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).

A Computer Vision Framework For Finger-Tapping Evaluation In Parkinson's Disease

Objective: To define and evaluate a Computer-Vision (CV) method for scoring Paced Finger-Tapping (PFT) in Parkinson's disease (PD) using quantitative motion analysis of index-fingers and to compare the obtained scores to the UPDRS (Unified Parkinson's Disease Rating Scale) finger-taps (FT). Background: The naked-eye evaluation of PFT in clinical practice results in coarse resolution to determine PD status. Besides, sensor mechanisms for PFT evaluation may cause patients discomfort. In order to avoid cost and effort of applying wearable sensors, a CV system for non-invasive PFT evaluation is introduced. Methods: A database of 221 PFT videos from 6 PD patients was processed. The subjects were instructed to position their hands above their shoulders besides the face and tap the index-finger against the thumb consistently with speed. They were facing towards a pivoted camera during recording. The videos were rated by two clinicians between symptom levels 0-to-3 using UPDRS-FT. The CV method incorporates a motion analyzer and a face detector. The method detects the face of testee in each video-frame. The frame is split into two images from face-rectangle center. Two regions of interest are located in each image to detect index-finger motion of left and right hands respectively. The tracking of opening and closing phases of dominant hand index-finger produces a tapping time-series. This time-series is normalized by the face height. The normalization calibrates the amplitude in tapping signal which is affected by the varying distance between camera and subject (farther the camera, lesser the amplitude). A total of 15 features were classified using K-nearest neighbor (KNN) classifier to characterize the symptoms levels in UPDRS-FT. The target ratings provided by the raters were averaged. Results: A 10-fold cross validation in KNN classified 221 videos between 3 symptom levels with 75% accuracy. An area under the receiver operating characteristic curves of 82.6% supports feasibility of the obtained features to replicate clinical assessments. Conclusions: The system is able to track index-finger motion to estimate tapping symptoms in PD. It has certain advantages compared to other technologies (e.g. magnetic sensors, accelerometers etc.) for PFT evaluation to improve and automate the ratings

Análise digital de imagem e estereologia da angiogênese em adenomas e no adenocarcinoma colorretal invasivo de submucosa

A angiogênese é essencial no desenvolvimento neoplásico, associando-se às metástases à distância e recorrência em diversas neoplasias malignas. Em carcinomas colorretais, os parâmetros da análise digital de imagem e estereologia da angiogênese foram pouco estudados. Objetivo: avaliar parâmetros tridimensionais e a quantificação microvascular bidimensional nas diferentes apresentações morfológicas dos adenomas colorretais e no adenocarcinoma colorretal restrito à submucosa, a fim de determinar o papel da angiogênese nas diferentes etapas da seqüência adenoma-carcinoma e sua relação com as diferentes apresentações das lesões precursoras do carcinoma colorretal. Material e métodos: foi realizado estudo histórico de delineamento transversal, incluindo 115 lesões neoplásicas colorretais, ressecadas endoscópica ou cirurgicamente no período de 1997 a 2001, obtidas de pacientes do Hospital de Clínicas de Porto Alegre e da Fundação Universitária de Gastroenterologia (FUGAST). Para análise da angiogênese foram utilizadas as técnicas de imuno-histoquímica, análise digital de imagem, quantificação microvascular e estereologia. Os resultados foram apresentados como mediana e intervalos interquartis. Resultados: a quantificação microvascular foi progressivamente mais elevada nas lesões polipóides com displasia de alto grau comparadas às de baixo grau. Quanto maior o grau de atipia observado, maior foi o número de microvasos (regressão linear, P < 0,05). O volume e extensão microvascular foram diferentes entre as fases evolutivas da neoplasia colorretal, resultando em aumento no volume 728 (416 - 1408) versus 178 (93 - 601) e extensão microvascular 242,4 (131,1 - 936,8) vs 24,0 (6,5 - 142,2) (P < 0,001) nas lesões polipóides com displasia de alto grau comparadas às de baixo grau, respectivamente. A quantificação microvascular foi progressivamente mais elevada, acompanhando a progressão neoplásica polipóide: displasia de baixo grau 41,8 (15,8 - 71,9), displasia de alto grau 60,0 (23,0 - 95,6) e carcinoma de submucosa 76,0 (37,5 - 132,6) (P < 0,001). Concomitante, o volume 956 (436 - 2188) vs 178 (93 - 601) e a extensão microvascular 534,6 (146,7 - 1262) vs 24,0 (6,5 - 142,2) foram mais elevados nos adenocarcinomas colorretais restritos à submucosa em relação às lesões polipóides com displasia de baixo grau, respectivamente (P < 0,001). Não foi encontrada diferença estatisticamente significativa na angiogênese entre os adenomas polipóides e não-polipóides através da quantificação 41,8 (15,8 - 71,9) vs 22 (16 - 40) e estimativa da extensão microvascular 24 (6,5-142,2) vs 17,5 (4,4-54,7), respectivamente. Conclusão: a utilização da análise digital de imagem e estereologia acrescentou maior objetividade e eficácia na metodologia de avaliação angiogênica, pois permitiu a precisa segmentação das áreas hipervasculares, a representação da morfologia tridimensional característica do suprimento vascular e a identificação de diferenças na microvascularização nas etapas evolutivas do câncer colorretal.

