Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation

The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry', that is, insulated from water fluctuations. We show that patterns of `dry' residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom's depth inside an interface. We analyze the correlation between Voronoi shelling order, dryness, and conservation on a set of 54 protein-protein complexes. Residues with high shelling order tend to be dry; evolutionary conservation also correlates with dryness and shelling order but, perhaps not surprisingly, is a much less accurate predictor of either property. Voronoi shelling order thus seems a meaningful and efficient descriptor of protein interfaces. Moreover, the strong correlation with dryness suggests that water dynamics within protein interfaces may, in first approximation, be described by simple diffusion models

From identifying to acting: how to guarantee good quality air in buildings

The massive health impacts of air pollution have gradually put it firmly in the media spotlight, and almost everything we hear about air quality these days seems to be alarmist or resigned. Moving beyond doom-mongering to solve a major portion of the problem will demand solutions that are reliable, long-lasting and deliver guaranteed results – just like the approaches used to tackle other types of hard-to-deal-with pollution such as in water, hazardous waste and ground pollution. The same applies to indoor air pollution, which is another major public health challenge because we spend over 80% of our time in enclosed spaces. This attitude reflects the idea of the exposome, which guides public policies seeking to cut people’s day-to-day exposure at every stage of their lives. It is also a response to strong pressure from society, which prefers to think of protection in terms of individuals.For Veolia, guaranteeing air quality in a building means addressing the issue through three complementary approaches. First, it requires polluting phenomena to be diagnosed and described, identifying the nature of this constant and invisible form of pollution, and assessing its level. This is what we do through our AIR Control service. Then the pollution has to be treated by deploying techniques appropriate to the type of remediation required, as a function of the building type. This is our AIR Performance service. Lastly, and bearing in mind the impacts of air quality on individual behavior, associating the various stakeholders is essential to obtaining lasting results. This is our AIR Human service. Schools, office buildings, hospitals and health care facilities, shopping malls, hotels, etc. – all are concerned and all need to provide good quality air to their users and occupants. New solutions are now available that rely on optimization of air treatment units developed for operating rooms and clean rooms, as well as on new continuous measurement technologies made possible by microsensors. Two levers are needed to support widespread rollout of these solutions: research and development to achieve commercial release of ever more innovative techniques that combine air quality with optimized energy use as a cost-effective package; and stronger regulation to introduce a performance obligation that will guarantee air of good quality, a process already seen in decisions recently enacted by some countries

PARAMETER IDENTIFICATION OF ADVANCED PLASTIC POTENTIALS AND IMPACT ON PLASTIC ANISOTROPY PREDICTION

In the work presented in this paper, several strain rate potentials are examined in order to analyze their ability to model the initial stress and strain anisotropy of several orthotropic sheet materials. Classical quadratic and more advanced non-quadratic strain rate potentials are investigated in the case of FCC and BCC polycrystals. Different identifications procedures are proposed, which are taking into account the crystallographic texture and/or a set of mechanical test data in the determination of the material parameters.International audienceIn the work presented in this paper, several strain rate potentials are examined in order to analyze their ability to model the initial stress and strain anisotropy of several orthotropic sheet materials. Classical quadratic and more advanced non-quadratic strain rate potentials are investigated in the case of FCC and BCC polycrystals. Different identifications procedures are proposed, which are taking into account the crystallographic texture and/or a set of mechanical test data in the determination of the material parameters

Testing the chondrule-rich accretion model for planetary embryos using calcium isotopes

