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See detailExploiting SNP Correlations within Random Forest for Genome-Wide Association Studies
Botta, Vincent ULg; Louppe, Gilles ULg; Geurts, Pierre ULg et al

in PLoS ONE (2014)

The primary goal of genome-wide association studies (GWAS) is to discover variants that could lead, in isolation or in combination, to a particular trait or disease. Standard approaches to GWAS, however ... [more ▼]

The primary goal of genome-wide association studies (GWAS) is to discover variants that could lead, in isolation or in combination, to a particular trait or disease. Standard approaches to GWAS, however, are usually based on univariate hypothesis tests and therefore can account neither for correlations due to linkage disequilibrium nor for combinations of several markers. To discover and leverage such potential multivariate interactions, we propose in this work an extension of the Random Forest algorithm tailored for structured GWAS data. In terms of risk prediction, we show empirically on several GWAS datasets that the proposed T-Trees method significantly outperforms both the original Random Forest algorithm and standard linear models, thereby suggesting the actual existence of multivariate non-linear effects due to the combinations of several SNPs. We also demonstrate that variable importances as derived from our method can help identify relevant loci. Finally, we highlight the strong impact that quality control procedures may have, both in terms of predictive power and loci identification. [less ▲]

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See detailModélisation 2D par éléments finis du contact : effet de l’utilisation de méthodes de représentation des surfaces présentant un ordre de continuité élevé et méthodes permettant de passer le patch test
Nguyen, Duc Tue ULg

Doctoral thesis (2014)

Ce travail de thèse concerne la mécanique numérique du contact entre les solides déformables. La simulation numérique des problèmes de contact comporte de nombreuses difficultés notamment dans un contexte ... [more ▼]

Ce travail de thèse concerne la mécanique numérique du contact entre les solides déformables. La simulation numérique des problèmes de contact comporte de nombreuses difficultés notamment dans un contexte de grands déplacements et de grandes déformations. Le but de ce travail est d’analyser l’influence de l’ordre de continuité élevé de la représentation de surface et de développer une méthode pour passer le patch test, à savoir qu’un élément passe le patch test si il transmet correctement des pressions de contact entre deux surfaces. Pour la discrétisation des éléments finis, l'interface de contact est représentée par une série de lignes et de courbes à continuité C0. Par conséquent, lors du passage du nœud esclave entre deux segments maîtres adjacents, il peut arriver avoir une discontinuité de la direction du vecteur normal. Cette situation peut mener à des problèmes de convergence de l'algorithme de résolution. Pour éviter ce problème, l’approche proposée consiste à développer les représentations de surface maître à ordre de continuité C1 ou C2 pour les éléments nœud-surface linéaires et quadratiques. Les éléments nœud-surface ne passent pas le patch test. Plus récemment, un élément linéaire utilisant la méthode des nœuds esclaves virtuels pour Passer le Patch Test (PPT) a été proposée dans la littérature. Cependant, cet élément est à ordre de continuité C0 et peut donner des grandes oscillations de la pression de contact à cause des pénétrations initiales des nœuds esclaves virtuels qui sont les pénétrations des nœuds esclaves virtuels dans la surface maître à l’état initial. Pour tenter de surmonter cette difficulté, une nouvelle approche repose sur un élément linéaire utilisant la méthode PPT et la représentation de surface à ordre de continuité C1 pour la surface maître et pour la surface esclave. L’élément quadratique nœud-surface donne des oscillations de pression de contact à cause de la distribution non-uniforme des forces nodales. Afin de résoudre ce problème, la méthode PPT est développée pour l’élément quadratique. [less ▲]

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See detailThe BANANA Project. V. Misaligned and Precessing Stellar Rotation Axes in CV Velorum
Albrecht, Simon; Winn, Joshua N.; Torres, Guillermo et al

in Astrophysical Journal (2014), 785

As part of the Binaries Are Not Always Neatly Aligned project (BANANA), we have found that the eclipsing binary CV Velorum has misaligned rotation axes. Based on our analysis of the Rossiter-McLaughlin ... [more ▼]

