Université libre de Bruxelles

About: Université libre de Bruxelles is a education organization based out in Brussels, Belgium. It is known for research contribution in the topics: Population & Breast cancer. The organization has 24974 authors who have published 56969 publications receiving 2084303 citations. The organization is also known as: ULB.

minet : A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

Abstract: This paper presents the R/Bioconductor package minet (version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical dependencies between genes and the weight of an edge quantifies the statistical evidence of a specific (e.g transcriptional) gene-to-gene interaction. Four different entropy estimators are made available in the package minet (empirical, Miller-Madow, Schurmann-Grassberger and shrink) as well as four different inference methods, namely relevance networks, ARACNE, CLR and MRNET. Also, the package integrates accuracy assessment tools, like F-scores, PR-curves and ROC-curves in order to compare the inferred network with a reference one. The package minet provides a series of tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive R Archive Network (CRAN) as well as from the Bioconductor website.

Molecular cloning of the thyrotropin receptor

Abstract: The pituitary hormone thyrotropin, or thyroid-stimulating hormone (TSH), is the main physiological agent that regulates the thyroid gland. The thyrotropin receptor (TSHR) was cloned by selective amplification with the polymerase chain reaction of DNA segments presenting sequence similarity with genes for G protein-coupled receptors. Out of 11 new putative receptor clones obtained from genomic DNA, one had sequence characteristics different from all the others. Although this clone did not hybridize to thyroid transcripts, screening of a dog thyroid complementary DNA (cDNA) library at moderate stringency identified a cDNA encoding a 4.9-kilobase thyroid-specific transcript. The polypeptide encoded by this thyroid-specific transcript consisted of a 398-amino acid residue amino-terminal segment, constituting a putative extracellular domain, connected to a 346-residue carboxyl-terminal domain that contained seven putative transmembrane segments. Expression of the cDNA conferred TSH responsiveness to Xenopus oocytes and Y1 cells and a TSH binding phenotype to COS cells. The TSHR and the receptor for luteinizing hormone-choriogonadotropin constitute a subfamily of G protein-coupled receptors with distinct sequence characteristics.

Local kinematics of K and M giants from CORAVEL/Hipparcos/Tycho-2 data: Revisiting the concept of superclusters

Abstract: The availability of the Hipparcos Catalogue has triggered many kinematic and dynamical studies of the solar neighbourhood. Nevertheless, those studies generally lacked the third component of the space velocities, i.e., the radial velocities. This work presents the kinematic analysis of 5952 K and 739 M giants in the solar neighbourhood which includes for the first time radial velocity data from a large survey performed with the CORAVEL spectrovelocimeter. It also uses proper motions from the Tycho-2 catalogue, which are expected to be more accurate than the Hipparcos ones. An important by-product of this study is the observed fraction of only 5.7% of spectroscopic binaries among M giants as compared to 13.7% for K giants. After excluding the binaries for which no center-of-mass velocity could be estimated, 5311 K and 719 M giants remain in the final sample. The UV -plane constructed from these data for the stars with precise parallaxes (%) reveals a rich small-scale structure, with several clumps corresponding to the Hercules stream, the Sirius moving group, and the Hyades and Pleiades superclusters. A maximum-likelihood method, based on a Bayesian approach, has been applied to the data, in order to make full use of all the available stars (not only those with precise parallaxes) and to derive the kinematic properties of these subgroups. Isochrones in the Hertzsprung-Russell diagram reveal a very wide range of ages for stars belonging to these groups. These groups are most probably related to the dynamical perturbation by transient spiral waves (as recently modelled by De Simone et al. [CITE]) rather than to cluster remnants. A possible explanation for the presence of young group/clusters in the same area of the UV -plane is that they have been put there by the spiral wave associated with their formation, while the kinematics of the older stars of our sample has also been disturbed by the same wave. The emerging picture is thus one of dynamical streams pervading the solar neighbourhood and travelling in the Galaxy with similar space velocities. The term dynamical stream is more appropriate than the traditional term supercluster since it involves stars of different ages, not born at the same place nor at the same time. The position of those streams in the UV -plane is responsible for the vertex deviation of for the whole sample. Our study suggests that the vertex deviation for younger populations could have the same dynamical origin. The underlying velocity ellipsoid, extracted by the maximum-likelihood method after removal of the streams, is not centered on the value commonly accepted for the radial antisolar motion: it is centered on km s-1 . However, the full data set (including the various streams) does yield the usual value for the radial solar motion, when properly accounting for the biases inherent to this kind of analysis (namely, km s-1 ). This discrepancy clearly raises the essential question of how to derive the solar motion in the presence of dynamical perturbations altering the kinematics of the solar neighbourhood: does there exist in the solar neighbourhood a subset of stars having no net radial motion which can be used as a reference against which to measure the solar motion?

A quasi maximum likelihood approach for large approximate dynamic factor models

Abstract: Is maximum likelihood suitable for factor models in large cross-sections of time series? We answer this question from both an asymptotic and an empirical perspective. We show that estimates of the common factors based on maximum likelihood are consistent for the size of the cross-section (n) and the sample size (T) going to infinity along any path of n and T and that therefore maximum likelihood is viable for n large. The estimator is robust to misspecification of the cross-sectional and time series correlation of the the idiosyncratic components. In practice, the estimator can be easily implemented using the Kalman smoother and the EM algorithm as in traditional factor analysis.