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).

Comparison of two extraction methods for evaluation of volatile constituents patterns in commercial whiskeys: Elucidation of the main odour-active compounds

An analytical procedure based on manual dynamic headspace solid-phase microextraction (HS-SPME) method and the conventional extraction method by liquid–liquid extraction (LLE), were compared for their effectiveness in the extraction and quantification of volatile compounds from commercial whiskey samples. Seven extraction solvents covering a wide range of polarities and two SPME fibres coatings, has been evaluated. The highest amounts extracted, were achieved using dichloromethane (CH2Cl2) by LLE method (LLECH2Cl2)(LLECH2Cl2) and using a CAR/PDMS fibre (SPMECAR/PDMS) in HS-SPME. Each method was used to determine the responses of 25 analytes from whiskeys and calibration standards, in order to provide sensitivity comparisons between the two methods. Calibration curves were established in a synthetic whiskey and linear correlation coefficient (r ) were greater than 0.9929 for LLECH2Cl2LLECH2Cl2 and 0.9935 for SPMECAR/PDMS, for all target compounds. Recoveries greater than 80% were achieved. For most compounds, precision (expressed by relative standard deviation, R.S.D.) are very good, with R.S.D. values lower than 14.78% for HS-SPME method and than 19.42% for LLE method. The detection limits ranged from 0.13 to 19.03 μg L−1 for SPME procedure and from 0.50 to 12.48 μg L−1 for LLE. A tentative study to estimate the contribution of a specific compound to the aroma of a whiskey, on the basis of their odour activity values (OAV) was made. Ethyl octanoate followed by isoamyl acetate and isobutyl alcohol, were found the most potent odour-active compounds.

Application of chemometric methods in the evaluation of chemical and spectroscopic data on organic matter from Oxisols in sewage sludge applications

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

Comparative study of analytical methods by direct and first-derivative UV spectrophotometry for evaluation of losartan potassium in capsules

O losartano potássico é um agente anti-hipertensivo não peptídico, que exerce sua ação por bloqueio específico dos receptores da angiotensina II. Este trabalho propôs a validação e aplicação de métodos analíticos orientados ao controle de qualidade de losartano potássico 50 mg na forma farmacêutica cápsula, utilizando a espectrofotometria direta e derivada de primeira ordem na região do UV. Baseado nas características espectrofotométricas de losartano potássico, um sinal a 205 nm do espectro de ordem zero e um sinal a 234 nm do espectro de primeira derivada foram adequados para a quantificação. Os resultados foram usados para comparar essas duas técnicas instrumentais. O coeficiente de correlação entre as respostas e as concentrações de losartano potássico na faixa de 3,0-7,0 mg L-1 e 6,0-14,0 mg L-1 para espectrofotometria direta e derivada de primeira ordem em solução aquosa, respectivamente, foi de (r) of 0,9999 para ambos os casos. Os métodos foram aplicados para quantificação de losartano potássico em cápsulas obtidas de farmácias de manipulação locais e demonstraram ser eficientes, fáceis de aplicar e de baixo custo. Além disso, não necessitam de reagentes poluentes e requerem equipamentos economicamente viáveis.

Parameterized fast decoupled power flow methods for obtaining the maximum loading point of power systems. Part II. Performance evaluation

The parameterized fast decoupled power flow (PFDPF), versions XB and BX, using either theta or V as a parameter have been proposed by the authors in Part I of this paper. The use of reactive power injection of a selected PVbus (Q(PV)) as the continuation parameter for the computation of the maximum loading point (MLP) was also investigated. In this paper, the proposed versions obtained only with small modifications of the conventional one are used for the computation of the MLP of IEEE test systems (14, 30, 57 and 118 buses). These new versions are compared to each other with the purpose of pointing out their features, as well as the influence of reactive power and transformer tap limits. The results obtained with the new approaches are presented and discussed. The results show that the characteristics of the conventional FDPF method are enhanced and the region of convergence around the singular solution is enlarged. In addition, it is shown that these versions can be switched during the tracing process in order to efficiently determine all the PV curve points with few iterations. A trivial secant predictor, the modified zero-order polynomial, which uses the current solution and a fixed increment in the parameter (V, theta, or mu) as an estimate for the next solution, is used for the predictor step. (C) 2003 Elsevier B.V. All rights reserved.

