Reliable ABC model choice via random forests

Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques. We propose a novel approach based on a machine learning tool named random forests to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with random forests and postponing the approximation of the posterior probability of the predicted MAP for a second stage also relying on random forests. Compared with earlier implementations of ABC model choice, the ABC random forest approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least fifty), and (iv) it includes an approximation of the posterior probability of the selected model. The call to random forests will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets. The proposed methodologies are implemented in the R package abcrf available on the CRAN.Comment: 39 pages, 15 figures, 6 table

Genome-wide analysis of the rice and arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining

<p>Abstract</p> <p>Background</p> <p>Plant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. Our objective was to characterize the complete <it>nsLtp </it>gene family in rice and arabidopsis and to perform wheat EST database mining for <it>nsLtp </it>gene discovery.</p> <p>Results</p> <p>In this study, we carried out a genome-wide analysis of <it>nsLtp </it>gene families in <it>Oryza sativa </it>and <it>Arabidopsis thaliana </it>and identified 52 rice <it>nsLtp </it>genes and 49 arabidopsis <it>nsLtp </it>genes. Here we present a complete overview of the genes and deduced protein features. Tandem duplication repeats, which represent 26 out of the 52 rice <it>nsLtp </it>genes and 18 out of the 49 arabidopsis <it>nsLtp </it>genes identified, support the complexity of the <it>nsLtp </it>gene families in these species. Phylogenetic analysis revealed that rice and arabidopsis nsLTPs are clustered in nine different clades. In addition, we performed comparative analysis of rice <it>nsLtp </it>genes and wheat (<it>Triticum aestivum</it>) EST sequences indexed in the UniGene database. We identified 156 putative wheat <it>nsLtp </it>genes, among which 91 were found in the 'Chinese Spring' cultivar. The 122 wheat non-redundant nsLTPs were organized in eight types and 33 subfamilies. Based on the observation that seven of these clades were present in arabidopsis, rice and wheat, we conclude that the major functional diversification within the nsLTP family predated the monocot/dicot divergence. In contrast, there is no type VII nsLTPs in arabidopsis and type IX nsLTPs were only identified in arabidopsis. The reason for the larger number of <it>nsLtp </it>genes in wheat may simply be due to the hexaploid state of wheat but may also reflect extensive duplication of gene clusters as observed on rice chromosomes 11 and 12 and arabidopsis chromosome 5.</p> <p>Conclusion</p> <p>Our current study provides fundamental information on the organization of the rice, arabidopsis and wheat <it>nsLtp </it>gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat <it>nsLtp </it>gene families and will strongly support further transcript profiling or functional analyses of <it>nsLtp </it>genes. Until such time as specific physiological functions are defined, it seems relevant to categorize plant nsLTPs on the basis of sequence similarity and/or phylogenetic clustering.</p

Les séries fluvio-éoliennes du "Cutler Group" :: Permien (Utah, USA). Modèle architectural et expression des unités génétiques

