Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

Comportamento de fundações superficiais apoiadas em aterros estabilizados com resíduos industriais

Neste trabalho foi estudado o comportamento de fundações superficiais apoiadas em sistema de dupla camada, quando a superior é cimentada. O estudo consistiu-se de três etapas, chamadas de Etapa de Laboratório, Etapa Numérica e Etapa de Campo. Na Etapa de Laboratório foi verificada a viabilidade técnica de utilizar os resíduos industriais cinza pesada e cal de carbureto na estabilização de um solo residual de arenito botucatu. Estudou-se a reatividade da cinza pesada com a cal de carbureto, a influência da temperatura e do tempo de cura no desenvolvimento das reações pozolânicas, a influência de diferentes teores de resíduos na resistência à compressão simples, compressão diametral e durabilidade, objetivando definir uma mistura ótima e, ainda, o impacto ambiental da utilização da mistura ótima, através de ensaios de lixiviação e solubilização. Na Etapa Numérica foi estudado, através do Método dos Elementos Finitos, o comportamento de fundações superficiais apoiadas em dupla camada. O modelo utilizado para representar o comportamento do material cimentado e não-cimentado foi o elástico-plástico com critério de ruptura de Drucker-Prager e fluxo não-associado. Verificou-se, através de análise paramétrica, a influência da espessura da camada cimentada e do diâmetro da fundação, bem como a influência dos parâmetros dos materiais cimentado e não-cimentado na resposta carga x recalque de fundações superficiais. Na Etapa de Campo foram construídos aterros experimentais utilizando a mistura ótima determinada na Etapa de Laboratório e, sobre estes aterros, foram executados provas de carga de placas. A análise dos resultados obtidos nas três etapas levou às seguintes conclusões: é possível utilizar cinza pesada e cal de carbureto para estabilizar o solo residual de botucatu; o comportamento de fundações superficiais sobre solos cimentados é controlado pela relação espessura da camada cimentada diâmetro da fundação; os parâmetros ângulo de atrito e módulo de elasticidade da camada cimentada não influenciam os resultados de prova de carga; a ruptura da fundação é função de dois mecanismos progressivos, os quais são função das tensões de tração geradas na parte inferior da camada cimentada e das tensões cisalhantes existentes logo abaixo das bordas da fundação.

Inibição do crescimento de Escherichia coli isolada de Queijo Minas Frescal por Lactobacillus acidophilus

Escherichia coli faz parte da microbiota anaeróbica facultativa normal, sendo também considerada um dos maiores patógenos entéricos predominantes no cólon dos animais e homem. Neste trabalho, realizaram-se ensaios in vitro para avaliar o grau de atividade antagonista de cinco cepas de Lactobacillus acidophilus, com capacidade probiótica sobre Escherichia coli BIA 26 (STEC) isolada de queijo Minas Frescal. Para tanto, foi utilizado o teste de inibição através do método de dupla camada em triplicata para avaliar zonas de inibição de crescimento. Todas as cepas de Lactobacillus mostraram-se capazes de inibir a E. coli, com zonas de inibição variando de 12 a 15mm de diâmetro, sendo que a maioria apresentou 14mm de diâmetro, consideradas como fortes halos de inibição.

Evaluation of the effect of the stoichiometric ratio of Ca/Cu on the electrical and microstructural properties of the CaCu3Ti4O12 polycrystalline system

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Modelagem Matemática e Computacional de fenômenos eletrocinéticos em meios porosos carregados eletricamente

In this work we present a mathematical and computational modeling of electrokinetic phenomena in electrically charged porous medium. We consider the porous medium composed of three different scales (nanoscopic, microscopic and macroscopic). On the microscopic scale the domain is composed by a porous matrix and a solid phase. The pores are filled with an aqueous phase consisting of ionic solutes fully diluted, and the solid matrix consists of electrically charged particles. Initially we present the mathematical model that governs the electrical double layer in order to quantify the electric potential, electric charge density, ion adsorption and chemical adsorption in nanoscopic scale. Then, we derive the microscopic model, where the adsorption of ions due to the electric double layer and the reactions of protonation/ deprotanaç~ao and zeta potential obtained in modeling nanoscopic arise in microscopic scale through interface conditions in the problem of Stokes and Nerst-Planck equations respectively governing the movement of the aqueous solution and transport of ions. We developed the process of upscaling the problem nano/microscopic using the homogenization technique of periodic structures by deducing the macroscopic model with their respectives cell problems for effective parameters of the macroscopic equations. Considering a clayey porous medium consisting of kaolinite clay plates distributed parallel, we rewrite the macroscopic model in a one-dimensional version. Finally, using a sequential algorithm, we discretize the macroscopic model via the finite element method, along with the interactive method of Picard for the nonlinear terms. Numerical simulations on transient regime with variable pH in one-dimensional case are obtained, aiming computational modeling of the electroremediation process of clay soils contaminated

Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A polaronic stacking fault defect model for CaCu3Ti4O12 material: an approach for the origin of the huge dielectric constant and semiconducting coexistent features

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Dielectric spectroscopy analysis of CaCu3Ti4O12 polycrystalline systems

Dielectric spectroscopy was used in this study to examine CaCu3Ti4O12 polycrystalline samples. The analysis involved systems presenting low non-Ohmic properties, and the grain's internal domain was evaluated separately from the contribution of barrier-layer capacitances associated with Schottky-type barriers in this type of material. The effect of oxygen-rich atmosphere and high cooling rate was evaluated, revealing a strong increase in the dielectric properties of the CaCu3Ti4O12 system under these conditions. This effect was attributed to a chemical change in the grain's internal domain, which may be considered an internal barrier-layer capacitance of the polycrystalline material. (c) 2006 American Institute of Physics.