As part of the Binaries Are Not Always Neatly Aligned project (BANANA), we have found that the eclipsing binary CV Velorum has misaligned rotation axes. Based on our analysis of the Rossiter-McLaughlin effect, we find sky-projected spin-orbit angles of β[SUB]p[/SUB] = -52° ± 6° and β[SUB]s[/SUB] = 3° ± 7° for the primary and secondary stars (B2.5V + B2.5V, P = 6.9 days). We combine this information with several measurements of changing projected stellar rotation speeds (vsin i [SUB]sstarf[/SUB]) over the last 30 yr, leading to a model in which the primary star's obliquity is ≈65°, and its spin axis precesses around the total angular momentum vector with a period of about 140 yr. The geometry of the secondary star is less clear, although a significant obliquity is also implicated by the observed time variations in the vsin i [SUB]sstarf[/SUB]. By integrating the secular tidal evolution equations backward in time, we find that the system could have evolved from a state of even stronger misalignment similar to DI Herculis, a younger but otherwise comparable binary. Based on observations made with ESOs 2.2 m Telescopes at the La Silla Paranal Observatory under programme ID 084.C-1008 and under MPIA guaranteed time. [less ▲]

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See detailUtilisation de biocapteurs microbiens GFP pour la caractérisation des performances des bioréacteurs
Brognaux, Alison ULg

Doctoral thesis (2014)

The scale-up of bioprocesses is a critical step during bioproducts development. Actually, the mixing operation’s efficiency drops when the reactor volume increases: gradients of glucose and oxygen appear ... [more ▼]

The scale-up of bioprocesses is a critical step during bioproducts development. Actually, the mixing operation’s efficiency drops when the reactor volume increases: gradients of glucose and oxygen appear when operating in fed-batch mode, causing losses of production. The aim of this project is the scale-up and sizing of bioreactors based on the direct physiological parameters to consider this heterogeneity. Concretely, it consists in obtaining an on-line signal of the physiological status of micro-organisms. The coding sequence of the Green Fluorescent Protein (GFP) has been inserted after gene promoters of interest in Escherichia coli to built biosensors. A particular focus has been paid on promoters responding to general stress or specifically to lack of glucose and on those responding to cell growth rate. The GFP biosensors of interest have been tested in scale-down bioreactors, allowing to reproduce industrial hydrodynamic conditions at a laboratory scale. A mini-bioreactor platform has also been developed to enable a high throughput screening of biosensors. The intracellular accumulation of GFP has been measured by flow cytometry and GFP release has been monitored by western blot analyses. For biosensors sensitive to stress general response or glucose limitation, GFP has been induced during a glucose limitation and repressed by comparison when glucose heterogeneities appear. The use of a destabilized GFP has been considered in this project for ribosomal biosensors to approach more instantaneous physiological responses of microorganisms. For these ones, the response is proportional to growth rate during the batch phase, but more complex mechanisms take part during a prolonged glucose limitation. Membrane permeability has also been studied and has been noticed more important in homogeneous fed-batch bioreactors than in scale-down reactors. As GFP leakage has been noted in the extracellular medium, a study has also been carry out about proteins released in the extracellular medium (leakage), and correlated with the cell permeability. Finally, an on-line flow cytometer has been developed for the characterization of physiological status of micro-organisms during the bioprocess, and a 3D-ORM probe allowed to measure their viability on-line [less ▲]

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See detail« Penser avec et contre Fanon : sur Achille Mbembe, ‘’Le fouet de Dieu’’ (in De la postcolonie) »
Melice, Anne ULg

Conference (2014, April 01)

Achille Mbembe remarque, pour le regretter, que la réflexion qu’il a intitulée « Le fouet de Dieu » n’a guère fait l’objet de lectures critiques. C’est précisément à dégager les enjeux de ce chapitre de ... [more ▼]

