pylori est une bactérie à Gram négatif qui colonise plus de 50% de la population humaine. Cette bactérie est l'un des pathogènes les plus présents dans la population et la colonisation se fait dans l'enfance et l'adolescence. H. pylori est responsable de l'apparition de maladies gastriques chez l'humain comme des ulcères gastriques, mais aussi des cancers gastriques. Plusieurs mécanismes contribuent aux maladies gastriques dont une infection chronique à long terme ainsi que des facteurs de virulence comme le système de sécrétion de type 4 (SST4). Le SST4 forme une seringue protéique utilisée par la bactérie pour injecter la protéine CagA dans les cellules humaines. Cette protéine a été la première protéine bactérienne classifiée comme une oncoprotéine par sa capacite à interférer et modifier de nombreuses fonctions et signaux métaboliques des cellules épithéliales gastriques. Afin d'éradiquer Helicobacter, une antibiothérapie est utilisée, cependant depuis les 10 dernières années plus de 50% des bactéries isolées de patients ont été identifiés comme étant porteuses de résistances contre aux moins un antibiotique de première ligne. L’utilisation de petites molécules organiques capables d'interférer avec les facteurs de virulence est une alternative intéressante à la thérapie aux antibiotiques. L'utilisation de ces molécules possède des avantages dont la faible pression de sélection de résistance parce qu’elles n’impactent pas des fonctions vitales des bactéries. Le SST4 de H. pylori est composé de nombreuses protéines essentielles qui pourraient être de potentielles cibles pour des molécules inhibitrices. Nous avons choisi la cible Cagα, une ATPase homologue à VirB11 de Agrobacterium tumefaciens. Cette protéine est essentielle pour l’injection de CagA. Précédemment, notre laboratoire a identifié une petite molécule nommée 1G2 qui était capable d’interagir avec Cagα et de diminuer l’induction de l’interleukine 8 produit par les cellules gastriques lors de l’infection par des souches de H. pylori possédant un SST4 fonctionnel. A partir d’une structure cristallographique de Cagα liée à 1G2 et nous avons créé des protéines Cagα avec des mutations aux site de liaison de 1G2. En utilisant la fluorimétrie différentielle à balayage (DSF) nous avons pu identifier les acides aminés qui contribuent à la liaison de 1G2 (K41, R73 et F39). Basé sur cette information nous avons utilisé la chimie médicinale pour créer une librairie de molécules dérivées de 1G2 dans le but d’identifier des inhibiteurs plus puissants. Après avoir éliminé les molécules ayant un effet toxique sur les cellules gastriques et H. pylori, nous avons sélectionné cinq molécules (1313, 1338, 2886, 2889 et 2902) qui inhibent la production d’IL-8 plus que 1G2 dans notre modèle d’infection cellulaire. Nous avons montré par DSF que les molécules interagissent toujours avec Cagα et 1338, 2889 et 2902 sont des inhibiteurs plus puissants de son activité d’ATPase. Avec le modèle d’infection, nous avons déterminé que les cinq molécules n’affectent par la présence de CagA dans le lysat de l’infection. Cependant, nous avons observé par microscopie électronique à balayage que le SST4 pilus n’était pas présent en présence des inhibiteurs. En plus, nous avons testé les effets de 1G2 sur des souches de H. pylori résistantes, à un ou plusieurs antibiotiques de première ligne, isolées de biopsie gastriques de patients. Comme dans le cas de la bactérie modèle de laboratoire, nous avons observé une diminution de l’induction des IL-8 lors de l’infection ainsi qu’une inhibition de la formation du SST4 pilus. Nous avons aussi identifié que le gène de la protéine Cagα d’une des bactéries résistantes à 1G2 (souche #3822) porte un remplacement de R73 à K ce qui pourrait expliquer la résistance à 1G2. Pour conclure, nous avons dans cette étude caractérisé le site de liaison de 1G2 à Cagα et nous avons identifié des molécules qui sont plus puissantes comme inhibiteurs que 1G2.Helicobacter pylori is a Gram-negative bacterium that colonizes more than 50% of the human population. This bacterium is one of the most common pathogens in the population and colonization occurs in childhood and adolescence. H. pylori is implicated in the manifestation of gastric diseases in humans such as gastric ulcers and also gastric cancer. Several mechanisms are involved in the formation of gastric diseases including long-term chronic infection as well as virulence factors such as the type 4 secretion system (T4SS). The T4SS forms a protein syringe used by the bacteria to inject the protein CagA into mammalian cells. This protein is the first bacterial protein classified as an oncoprotein by its ability to interact with numerous metabolic functions of gastric epithelial cells. To eradicate Helicobacter, antibiotic therapy is used, but for the last 10 years more than 50% of the bacteria isolated from patients have been identified as carrying resistance against at least one first-line antibiotic. The use of small molecules capable of interfering with virulence factors is being studied as an alternative to antibiotic therapy. The use of these molecules has many advantages, and they may cause lower selection pressure for resistance than antibiotics. The H. pylori T4SS is composed of many essential proteins that could be potential targets for inhibitory molecules. We chose the target Cagα, an ATPase homologous to the model VirB11 from Agrobacterium tumefaciens. This protein is essential for the injection of CagA. Previously, our laboratory identified a small molecule coined 1G2 that interacts with Cagα and decreases the induction of interleukin-8 produced by gastric cells upon infection with H. pylori strains with functional T4SS. Based on a crystallographic study of Cagα bound to 1G2, we created Cagα proteins with mutations at the 1G2 binding site. Using differential scanning fluorimetry, we identified amino acids that contribute to 1G2 binding (K41, R73 and F39). Based on these observations, we used medicinal chemistry to create a library of molecules derived from 1G2 to create more potent inhibitors. After eliminating the molecules with a toxic effect on gastric cells and H. pylori growth, we selected five molecules with stronger effects than 1G2 on IL8 induction in our cell infection model (1313, 1338, 2886, 2889 and 2902). We observed by DSF that the molecules interact with Cagα and 1338, 2889 and 2902 are stronger inhibitors of the ATPase 8 activity than 1G2. With our infection model, we determined that the five molecules do not affect the presence of CagA. However, by scanning electron microscopy we observed that the T4SS pilus was not present. In addition to the tests on a laboratory model bacterium, we evaluated 1G2 on resistant strains of H. pylori isolated from gastric biopsy from patients. Similar to the laboratory model bacterium, 1G2 decreased IL-8 induction and inhibited T4SS pilus formation. We have also identified that strain #3822 that is resistant to 1G2 carries a R73 to K mutation in the Cagα gene, which could explain the 1G2 resistance. To conclude, we have here characterized the 1G2 binding site on Cagα and we created inhibitors that are more potent than 1G2

