maigesPack: A Computational Environment for Microarray Data Analysis

Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies focused on systems biology. One of its main problem is complexity of experimental procedure, presenting several sources of variability, hindering statistical modeling. So far, there is no standard protocol for generation and evaluation of microarray data. To mitigate the analysis process this paper presents an R package, named maigesPack, that helps with data organization. Besides that, it makes data analysis process more robust, reliable and reproducible. Also, maigesPack aggregates several data analysis procedures reported in literature, for instance: cluster analysis, differential expression, supervised classifiers, relevance networks and functional classification of gene groups or gene networks

Shape, spin and baryon fraction of clusters in the MareNostrum Universe

The MareNostrum Universe is one of the largest cosmological SPH simulation done so far. It consists of $1024^3$ dark and $1024^3$ gas particles in a box of 500 $h^{-1}$ Mpc on a side. Here we study the shapes and spins of the dark matter and gas components of the 10,000 most massive objects extracted from the simulation as well as the gas fraction in those objects. We find that the shapes of objects tend to be prolate both in the dark matter and gas. There is a clear dependence of shape on halo mass, the more massive ones being less spherical than the less massive objects. The gas distribution is nevertheless much more spherical than the dark matter, although the triaxiality parameters of gas and dark matter differ only by a few percent and it increases with cluster mass. The spin parameters of gas and dark matter can be well fitted by a lognormal distribution function. On average, the spin of gas is 1.4 larger than the spin of dark matter. We find a similar behavior for the spins at higher redshifts, with a slightly decrease of the spin ratios to 1.16 at $z=1.$ The cosmic normalized baryon fraction in the entire cluster sample ranges from $Y_b = 0.94$, at $z=1$ to $Y_b = 0.92$ at $z=0$. At both redshifts we find a slightly, but statistically significant decrease of $Y_b$ with cluster mass.Comment: 7 pages, 6 figures. Accepted for publication in The Astrophysical Journa

Vacuum solutions with nontrivial boundaries for the Einstein-Gauss-Bonnet theory

The classification of certain class of static solutions for the Einstein-Gauss-Bonnet theory in vacuum is presented. The spacelike section of the class of metrics under consideration is a warped product of the real line with a nontrivial base manifold. For arbitrary values of the Gauss-Bonnet coupling, the base manifold must be Einstein with an additional scalar restriction. The geometry of the boundary can be relaxed only when the Gauss-Bonnet coupling is related with the cosmological and Newton constants, so that the theory admits a unique maximally symmetric solution. This additional freedom in the boundary metric allows the existence of three main branches of geometries in the bulk, containing new black holes and wormholes in vacuum.Comment: Prepared for the proceedings of the 7th Alexander Friedmann International Seminar on Gravitation and Cosmology, July 2008, Joao Pessoa, Brasil. 4 pages, References adde

Analytical infrared intensities for periodic systems with local basis sets

We report a method for the efficient evaluation of analytic infrared (IR) intensities within generalized Kohn-Sham density functional theory using Gaussian orbitals and periodic boundary conditions. A discretized form of the Berry phase is used to evaluate a periodic dipole moment and its derivatives with respect to in-phase nuclear coordinate displacements. Benchmark calculations are presented for one-dimensional chains of water molecules and poly(paraphenylenevinylene).Comment: 16 pages, 3 figures, 4 tables, submitted to Phys. Rev.

What makes representative constructivism democratic?

This article connects J. S. Mill’s democratic theory and practice with the contemporary debate surrounding representative constructivism and argues that Mill’s advocacy of female suffrage affords an empirical example of the mobilization power of representative constructivism. Studying this concrete example of constructivism alongside Mill’s theory of political representation clarifies that constructivism is democratic to the extent it seeks to make citizens themselves appropriate and contest the claims that their representatives construct on their behalf