Achille Mbembe remarque, pour le regretter, que la réflexion qu’il a intitulée « Le fouet de Dieu » n’a guère fait l’objet de lectures critiques. C’est précisément à dégager les enjeux de ce chapitre de son livre De la postcolonie que vise mon intervention. J’avais été très impressionnée, lors de mes recherches doctorales sur le kimbanguisme, par les analyses relatives au christianisme figurant dans Afriques indociles. Ces thèses sont tout à la fois creusées et déplacées dans « Le fouet de Dieu ». L’avant-propos de la deuxième édition du livre suggère brièvement une mise en perspective stimulante de ces pages. Prenant acte de la nécessité de désormais « penser avec et contre Fanon », Mbembe y souligne qu’elles ouvrent sur une conception du rapport éthique à autrui, qui prend chez lui la forme d’une prescription inconditionnelle : « donner la mort à la mort ». Mon interrogation se resserre autour de la thématique de l’altérité. En rassemblant en gerbe les problématiques du désir, de la domination et de la liberté, elle met au jour l’articulation profonde du religieux et du politique. [less ▲]

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See detailL’antonymie. Définition de l’antonymie en langue et description des fonctions sémantico-référentielles de la co-présence antonymique en discours
Steffens, Marie ULg

Doctoral thesis (2014)

Grâce à un examen critique des travaux consacrés à l’antonymie, nous avons pu définir l’antonymie comme une relation multiforme qui touche des unités très différentes sur les plans sémantique et morpho ... [more ▼]

Grâce à un examen critique des travaux consacrés à l’antonymie, nous avons pu définir l’antonymie comme une relation multiforme qui touche des unités très différentes sur les plans sémantique et morpho-syntaxique mais dont l’unicité réside dans une opposition binaire fondamentale enracinée lexicalement. Nous avons ainsi dépassé la simple distinction entre contraires et contradictoires pour entrer dans la fascinante diversité de l’opposition et montrer comme les notions de graduation, de graduabilité, de scalarité, de borne et de seuil se combinent pour forger l’identité sémantique de chaque paire d’antonymes, la rapprocher ou la distinguer des autres. Grâce à l’analyse empirique d’énoncés extraits du journal Le Monde, nous avons montré que la co-présence antonymique en contexte s’appuie pour faire sens sur les relations antonymiques inscrites dans la mémoire linguistique des locuteurs, où sont fortement associées la forme et le sens des antonymes. Nous avons également montré comment la plongée de deux antonymes dans un contexte d’emploi peut moduler leur opposition et la définition du lexème neutre ou intermédiaire, lorsqu’il existe. Les antonymes co-présents, grâce aux rôles sémantico-syntaxiques qu’ils peuvent jouer, contribuent à la structuration des énoncés dans lesquels ils sont employés parce qu’ils organisent les unités qui les entourent sur le plan sémantico-référentiel. [less ▲]

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See detailTheoretical studies of gravitational lensing phenomena: the case of multiply imaged quasars
Wertz, Olivier ULg

Doctoral thesis (2014)

In the early 1960s, gravitational lensing has received a special attention when S. Liebes and S. Refsdal have derived in detail some of the basic equations of the theory. While Liebes (1964) discussed the ... [more ▼]