Interactive book-reading to improve inferencing abilities in kindergarten classrooms : a clinical project

Inferencing abilities are crucial to development of reading comprehension. However, few studies addressed those abilities in interventions promoting early literacy skills, especially in kindergartners. The aim of this study was to measure the efficacy of an interactive book-reading intervention targeting inferencing abilities, delivered by a school-based speech-language pathologist (SLP) in whole group kindergarten classes. Two hundred and forty-nine 5-year-old kindergartners from low socio-economic settings were quasi-randomly assigned to either one of the experimental groups (EG1 and EG2) or an active control group (CG). EG1 received a 7-week interactive book-reading intervention followed by a 7-week period where it was up to the teachers to implement aspects of the intervention in their teaching or not. EG2 received the 7-week interactive book-reading intervention only and the active control group received an initial workshop only. Three subtests targeting (1) causal inferences during book-reading, (2) causal inferences in a formal task, and (3) referential inferences in a formal task were performed at pre- and post-intervention assessments. There was a significant Time × Group interaction effect for the first subtest indicating an advantage for EG1 compared to CG over time. EG2 appeared as an intermediary group as its results were not different from EG1 and showing only a trend toward significance (p = 0.064) when compared to CG. There was no significant Time × Group interaction effect for the second subtest. A significant Time × Group interaction effect was present for the third subtest, EG1 and EG2 showing larger improvement than CG