National audienceL'essor qu'a connu la stratigraphie séquentielle dans les environnements continentaux a permis de définir des modèles architecturaux pour des séries fluvio-lacustres. Plus récemment, les modèles proposés ont intégré les dépôts éoliens dans les systèmes continentaux côtiers ou lacustres (préservation de l'éolien vs variations de la table d'eau, e.g. Carr-Crabaugh & Kocurek, 1998) ou dans les systèmes continentaux endoréiques (préservation de l'éolien vs climat (e.g. Clemmensen et al., 1998) ou préservation de l'éolien vs accommodation et flux de sédiments, e.g. Bourquin et al., 2009). Cependant, peu de modèles discutent les variations de préservation des dépôts éoliens par rapport aux environnements continentaux associés (fluvial, lac, playa) afin de prédire un modèle architectural des dépôts éoliens (du réservoir au bassin) en fonction du contexte géodynamique. L'objectif de cet exposé est de contraindre l'expression des unités génétiques et de proposer un modèle architectural montrant les variations de préservation des dépôts éoliens en fonction du contexte tectonique, climatique et eustatique. L'étude des séries du Permien inférieur, " Cutler Group ", du " Paradox Basin " (SE Utah), caractérisées par des dépôts fluvio-éoliens (e.g. Condon, 1997), a été réalisée à partir de 5 sections sédimentologiques. Elles sont localisées sur un profil proximal représenté par des dépôts dominés fluvial jusqu'à des dépôts dominés éolien dans le domaine distal (e.g. Mountney & Jagger, 2004). Une étude sédimentologique et stratigraphique détaillée permet de proposer une évolution spatiale et temporelle des environnements de dépôt. Nous avons ainsi mis en évidence (1) les variations d'expression des unités génétiques d'un environnement proximal à un environnement distal en climat semi-aride, (2) plusieurs modèles architecturaux montrant l'évolution verticale depuis un contexte de bassin côtier, à dunes éoliennes faiblement préservées, vers des environnements plus continentaux dominés éolien puis vers des systèmes fluvio-lacustres à faible préservation des dépôts éoliens

Modulation of sodium-coupled uptake and membrane fluidity by cisplatin in renal proximal tubular cells in primary culture and brush-border membrane vesicles

Modulation of sodium-coupled uptake and membrane fluidity by cisplatin in renal proximal tubular cells in primary culture and brush-border membrane vesicles. The proximal tubule appears to be the main target for the adverse effects of cis-diamminedichloroplatinum (II) (cDDP). We evaluated the early effects of cDDP at concentrations (3 to 67 µM) lower that those which alter cell viability, on three apical transport systems and on the physical state of the brush border membrane (BBM) in rabbit proximal tubule (RPT) cells in primary culture. The maximal effect, corresponding to a 30% decrease in Na+-coupled uptake of phosphate (Pi) and α-methylglucopyranoside (MGP) and a twofold increase in Na+-coupled alanine uptake, was obtained at 17 µM (5 µg/ml) cDDP and occurred through a modification of their affinity. At this concentration, cDDP increased BBM fluidity and decreased the BBM cholesterol content by 28%, without increasing the permeability of tight junctions. To clarify the role of cDDP-induced increase in BBM fluidity on alterations of Na+-coupled uptake, these parameters were also investigated in BBM vesicles isolated from rabbit renal cortex directly exposed to cDDP. cDDP induced a concentration-dependent inhibition of Na+-coupled uptake of MGP, Pi and alanine in BBM vesicles from the renal cortex, associated with a decrease in protein sulfhydryl content, without modifying BBM fluidity. Our findings strongly suggest that the cDDP-induced increase in BBM fluidity in RPT cells results from an indirect mechanism, possibly an alteration of cholesterol metabolism, and did not play a major role in the cDDP-induced inhibition of Na+/Pi and Na+/ glucose cotransport systems that may be mainly mediated through a direct chemical interaction with essential sulfhydryl groups of the transporters

On the evaluation of the conversational speech quality in telecommunications

International audienceIn this paper we propose an objective method to assess speech quality in the conversational context by taking into account the talking and listening speech qualities and the impact of delay. This approach is applied to the results of four subjective tests on the effects of echo, delay, packet loss and noise. The dataset is divided into training and validation sets. For the training set, a multiple linear regression is applied to determine a relationship between conversational, talking and listening speech qualities and the delay value. The multiple linear regression leads to an accurate estimation of the conversational scores with high correlation and low error between subjective and estimated scores, both on the training and validation sets. In addition, a validation is performed on the data of a subjective test found in the literature which confirms the reliability of the regression. The relationship is then applied to an objective level by replacing talking and listening subjective scores with talking and listening objective scores provided by existing objective models, fed by speech signals recorded during the subjective tests. The conversational model achieves high perfor- mance as revealed by comparison with the test results and with the existing standard methodology “E-model”, presented in the ITU-T (International Telecommunication Union) Recommendation G.107