In the early 1960s, gravitational lensing has received a special attention when S. Liebes and S. Refsdal have derived in detail some of the basic equations of the theory. While Liebes (1964) discussed the probability of detecting these effects and considered several astrophysical applications, Refsdal (1964) derived, inter alia, his famous relation which links the Hubble parameter (H0) to the expected time delays between pairs of lensed images. From that moment, the scientific community fully realized that gravitational lensing effects offer a new way of probing cosmology. However, an important fact has been to accept that the determination of H0 seems to be model dependent, not only on the universe model, but also on the mass distribution of the deflector. The main topic of the present thesis constitutes a straight continuation of this inquiry. We have been sounding parts of the mathematical lensing framework on two fronts. First, considering to first order a very small misalignment between the source, the lens and the observer, we have derived the expressions of the lensed image positions along with their amplification ratios, for the case of power-law axially symmetric mass distributions, the so-called ε-γ family of models (Wertz, Pelgrims & Surdej, 2012). After combining these results, it has allowed us to derive an expression for H0 independently of the model parameters. We have extended this study to the ε-γ family of models with external shear, as well as to the singular isothermal ellipsoid (SIE) models. For both these types of models, we have obtained an expression of H0 which is once again independent, to first order, of the model parameters. Furthermore, even though these families of models remain rigorously distinct, except for the singular isothermal sphere (SIS) and the perfect alignment, the expression of H0 in terms of observable quantities and of the source position takes surprisingly the same simple form. In addition, we have demonstrated the feasibility of analytically constraining to first order the model parameters by only using the astrometric positions of the lensed images. Therefore, for the case of a small misalignment between the source, the deflector and the observer, it is straightforward to determine whether the ε-γ or SIE family of models constitutes a judicious representation of the mass distribution of the deflector. It is conceivable that similar results can be deduced for other families of models. Secondly, we have developed a new analytical approach in order to determine the expression of the deflection angle, hereafter α. Since the latter depends on the deflector mass distribution, there exists no global explicit expression but only an implicit definition of α. Therefore, the analytical methods used to obtain the explicit expression differ for different types of mass distribution. However, using the Fourier transform theory, one may basically express α in terms of the Fourier transform of the surface mass density. Such a method allows us to approach any mass distribution in a unique way. As a first application, we have separately derived the expression of the two components of α for the case of homoeoidal symmetric lenses (Wertz & Surdej, 2013). This original result constitutes a first proof that the Fourier approach constitutes a promising alternative to the complex formalism introduced by Bourassa & Kantowski (1975, corrected by Bray 1984). A particular case of homoeoidal symmetric lenses lies in the non-singular isothermal ellipsoid (NSIE) family of models for which the analytical treatment has been somewhat limited (Kormann & al. 1994). The use of the Fourier approach has made possible to derive a complete analytical treatment of the NSIE, i.e. the expressions of the deflection angle, the deflection potential, and the critical and caustic curves even off the axis (Wertz & Surdej, submitted to MNRAS in february 2014). This original result has allowed us to investigate and better understand this family of models. Furthermore, it is of great interest for mass distribution modeling and to rigorously determine the expected time delays between pairs of lensed images. The previous analytical treatments mainly consisted of parametrical models for the deflector. An alternative way to grasp lenses consists in modeling their mass distribution using non-parametric models. With this aim in mind, we have proceeded as follows: we tessellate the lens plane with squared pixels, and associate to each of them a constant surface mass density. Making use of the Fourier approach, we have derived the expression of the deflection angle for the whole grid. This result contains the main advantage of the non-parametric models, i.e. to model any type of mass distribution without any preconception, and the usefulness of handling quantities which can be described with analytical functions. [less ▲]

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See detailStudy of the Bacillus subtilis PBP4* and RacX, YlmE racemases in relation with disassembly of biofilms
Vanden Broeck, Arnaud ULg

Conference (2014, April 01)

Bacillus subtilis is a PGPR (Plant Growth Promoting Rhizobacterium) Gram positive bacterium and a model for studying the in vitro formation or disruption of biofilms. At the liquid/air interface of ... [more ▼]

Bacillus subtilis is a PGPR (Plant Growth Promoting Rhizobacterium) Gram positive bacterium and a model for studying the in vitro formation or disruption of biofilms. At the liquid/air interface of standing cultures, B. subtilis forms thick pellicles of limited lifetimes. Some D-amino acids have been reported among the factors playing a role in the disassembly of B. subtilis biofilms and ylmE or racX mutants (in which the racemases YlmE or RacX are absent) show a delay in pellicle disruption. The racX encoding gene is part of a bicistronic operon in which the second gene (pbpE) codes for a Penicillin-Binding Protein, the PBP4* whose function is not characterized in Bacillus. Our studies aim to produce, purify and characterize the role of the PBP4* and RacX, YlmE racemases in relation with the disassembly of biofilms. Biochemical and structural data have been obtained and the role of the three proteins has been partly solved. X-ray structures will permit us to create inhibitor molecules against Bacillus subtilis biofilm formation or disassembly. [less ▲]

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See detailComportements à risque et maladies cardio-vasculaires. Comment infléchir le cours des choses?
Etienne, Anne-Marie ULg; Krzesinski, Jean-Marie ULg; André, Jean-François

Scientific conference (2014, April 01)

«Comportements à risques et maladies cardio-vasculaires, comment infléchir le cours des choses ?» Entre recommandations, croyances et attitudes des médecins, croyances, attitudes et vécu des patients ... [more ▼]

