A Bayesian Semiparametric Approach for Solving the Discrete Calibration Problem

In this article, we introduce a semi-parametric Bayesian approach based on Dirichlet process priors for the discrete calibration problem in binomial regression models. An interesting topic is the dosimetry problem related to the dose-response model. A hierarchical formulation is provided so that a Markov chain Monte Carlo approach is developed. The methodology is applied to simulated and real data.

Influence of neodymium ions on photocatalytic activity of TiO(2) synthesized by sol-gel and precipitation methods

Titanium dioxide with and without the addition of neodymium ions was prepared using sol-gel and precipitation methods. The resulting catalysts were characterized by thermal analysis, X-ray diffraction and BET specific surface area. Neodymium addition exerted a remarkable influence on the phase transition temperature and the surface properties of the TiO(2) matrix. TiO(2) samples synthesized by precipitation exhibit an exothermic event related from the amorphous to anatase phase transition at 510 degrees C, whereas in Nd-doped TiO(2) this transition occurred at 527 degrees C. A similar effect was observed in samples obtained using sol-gel method. The photocatalytic reactivity of the catalysts was evaluated by photodegradation of Remazol Black B (RB) under ultraviolet irradiation. Nd-doped TiO(2) showed enhanced photodegradation ability compared to undoped TiO(2) samples, independent of the method of synthesis. In samples obtained by sol-gel, RB decoloration was enhanced by 16% for TiO(2) doped with 0.5% neodymium ions. (C) 2010 Elsevier B.V. All rights reserved.

Effect of culture medium on biocalcification by Pseudomonas Putida, Lysinibacillus Sphaericus and Bacillus Subtilis

The objective of this study is to investigate the efficiency of calcium carbonate bioprecipitation by Lysinibacillus sphaericus, Bacillus subtilis and Pseudomonas putida, obtained from the Coleção de Culturas do Instituto Nacional de Controle de Qualidade em Saúde (INCQS), as a first step in determining their potential to protect building materials against water uptake. Two culture media were studied: modified B4 containing calcium acetate and 295 with calcium chloride. Calcium consumption in the two media after incubation with and without the bacterial inoculum was determined by atomic absorption analysis. Modified B4 gave the best results and in this medium Pseudomonas putida INQCS 113 produced the highest calcium carbonate precipitation, followed by Lysinibacillus sphaericus INQCS 414; the lowest precipitation was produced by Bacillus subtilis INQCS 328. In this culture medium XRD analysis showed that Pseudomonas putida and Bacillus subtilis precipitated calcite and vaterite polymorphs while Lysinibacillus sphaericus produced only vaterite. The shape and size of the crystals were affected by culture medium, bacterial strain and culture conditions, static or shaken. In conclusion, of the three strains Pseudomonas putida INQCS 113 in modified B4 medium gave the best results precipitating 96% of the calcium, this strain thus has good potential for use on building materials.

The full Bayesian significance test for mixture models: results in gene expression clustering

Gene clustering is a useful exploratory technique to group together genes with similar expression levels under distinct cell cycle phases or distinct conditions. It helps the biologist to identify potentially meaningful relationships between genes. In this study, we propose a clustering method based on multivariate normal mixture models, where the number of clusters is predicted via sequential hypothesis tests: at each step, the method considers a mixture model of m components (m = 2 in the first step) and tests if in fact it should be m - 1. If the hypothesis is rejected, m is increased and a new test is carried out. The method continues (increasing m) until the hypothesis is accepted. The theoretical core of the method is the full Bayesian significance test, an intuitive Bayesian approach, which needs no model complexity penalization nor positive probabilities for sharp hypotheses. Numerical experiments were based on a cDNA microarray dataset consisting of expression levels of 205 genes belonging to four functional categories, for 10 distinct strains of Saccharomyces cerevisiae. To analyze the method's sensitivity to data dimension, we performed principal components analysis on the original dataset and predicted the number of classes using 2 to 10 principal components. Compared to Mclust (model-based clustering), our method shows more consistent results.