Understanding the composition of raw materials that formed the Earth is a crucial step towards understanding the formation of terrestrial planets and their bulk composition. Calcium is the fifth most abundant element in terrestrial planets and, therefore, is a key element with which to trace planetary composition. However, in order to use Ca isotopes as a tracer of Earth's accretion history, it is first necessary to understand the isotopic behavior of Ca during the earliest stages of planetary formation. Chondrites are some of the oldest materials of the Solar System, and the study of their isotopic composition enables understanding of how and in what conditions the Solar System formed. Here we present Ca isotope data for a suite of bulk chondrites as well as Allende (CV) chondrules. We show that most groups of carbonaceous chondrites (CV, CI, CR and CM) are significantly enriched in the lighter Ca isotopes ($\delta^{44/40}Ca$ = +0.1 to +0.93 permill) compared with bulk silicate Earth ($\delta^{44/40}Ca$ = +1.05 $\pm$ 0.04 permill, Huang et al., 2010) or Mars, while enstatite chondrites are indistinguishable from Earth in Ca isotope composition ($\delta^{44/40}Ca$ = +0.91 to +1.06 permill). Chondrules from Allende are enriched in the heavier isotopes of Ca compared to the bulk and the matrix of the meteorite ($\delta^{44/40}Ca$ = +1.00 to +1.21 permill). This implies that Earth and Mars have Ca isotope compositions that are distinct from most carbonaceous chondrites but that may be like chondrules. This Ca isotopic similarity between Earth, Mars, and chondrules is permissive of recent dynamical models of planetary formation that propose a chondrule-rich accretion model for planetary embryos.Comment: 39 pages, 5 figures, 2 tables 1 supplementary material (1 table

Etude de l'évolution de la microstructure d'un alliage d'aluminium à hautes perfomances mécaniques soumis à une déformation thermomécanique à chaud

Les alliages d'aluminium sont grandement utilisés dans divers industries dont l'automobile pour la fabrication de pièces liaison au sol. Nous nous intéressons au comportement microstructural d'un alliage d'aluminium (appelé HMP ou High Mechanical Properties) hybride de fonderie/forge soumis à une déformation thermomécanique. Après une déformation à chaud et un traitement thermique T6, les caractéristiques mécaniques sont accrues (limite d'élasticité et contrainte maximale augmenté), tout en gardant un allongement intéressant. L'utilisation du logiciel Thermocalc© nous permet de tenir compte de températures limites à ne pas dépasser pour effectuer des traitements thermiques efficaces. Des essais de compression plane (Channel die) ont été menés afin d'étudier l'évolution de la sous-structure de cet alliage à différents niveaux et vitesses de déformation. Des observations en EBSD ont permis de caractériser les phénomènes de restauration et/ou recristallisation. En dehors du fait qu'un phénomène de sous-structuration induite par la déformation à chaud s'opère, la durée de vie en fatigue est bien supérieure à celle de l'alliage AS7G03 couramment utilisé dans l'industrie automobile

First results on a sensor bio-inspired by electric fish

This article presents the first results of a work which aims at designing an active sensor inspired by the electric fish. Its interest is its potential for robotics underwater navigation and exploration tasks in conditions where vision and sonar would meet difficulty. It could also be used as a complementary omnidirectional, short range sense to vision and sonar. Combined with a well defined engine geometry, this sensor can be modeled analytically. In this article, we focus on a particular measurement mode where one electrode of the sensor acts as a current emitter and the others as current receivers. In spite of the high sensitivity required by electric sense, the first results show that we can obtain a detection range of the order of the sensor length, which suggests that this sensor principle could be used in future for robotics obstacle avoidance

Sensor model for the navigation of underwater vehicles by the electric sense

International audienceWe present an analytical model of a sensor for the navigation of underwater vehicles by the electric sense. This model is inspired from the electroreception structure of the electric fish. In our model, that we call the poly-spherical model (PSM), the sensor is composed of n spherical electrodes. Some electrodes play the role of current-emitters whereas others play the role of current-receivers. By imposing values of the electrical potential on each electrode we create an electric field in the vicinity of the sensor. The region where the electric field is created is considered as the bubble of perception of the sensor. Each object that enters this bubble is electrically polarized and creates in return a perturbation. This perturbation induces a variation of the measured current by the sensor. The model is tested on objects for which the expression of the polarizability is known. A unique off-line calibration of the poly-spherical model permits to predict the measured current of a real immersed sensor in an aquarium. Comparisons in a basic scene between the predicted current given by the poly-spherical model and the measured current given by our test bed show a very good agreement, which confirms the interest of using such fast analytical models for the purpose of navigation