«Comportements à risques et maladies cardio-vasculaires, comment infléchir le cours des choses ?» Entre recommandations, croyances et attitudes des médecins, croyances, attitudes et vécu des patients, comment améliorer la prévention dans le domaine cardio-vasculaire ? [less ▲]

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See detailConceptual metaphors as a tool for the efficient teaching of Dutch and German posture verbs
De Knop, Sabine; Perrez, Julien ULg

in Review of Cognitive Linguistics (2014), 12(1), 1-29

The article deals with the typological differences between the Romance lan- guage French and the Germanic languages German and Dutch for the linguistic expressions of posture and location. It describes ... [more ▼]

The article deals with the typological differences between the Romance lan- guage French and the Germanic languages German and Dutch for the linguistic expressions of posture and location. It describes how these typological differ- ences can be problematic for French-speaking learners of German and Dutch. The main difference between both types of languages is that posture and loca- tion tend to be encoded by posture verbs in Germanic languages and by very general verbs in Romance languages (Talmy 2000). After a detailed description of the semantic networks of the German and Dutch posture verbs, the paper takes a critical look at how these expressions are dealt with in teaching manuals. It further presents strategies for the efficient teaching of posture verbs to foreign language learners. These strategies are among others awareness-raising exercis- es about the compulsory use of posture verbs in Germanic languages and the description of conceptual metaphors in different languages. These pedagogical avenues for the efficient teaching of the Dutch and German posture verbs con- stitute a first step towards the elaboration of an experimental set-up aiming at verifying them. [less ▲]

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See detailComportements à risques et maladies cardio-vasculaires, comment infléchir le cours des choses?
Krzesinski, Jean-Marie ULg; andre, Jean-François

Conference (2014, April 01)

Entre recommandations, croyances et attitudes des médecins, croyances, attitudes et vécu des patients, comment améliorer la prévention dans le domaine cardio-vasculaire?

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See detailValoriser un corpus secondaire : le cas des jeux en histoire
Saal, Caroline ULg

Scientific conference (2014, April 01)

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See detailDétermination de la broyabilité des plaquettes et des pellets de bois
Temmerman, Michaël ULg

Doctoral thesis (2014)

The literature about energy requirements for product milling in mining industry shows the subject has been, and still is, considered by numerous authors. Several milling theories have been proposed for ... [more ▼]

The literature about energy requirements for product milling in mining industry shows the subject has been, and still is, considered by numerous authors. Several milling theories have been proposed for these industries, especially concerning ores milling. Biomass milling, prior to its use as biofuel, has been, by far, less studied. Nevertheless, few measurements are available about energy needed for milling of particular biomass, in particular systems. But studies taking into account enough characteristic of the milled material (origin, moisture content, particle size distribution) are scarce. Moreover, the methods used to measure these properties are generally different. In consequence, nearly none biomass milling model has been proposed. Concerning wood densified product (pellets & briquettes) apparently no data are available yet. . This study draws upon the milling theories developed for the ore processing industry (Von Rittinger, Kick and Bond theories which have been merged by Charles and Hukki) in order to define a method for characterizing wood chip and pellet energy consumption during milling. Thus it proposes parameters and measurement methods that have to be taken into account when milling modelling comes to an end for biomass or densified biomass Energy consumption during wood milling depends on three main factors: the material moisture content, the particle size difference between the feed and the milled product, and the material itself. The latter may be characterized by a single grindability parameter based on an adaptation of Von Rittinger’s constant. A relation characterizing wood pellet energy consumption as a function of the particle size distribution of the pellet ingredients and the milled pellets is proposed as well. This is characteristic of each type of pellet for each moisture content value considered [less ▲]

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See detailÀ la (re)découverte du temple d’Isis à Pompéi
Veymiers, Richard ULg

Scientific conference (2014, April 01)

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See detailIntegration of near-surface geophysical, geological and hydrogeological data with multiple-point geostatistics in alluvial aquifers
Hermans, Thomas ULg

Doctoral thesis (2014)

Alluvial plains constitute essential geological bodies for environmental studies such as contaminated sites remediation, low-enthalpy geothermal energy or groundwater resources. The heterogeneity of these ... [more ▼]