Influence of Annealing Heat Treatment and Cr, Mg, and Ti Alloying on the Mechanical Properties of High-Silicon Cast Iron

The influence of annealing on the mechanical properties of high-silicon cast iron for three alloys with distinct chromium levels was investigated. Each alloy was melted either with or without the addition of Ti and Mg. These changes in the chemical composition and heat treatment aimed to improve the material's mechanical properties by inhibiting the formation of large columnar crystals, netlike laminae, precipitation of coarse packs of graphite, changing the length and morphology of graphite, and rounding the extremities of the flakes to minimize the stress concentration. For alloys with 0.07 wt.% Cr, the annealing reduced the impact resistance and tensile strength due to an enhanced precipitation of refined carbides and the formation of interdendritic complex nets. Annealing the alloys containing Ti and Mg led to a decrease in the mechanical strength and an increase in the toughness. Alloys containing approximately 2 wt.% Cr achieved better mechanical properties as compared to the original alloy. However, with the addition of Ti and Mg to alloys containing 2% Cr, the chromium carbide formation was inhibited, impairing the mechanical properties. In the third alloy, with 3.5 wt.% of Cr additions, the mechanical strength improved. The annealing promoted a decrease in both hardness and amount of iron and silicon complex carbides. However, it led to a chromium carbide formation, which influenced the mechanical characteristics of the matrix of the studied material.

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

Background: With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. Results: In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. Conclusion: A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.

Disequilibrium Coefficient: A Bayesian Perspective

Hardy-Weinberg Equilibrium (HWE) is an important genetic property that populations should have whenever they are not observing adverse situations as complete lack of panmixia, excess of mutations, excess of selection pressure, etc. HWE for decades has been evaluated; both frequentist and Bayesian methods are in use today. While historically the HWE formula was developed to examine the transmission of alleles in a population from one generation to the next, use of HWE concepts has expanded in human diseases studies to detect genotyping error and disease susceptibility (association); Ryckman and Williams (2008). Most analyses focus on trying to answer the question of whether a population is in HWE. They do not try to quantify how far from the equilibrium the population is. In this paper, we propose the use of a simple disequilibrium coefficient to a locus with two alleles. Based on the posterior density of this disequilibrium coefficient, we show how one can conduct a Bayesian analysis to verify how far from HWE a population is. There are other coefficients introduced in the literature and the advantage of the one introduced in this paper is the fact that, just like the standard correlation coefficients, its range is bounded and it is symmetric around zero (equilibrium) when comparing the positive and the negative values. To test the hypothesis of equilibrium, we use a simple Bayesian significance test, the Full Bayesian Significance Test (FBST); see Pereira, Stern andWechsler (2008) for a complete review. The disequilibrium coefficient proposed provides an easy and efficient way to make the analyses, especially if one uses Bayesian statistics. A routine in R programs (R Development Core Team, 2009) that implements the calculations is provided for the readers.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models

Survival or longevity is an economically important trait in beef cattle. The main inconvenience for its inclusion in selection criteria is delayed recording of phenotypic data and the high computational demand for including survival in proportional hazard models. Thus, identification of a longevity-correlated trait that could be recorded early in life would be very useful for selection purposes. We estimated the genetic relationship of survival with productive and reproductive traits in Nellore cattle, including weaning weight (WW), post-weaning growth (PWG), muscularity (MUSC), scrotal circumference at 18 months (SC18), and heifer pregnancy (HP). Survival was measured in discrete time intervals and modeled through a sequential threshold model. Five independent bivariate Bayesian analyses were performed, accounting for cow survival and the five productive and reproductive traits. Posterior mean estimates for heritability (standard deviation in parentheses) were 0.55 (0.01) for WW, 0.25 (0.01) for PWG, 0.23 (0.01) for MUSC, and 0.48 (0.01) for SC18. The posterior mean estimates (95% confidence interval in parentheses) for the genetic correlation with survival were 0.16 (0.13-0.19), 0.30 (0.25-0.34), 0.31 (0.25-0.36), 0.07 (0.02-0.12), and 0.82 (0.78-0.86) for WW, PWG, MUSC, SC18, and HP, respectively. Based on the high genetic correlation and heritability (0.54) posterior mean estimates for HP, the expected progeny difference for HP can be used to select bulls for longevity, as well as for post-weaning gain and muscle score.

New constraints on the chemical evolution of the solar neighbourhood and Galactic disc(s) Improved astrophysical parameters for the Geneva-Copenhagen Survey

We present a re-analysis of the Geneva-Copenhagen survey, which benefits from the infrared flux method to improve the accuracy of the derived stellar effective temperatures and uses the latter to build a consistent and improved metallicity scale. Metallicities are calibrated on high-resolution spectroscopy and checked against four open clusters and a moving group, showing excellent consistency. The new temperature and metallicity scales provide a better match to theoretical isochrones, which are used for a Bayesian analysis of stellar ages. With respect to previous analyses, our stars are on average 100 K hotter and 0.1 dex more metal rich, which shift the peak of the metallicity distribution function around the solar value. From Stromgren photometry we are able to derive for the first time a proxy for [alpha/Fe] abundances, which enables us to perform a tentative dissection of the chemical thin and thick disc. We find evidence for the latter being composed of an old, mildly but systematically alpha-enhanced population that extends to super solar metallicities, in agreement with spectroscopic studies. Our revision offers the largest existing kinematically unbiased sample of the solar neighbourhood that contains full information on kinematics, metallicities, and ages and thus provides better constraints on the physical processes relevant in the build-up of the Milky Way disc, enabling a better understanding of the Sun in a Galactic context.

Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall.

The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data

Background: The thin-spined porcupine, also known as the bristle-spined rat, Chaetomys subspinosus (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus Chaetomys was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome b gene and karyotypic information to address this issue. Our molecular analyses included one individual of Chaetomys subspinosus from the state of Bahia in northeastern Brazil, and other hystricognaths. Results: All topologies recovered in our molecular phylogenetic analyses strongly supported Chaetomys subspinosus as a sister clade of the erethizontids. Cytogenetically, Chaetomys subspinosus showed 2n = 52 and FN = 76. Although the sexual pair could not be identified, we assumed that the X chromosome is biarmed. The karyotype included 13 large to medium metacentric and submetacentric chromosome pairs, one small subtelocentric pair, and 12 small acrocentric pairs. The subtelocentric pair 14 had a terminal secondary constriction in the short arm, corresponding to the nucleolar organizer region (Ag-NOR), similar to the erethizontid Sphiggurus villosus, 2n = 42 and FN = 76, and different from the echimyids, in which the secondary constriction is interstitial. Conclusion: Both molecular phylogenies and karyotypical evidence indicated that Chaetomys is closely related to the Erethizontidae rather than to the Echimyidae, although in a basal position relative to the rest of the Erethizontidae. The high levels of molecular and morphological divergence suggest that Chaetomys belongs to an early radiation of the Erethizontidae that may have occurred in the Early Miocene, and should be assigned to its own subfamily, the Chaetomyinae.

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

Marinussaurus curupira, a new genus and species of Gymnophthalmidae lizard is described from Iranduba, state of Amazonas, Brazil. The genus is characterized by an elongate body; short and stout pentadactyl limbs; all digits clawed; single frontonasal; two prefrontals; absence of frontoparietals; interparietal and parietals forming a straight posterior margin, with interparietal shorter than parietals; distinctive ear opening and eyelid; few temporals; three pairs of chin shields; nasal divided; a distinct collar; smooth, mainly hexagonal, dorsal scales; smooth quadrangular ventral scales; two precloacal and three femoral pores on each side in males; pores between three or four scales. Parsimony (PAR) and partitioned Bayesian (BA) phylogenetic analyses with morphological and molecular data recovered the new genus as a member of the Ecpleopodini radiation of the Cercosaurinae. A close relationship of the new genus with Arthrosaura is postulated.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

INFERENCE FOR EIGENVALUES AND EIGENVECTORS OF GAUSSIAN SYMMETRIC MATRICES

This article presents maximum likelihood estimators (MLEs) and log-likelihood ratio (LLR) tests for the eigenvalues and eigenvectors of Gaussian random symmetric matrices of arbitrary dimension, where the observations are independent repeated samples from one or two populations. These inference problems are relevant in the analysis of diffusion tensor imaging data and polarized cosmic background radiation data, where the observations are, respectively, 3 x 3 and 2 x 2 symmetric positive definite matrices. The parameter sets involved in the inference problems for eigenvalues and eigenvectors are subsets of Euclidean space that are either affine subspaces, embedded submanifolds that are invariant under orthogonal transformations or polyhedral convex cones. We show that for a class of sets that includes the ones considered in this paper, the MLEs of the mean parameter do not depend on the covariance parameters if and only if the covariance structure is orthogonally invariant. Closed-form expressions for the MLEs and the associated LLRs are derived for this covariance structure.

FORAMINIFERAL RECORD OF CHANGES IN SUMMER MONSOON PRECIPITATION AT THE SOUTHEASTERN BRAZILIAN CONTINENTAL MARGIN SINCE THE LAST GLACIAL MAXIMUM

Changes in the oxygen isotopic composition of the planktonic foraminifer Globigerinoides ruber and in the foraminifera faunal composition in a core retrieved from the southeastern Brazilian continental margin were used to infer past changes in the hydrological balance and monsoon precipitation in the western South Atlantic since the Last Glacial Maximum (LGM). The results suggest a first-order orbital (precessional) control on the South American Monsoon precipitation. This agrees with previous studies based on continental proxies except for LGM estimates provided by pollen records. The causes for this disagreement are discussed.