An Unified FPT Algorithm for Width of Partition Functions

During the last decades, several polynomial-time algorithms have been designed that decide whether a graph has tree-width (resp., path-width, branch-width, etc.) at most k, where k is a fixed parameter. Amini et al. (Discrete Mathematics'09) use the notions of partitioning-trees and partition functions as a generalized view of classical decompositions of graphs, namely tree decomposition, path decomposition, branch decomposition, etc. In this paper, we propose a set of simple sufficient conditions on a partition function Φ, that ensures the existence of a linear-time explicit algorithm deciding if a set A has Φ-width at most k (k fixed). In particular, the algorithm we propose unifies the existing algorithms for tree-width, path-width, linear-width, branch-width, carving-width and cut-width. It also provides the first Fixed Parameter Tractable linear-time algorithm to decide if the q-branched tree-width, defined by Fomin et al. (Algorithmica'09), of a graph is at most k (k and q are fixed). Moreover, the algorithm is able to decide if the special tree-width, defined by Courcelle (FSTTCS'10), is at most k, in linear-time where k is a Fixed Parameter. Our decision algorithm can be turned into a constructive one by following the ideas of Bodlaender and Kloks (J. of Alg. 1996).Au cours de ces dernières années, plusieurs algorithmes polynomiaux ont été conçus pour décider si un graphe a largeur arborescente (resp., largeur en chemin, branch-width, etc) au plus k, où k est un paramètre fixe. Amini et al. (Discrete Mathematics'09) ont utilisé les notions d'arbres de partition et de fonctions de partition comme une vision généralisée des décompositions des graphes classiques, à savoir la décomposition arborescente, la décomposition en chemin, la décomposition en branche, etc. Dans cet article, nous proposons un ensemble de conditions sur une fonction de partition Φ, qui assure l'existence d'un algorithme explicite en temps linéaire pour décider si un ensemble A a Φ-largeur au plus k (oú k est fixé). En particulier, l'algorithme que nous proposons unifie les algorithmes existants pour la largeur arborescente, largeur en chemin, la largeur linéaire, la largeur de branche, cut-width et carving-width. Il est également le premier algorithme FPT pour décider si la largeur arborescente q-ramifié, définie par Fomin et al. (Algorithmica'09), d'un graphe est au plus k (k et q sont fixées). De plus, l'algorithme est capable de décider si la largeur arborescente spéciale, définie par Courcelle (FSTTCS'10), est plus k, où k est un paramètre fixé. Notre algorithme de décision peut être transformé en un algorithme constructif en suivant les idées de Bodlaender et Kloks (J. of Alg., 1996)

Parameter identification of advanced plastic potentials and impact on plastic anisotropy prediction

In the work presented in this paper, several strain rate potentials are examined in order to analyze their ability to model the initial stress and strain anisotropy of several orthotropic sheet materials. Classical quadratic and more advanced non-quadratic strain rate potentials are investigated in the case of FCC and BCC polycrystals. Different identifications procedures are proposed, which are taking into account the crystallographic texture and/or a set of mechanical test data in the determination of the material parameters

Pattern of DAP12 Expression in Leukocytes from Both Healthy and Systemic Lupus Erythematosus Patients

DAP12 is an ITAM-bearing transmembrane adaptor originally identified on the surface of Natural Killer cells. A broad expression among other immune cells was later found in myeloid and lymphoid cells. However, data on DAP12 expression pattern rely only on immunoblot and microarray analysis. Here, we describe the generation and the characterization of an anti-DAP12 monoclonal antibody. Using this novel reagent, we show that DAP12 expression is restricted to innate immune cells in basal condition. Since a decreased expression of DAP12 has been suggested in NK cells of systemic lupus erythematosus patients, we have further investigated the NK cell receptor repertoire and leukocyte expression of DAP12 in these patients and no major changes were detectable when compared to controls