Alluvial plains constitute essential geological bodies for environmental studies such as contaminated sites remediation, low-enthalpy geothermal energy or groundwater resources. The heterogeneity of these deposits governs flow processes and needs to be quantified. A proper description of such complex deposits requires an integrated approach combining geological, geophysical and hydrogeological data. Solving such spatial inverse problems in the Earth Sciences remains a considerable challenge given the large number of parameters to invert for, the non-linearity of forward models and, as a result, the ill-posedness of the problem. Geostatistics is therefore needed to specify prior models, more particularly, information to control the spatial features of the inverse solutions. Two-point geostatistical approaches have been developed to describe the heterogeneity of one geological formation but fail to reproduce the heterogeneity of fluvial deposits with multiple facies. Multiple-point statistics (MPS) introduced the training image (TI) concept to replace the variogram within an extended sequential simulation framework. The use of geophysics to constrain such simulations has been studied in the petroleum industry with wave-based methods (seismic reflection), but little research has been done to assess the use of near-surface potential methods to condition MPS in environmental studies. In this work, we propose to integrate geological (borehole logs), geophysical (electrical resistivity tomography (ERT) profiles) and hydrogeological (hydraulic heads) data within MPS models on the alluvial plain of the Meuse River, Belgium. Potential-based geophysical methods being integrative, they suffer from a relatively poor resolution. We first study how we can improve the informative content of geophysical inversion by including prior information in the ERT inverse problem. Three methods are tested and compared in several field cases, namely the reference model inversion, the structural inversion and the regularized geostatistical inversion. If every method has advantages and drawbacks, the best suited method for the considered problem is the regularized geostatistical method. Electromagnetic borehole logs enable to derive the vertical correlation length of electrical resistivity in the deposits and to subsequently use it to constrain the inversion. In addition to the knowledge of the bedrock position, it enables to retrieve an electrical resistivity distribution of the deposits close to direct observations. This ensures that geophysical models will be informative to constrain MPS simulations. Given the lack of geological and sedimentological data to build accurate TIs, a data base of TIs is built using several different parameters and scenarios. They are all based on a three facies description: clay/loam, sand and gravel corresponding to low, intermediate and high hydraulic conductivity. Then, we develop a methodology to verify the consistency of independently-built TIs with geophysical data. Our methodology starts by creating subsurface models with each TI. From these models we create synthetic geophysical data and from this synthetic data, synthetic inverted models. These models are now compared with a single inverted model obtained from the field survey, allowing for our definition of what is ``consistent''. To that extent, we calculate the Euclidean distance between any two inverted models as well as field data and visualize the results in a 2D or 3D space using multidimensional scaling (MDS). With this technique, it is possible to verify if field cases fall in the distribution represented by synthetic cases, and thus are consistent with them. In a second step, we present a cluster analysis on the MDS-map to highlight which parameters are the most sensitive for the construction of TI. Based on this analysis, a probability of each geological scenario is computed through kernel smoothing of the densities in reduced projected metric space. The integration of hydrogeological data is made through a stochastic inversion method: the probability perturbation method (PPM), using MPS constrained with geophysical data to generate models. The PPM algorithm automatically seeks solutions fitting both hydrogeological data and training-image based geostatistical constraints. Only geometrical features of the model are affected by the perturbation, i.e. we do not attempt to directly find the optimal value of hydrogeological parameters (chosen a priori), but the optimal spatial distribution of facies whose prior distribution is quantified in a training image. Tracing experiments may be used to further constrain hydrogeological models. ERT has proven its ability to monitor salt tracer tests, but few studies have investigated its performances in thermal tracing experiments. In this study, we demonstrate the ability of surface and crosshole ERT to image quantitatively temperature changes during heat injection experiments. Such resistivity data provides important information to improve hydrogeological models. Our study proves that ERT, especially crosshole ERT, is a reliable tool to follow thermal tracing experiments. It also confirms that ERT should be included to in situ techniques to characterize heat transfer in the subsurface and to monitor geothermal resources exploitation. [less ▲]

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See detailNeuropathies proximales du membre supérieur
WANG, François-Charles ULg

Conference (2014, April 01)

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