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

Hydrogen Recombination with Multilevel atoms

Hydrogen recombination is one of the most important atomic processes in many astrophysical objects such as Type II supernova (SN~II) atmospheres, the high redshift universe during the cosmological recombination era, and H II regions in the interstellar medium. Accurate predictions of the ionization fraction can be quite different from those given by a simple solution if one takes into account many angular momentum sub-states, non-resonant processes, and calculates the rates of all atomic processes from the solution of the radiative transfer equation instead of using a Planck function under the assumption of thermal equilibrium. We use the general purpose model atmosphere code PHOENIX 1D to compare how the fundamental probabilities such as the photo-ionization probability, the escape probability, and the collisional de-excitation probability are affected by the presence of other metals in the environment, multiple angular momentum sub-states, and non-resonant processes. Our comparisons are based on a model of SN 1999em, a SNe Type II, 20 days after its explosion.Comment: 29 pages, 12 figures, MNRAS, in pres

Implications of a Minimal SO(10) Higgs Structure

A minimal SO(10) Higgs structure involving a single adjoint field along with spinors, vectors and singlets has been shown to break the SO(10) gauge symmetry to the standard model while stabilizing the F-flat directions and solving the doublet-triplet splitting problem naturally. With this minimal set of Higgs fields, we show how to construct quark and lepton mass matrices which explain well the many features of the observed spectrum, including the Georgi-Jarlskog mass relations. A large mixing of the muon- and tau-neutrinos results naturally as observed in the atmospheric neutrino data. A particular model relying on a family symmetry has been constructed which realizes the desired mass matrices.Comment: 10 pages, REVTEX, contribution submitted to NEUTRINO 98 Conferenc

Resonant recoil in extreme mass ratio binary black hole mergers

The inspiral and merger of a binary black hole system generally leads to an asymmetric distribution of emitted radiation, and hence a recoil of the remnant black hole directed opposite to the net linear momentum radiated. The recoil velocity is generally largest for comparable mass black holes and particular spin configurations, and approaches zero in the extreme mass ratio limit. It is generally believed that for extreme mass ratios eta<<1, the scaling of the recoil velocity is V {\propto} eta^2, where the proportionality coefficient depends on the spin of the larger hole and the geometry of the system (e.g. orbital inclination). Here we show that for low but nonzero inclination prograde orbits and very rapidly spinning large holes (spin parameter a*>0.9678) the inspiralling binary can pass through resonances where the orbit-averaged radiation-reaction force is nonzero. These resonance crossings lead to a new contribution to the kick, V {\propto} eta^{3/2}. For these configurations and sufficiently extreme mass ratios, this resonant recoil is dominant. While it seems doubtful that the resonant recoil will be astrophysically significant, its existence suggests caution when extrapolating the results of numerical kick results to extreme mass ratios and near-maximal spins.Comment: fixed references; matches PRD accepted version (minor revision); 9 pages, 2 figure

Superconductivity in metal rich Li-Pd-B ternary Boride

8K superconductivity was observed in the metal rich Li-Pd-B ternary system. Structural, microstructural, electrical and magnetic investigations for various compositions proved that Li2Pd3B compound, which has a cubic structure composed of distorted Pd6B octahedrons, is responsible for the superconductivity. This is the first observation of superconductivity in metal rich ternary borides containing alkaline metal and Pd as a late transition metal. The compound prepared by arc melting has high density, is stable in the air and has an upper critical field, Hc2(0), of 6T.Comment: 4 pages, 5 figur

Growth and mineral nutrition responses of mycorrhizal and non-mycorrhizal cowpea, pigeon pea and groundnut to phosphorus sources of different solubilities

The effects of a superphosphate (SP) and a rock phosphate (RP), with equal total P contents, on the growth and mineral nutrition responses of mycorrhizal and nonmycorrhizal cowpea, pigeon pea and groundnut were investigated in a pot experiment using an air-dry gamma ray-sterilized (1.5Mrad) Andisol subsoil. Adequate amounts of micronutrients were added to the pot soils as supplements. The plants were inoculated with surface-sterilized 100 spores/pot of Glomus etunicatum or none and with Rhizobium strains. At their maturities, dry weights of plant parts and nodule number, root length, arbuscular mycorrhizal fungal (AMF) colonization of roots and AMF spore production were also measured. Shoot nitrogen and phosphorus concentrations were determined by the Micro-Kjeldahl distillation and ammonium-molybdenum blue methods, respectively. Shoot copper and iron concentrations were measured by the atomic absorption spectrophotometry. Mycorrhiza formation was greater with superphosphate than with rock phosphate treatments. Rock phosphate enhanced mycorrhization in cowpea and pigeon pea but it decreased it in groundnut. Superphosphate-treated cowpea and pigeon pea plants were larger than RP-treated plants whether mycorrhizal or not but in groundnut growth increased only when the plant was treated with SP and inoculated with AMF. Mycorrhizal enhancement of shoot growth in superphosphate-fertilized groundnut could be a direct consequence of improved P nutrition resulting from increased hyphal uptake and/or enlarged absorptive root surface due to increased root fineness. There were similarities in shoot dry matter yields as well as shoot P uptakes of both mycorrhizal and non-mycorrhizal RP-treated plants suggesting that the legumes were so unresponsive to the RP that even mycorrhization could not trigger any response in them. The increased contents of N, Cu and Fe in the shoots of mycorrhizal SP-fertilized plants were observed to be the result of larger shoot sizes except with Fe in groundnut shoot whose enhancement could be related to a good mycorrhiza formation and a concomitant improvement in P nutrition which may further have been influenced by its fine root structure. There was a very close interdependency of fine root structure, AMF colonization, AMFspore production and improved P and Fe nutrition in groundnut as a result of soluble phosphate application.Journal of Science & Technology (Ghana) Vol. 27 (2) 2007: pp. 43-5