Development of a procedure for the evaluation of spouses' and persons with aphasia's contributions an interview situation

Person with aphasia’s participation in group conversations in presence of her/his spouse have not been extensively studied. The development of a procedure that addresses the spouses’contributions (i.e., ‘repair’, ‘speaking for’ and ‘support’) as well as the reaction and participation of the person with aphasia in an interview situation is presented. Results from eight couples indicate that spouses are quite active when the aphasic person has the floor. Aphasic persons most often approve what the spouse has contributed and continue to participate fully. However, unsolicited ‘speaking for’ behaviors are sometimes followed by a decrease participation in conversation of people with aphasia

True and False Recognition Memories of Odors Induce Distinct Neural Signatures

Neural bases of human olfactory memory are poorly understood. Very few studies have examined neural substrates associated with correct odor recognition, and none has tackled neural networks associated with incorrect odor recognition. We investigated the neural basis of task performance during a yes–no odor recognition memory paradigm in young and elderly subjects using event-related functional magnetic resonance imaging. We explored four response categories: correct (Hit) and incorrect false alarm (FA) recognition, as well as correct (CR) and incorrect (Miss) rejection, and we characterized corresponding brain responses using multivariate analysis and linear regression analysis. We hypothesized that areas of the medial temporal lobe were differentially involved depending on the accuracy of odor recognition. In young adults, we found that significant activity in the hippocampus and the parahippocampal gyrus was associated with correct (true) recognition of odors, whereas the perirhinal cortex was associated with FAs and Misses. These findings are consistent with literature regarding hypothetical functional organization for memory processing. We also found that for correct recognition and rejection responses, the involvement of the hippocampus decreased when memory performances improved. In contrast to young individuals, elderly subjects were more prone to false memories and exhibited less specific activation patterns for the four response categories. Activation in the hippocampus and the parahippocampal gyrus was positively correlated with response bias scores for true and false recognition, demonstrating that conservative subjects produced an additional search effort leading to more activation of these two medial temporal lobe regions. These findings demonstrate that correct and incorrect recognition and rejection induce distinct neural signatures

Hsp83 loss suppresses proteasomal activity resulting in an upregulation of caspase-dependent compensatory autophagy

The 2 main degradative pathways that contribute to proteostasis are the ubiquitin-proteasome system and autophagy but how they are molecularly coordinated is not well understood. Here, we demonstrate an essential role for an effector caspase in the activation of compensatory autophagy when proteasomal activity is compromised. Functional loss of Hsp83, the Drosophila ortholog of human HSP90 (heat shock protein 90), resulted in reduced proteasomal activity and elevated levels of the effector caspase Dcp-1. Surprisingly, genetic analyses showed that the caspase was not required for cell death in this context, but instead was essential for the ensuing compensatory autophagy, female fertility, and organism viability. The zymogen pro-Dcp-1 was found to interact with Hsp83 and undergo proteasomal regulation in an Hsp83-dependent manner. Our work not only reveals unappreciated roles for Hsp83 in proteasomal activity and regulation of Dcp-1, but identifies an effector caspase as a key regulatory factor for sustaining adaptation to cell stress in vivo

Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

Background: The Wuschel related homeobox (WOX) family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG) using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. Results: The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Conclusion: Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most likely by preventing premature differentiation. The future use of Ostreococcus tauri and Physcomitrella patens as biological models should allow us to obtain a better insight into the functional importance of WOX13 OG genes

The concept of frozen elastic energy as a consequence of change in microstructure morphology

Une approche micromécanique et multi-échelle pour la modélisation des tissus mous explique la non-linéarité de leur réponse au chargement mécanique, la dépendance de leur réponse mécanique vis-à-vis de la trajectoire de déformation ainsi que l'éventuelle énergie stockée, comme conséquences du changement de morphologie de la microstructure