Electrochemical study of perchlorate reduction at tin electrodes

The electrochemical behaviour of tin in de-aerated sodium perchlorate was studied using potentiodynamic and potentiostatic techniques. Tin behaviour in sodium perchlorate has been complicated unexpectedly by the reduction of the perchlorate anion. It is shown that the reduction process takes place within a potential region comprising the negative side of the double layer region and the positive side of the hydrogen region (-0.7 less than or equal to E less than or equal to -1.3 V). The presence of oxide on the electrode surface favours the reduction reaction, which may occur in two steps: the formation of basic tin(II) chloride followed by its reduction, producing chloride.

Role of the surface state and structural feature in the thermoreversible sol-gel transition of a zirconyl aqueous precursor modified by sulfuric acid

The sols produced by admixture of ZrOCl2 acidified solutions to hot H2SO4 aqueous solutions were studied to clarify the effects of Cl- and SO42- ions on the kinetic stability of nanoparticles and to obtain some new evidence concerning the mechanism of a thermoreversible sol-gel transition observed in this system. The study of suspensions prepared with different molar ratios R-S = [Zr]/[SO42-] and R-Cl = [Zr]/[Cl-] revealed domains of composition of formation of thermoreversible gels, thermostable sols, and powder precipitation. The effects of R-S and R-Cl on the structural features of nanoparticles and on the particle solution interface were systematically analyzed for samples of thermoreversible and thermostable sol domains. Small-angle X-ray scattering measurements revealed the presence of small fractal aggregates in all samples of thermoreversible domains, while compact packing aggregates of primary particles are present in the thermostable sol. Extended X-ray absorption fine structure and elemental chemical analysis revealed that irrespective of the nominal value of R-S and R-Cl all studied samples of the thermoreversible domain are constituted by a well-defined compound possessing an inner core made of hydroxyl and oxo groups bridging together zirconium atoms surrounded on the surface by complexing sulfate ligands. zeta potentials of powders extracted by freeze-drying from the thermoreversible gel revealed a point of surface charge inversion attributed to the specific adsorption of SO42- ion. Thermoreversible gel formation is rationalized by considering the effect of the specific adsorption on the electrical double-layer repulsion together with the temperature dependency of the physical chemical properties of ions in solution.

Effect of spin-polarized subbands in the inhomogeneous hole gas providing the indirect exchange in GaMnAs bilayers

The magnetic order resulting from the indirect exchange in the metallic phase of a (Ga,Mn)As/GaAs double layer structure is studied via Monte Carlo simulation. The polarization of the hole gas is taken into account, establishing a self-consistency between the magnetic order and the electronic structure. The Curie-Weiss temperatures calculated for these low-dimensional systems are in the range of 50-80 K, and the dependence of the transition temperature with the GaAs separation layer is established. (C) 2003 Published by Elsevier B.V.

Nanoscale effects and polaronic relaxation in CaCu3Ti 4O12 compounds

In the present communication, by using dielectric spectroscopy measurement, the correlations between Nanosized Barrier Layer Capacitance (NBLC) (Bueno et al. (2009) [7]) and the high frequency polaronic near-Debye dipolar relaxation found in CaCu3Ti4O12 compounds was discussed. The polaronic process was confirmed to be closely associated with the ultrahigh dielectric features of CaCu3Ti4O12 materials and its concomitant dielectric loss. Herein, the shift in relaxation frequency as a function of temperature was used for calculating the activation energy for hopping electronic conduction. The value obtained was 33 meV, an energy whose magnitude is compatible and confirmed the hypothesis of polaronic features for this high frequency dipolar relaxation process. Furthermore, it is shown that the nanosized barrier inferred from the NBLC model has a polaronic feature with dielectric permittivity exiting orthogonally to dielectric loss, a phenomenological pattern that contradicts the normally observed behavior for traditional dielectrics but explain the dielectric and conductivity feature of CaCu3Ti4O12 compounds. © 2010 Elsevier Ltd. All rights reserved.

Estudo do comportamento coloidal de suspensão de fibra de celulose, carbonato de cálcio, amido catiônico: variação da força iônica e do pH

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Trocas gasosas e eficiência de uso da água da cultura do arroz irrigado por aspersão em função da aplicação de silício

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Espectroscopia de impedância em soluções iônicas e mistura de etanol/água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)