An in vitro evaluation of apicoectomies and retropreparations using different methods

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

Evaluation of two alternative methods for disinfection of toothbrushes and tongue scrapers

Objective: The aim of this study was to investigate the effectiveness of two alternatives methods for the disinfection of oral cleaning devices. Methods: One type of toothbrush and two types of tongue scrapers (steel and plastic) were tested in this study. Sixteen specimens of each group were cut with standardized dimensions, contaminated separately with Candida albicans, Streptococcus mutans and Staphylococcus aureus and incubated for 24 h. After this, oral cleaning devices were washed in saline solution to remove non-adhered cells and divided into two groups (n = 8), one irradiated in microwave and other immersed in 3.78% sodium perborate solution, and evaluated for microbial recovery. The values of cfu of each group of microorganism after disinfection were compared by Kruskal-Wallis and Dunn non-parametric test, considering 95% of confidence. Results: The toothbrush harboured a significant larger number of viable organisms than the tongue scrapers. The steel tongue scraper was less susceptible to adhesion of the three oral microorganisms. The time required to inactivate all contaminating microorganisms using microwave oven was 1 min and, for the immersion in 3.78% sodium perborate solution, was 2 and 3 h, respectively, for C. albicans and S. mutans/S. aureus. Conclusion: Microwave irradiation proved to be an effective alternative method to the disinfection of tongue cleaners and toothbrushes.

Research on Candida dubliniensis in a Brazilian yeast collection obtained from cardiac transplant, tuberculosis, and HIV-positive patients, and evaluation of phenotypic tests using agar screening methods

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

Evaluation of Staining Methods for Cytologic Diagnosis of Oral Lesions

ObjectiveTo compare the efficacy of Papanicolaou, hematoxylin-eosin (H-E), Leishman and periodic acid-Schiff (PAS) staining for Cytologic diagnosis of oral lesions.Study DesignPatients from the Discipline of Stomatology, Sao Jose dos Campos Dental School, from the wards of Hospital Heliopolis and from the dentistry outpatient clinic of the University Hospital, University of São Paulo Medical School, with the following diseases, were selected: erythematous candidiasis (n = 9), pseudomembranous candidiasis (n = 10), squamous cell carcinoma In = 19), herpes simplex (n = 8), paracoccidioidomycosis In = 8) and pemphigus vulgaris (n = 1).ResultsThe different staining methods were compared regarding the quality of definition of cytoplasmic and nuclear morphologic characteristics and the identification of bacteria, fungi, inflammatory cells and secretions. Papanicolaou and H-E staining were considered better methods. In cases of fungal infections, PAS staining is useful and should be applied as a complementary method.ConclusionWithin the limitations of this study, it can be concluded that the cytologic diagnosis of oral lesions along with different staining methods is a useful tool for oral diagnosis. (Acta Cytol 2008;52:697-701)

Resin Bonding to a Feldspar Ceramic After Different Ceramic Surface Conditioning Methods: Evaluation of Contact Angle, Surface pH, and Microtensile Bond Strength Durability

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

Evaluation of different electrochemical methods on the oxidation and degradation of Reactive Blue 4 in aqueous solution

The oxidation of a reactive dye, Reactive Blue 4, RB4, (C.I. 61205), widely used in the textile industries to color natural fibers, was studied by electrochemical techniques. The oxidation on glassy carbon electrode and reticulated vitreous carbon electrode occurs in only one step at 2.0 < PH < 12 involving a two-electron transfer to the amine group leading to the imide derivative. Dye solution was not decolorized effectively in this electrolysis process. Nevertheless, the oxidation of this dye on Ti/SnO2/SbOx (3% mol)/RuO2 (1% mol) electrode showed 100% of decolorization and 60% of total organic carbon removal in Na2SO4 0.2 M at PH 2.2 and potential of +2.4 V. Experiments on degradation photoelectrocatalytic were also carried out for RB4 degradation in Na2SO4 0.1 K PH 12, using a Ti/TiO2 photoanode biased at +1.0 V and UV light. After 1 h of electrolysis the results indicated total color removal and 37% of mineralization. (c) 2004 Elsevier Ltd. All rights reserved.