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.

COMPARATIVE EVALUATION of OCULOMETRIC VARIABLES IN GRAVES' OPHTHALMOPATHY

OBJECTIVES: To estimate oculometric parameters of Graves' ophthalmopathy in comparison to healthy eyes using digital photography and digital image analysis.INTRODUCTION: Graves' ophthalmopathy is the main cause of eye proptosis. Because these protrusions cause clinically perceived distortions in orbital architecture, digital photographs can be used to detect and quantify these changes.METHODS: We carried out a cross-sectional study comprising 12 healthy volunteers and 15 Graves' ophthalmopathy patients with the purpose of evaluating the use of simple, non-invasive digital photography to estimate oculometric parameters of Graves' ophthalmopathy and compare them with the parameters of unaffected eyes. Facial photographs of cases and controls were taken in a standardized manner. Oculometric parameters were compared between the groups and then correlated to proptometer measures.RESULTS: All estimated oculometric variables showed significant differences between the groups, in particular with regard to mediopupilar aperture, lateral height, distance from the iris edge to the lateral boundary of the palpebral fissure, and distance from the higher point of the iris to the lateral limit of the palpebral fissure. The product of medial aperture and horizontal palpebral fissure also revealed greater discrepancy between the groups. Proptometer measures showed significant linear correlation between the distance from the iris edge to the lateral boundary of the palpebral fissure and between the distance from the higher point of the iris to the lateral limit of palpebral fissure (p<0.05).CONCLUSIONS: Comparative analysis of oculometric parameters in Graves' ophthalmopathy suggests that eye proptosis is related to an asymmetric increase in lateral oculometric measures. Standardized digital photographs can be used in clinical practice to objectively estimate oculometric parameters of Graves' ophthalmopathy patients.

Application of wavelets to the evaluation of phantom images for mammography quality control

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluation of the color stability of two techniques for reproducing artificial irides after microwave polymerization

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

Accuracy of zoomed digital image in the detection of periodontal bone defect: in vitro study

Objectives: (1) To evaluate the intraobserver agreement related to image interpretation and (2) to compare the accuracy of 100%, 200% and 400% zoomed digital images in the detection of simulated periodontal bone defects.Methods: Periodontal bone defects were created in 60 pig hemi-mandibles with slow-speed burs 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm and 3.0 mm in diameter. 180 standardized digital radiographs were made using Schick sensor and evaluated at 100%, 200% and 400% zooming. The intraobserver agreement was estimated by Kappa statistic (kappa). For the evaluation of diagnostic accuracy receiver operating characteristic (ROC) analysis was performed followed by chi-square test to compare the areas under ROC curves according to each level of zooming.Results: For 100%, 200% and 400% zooming the intraobserver agreement was moderate (kappa = 0.48, kappa = 0.54 and kappa = 0.43, respectively) and there were similar performances in the discrimination capacity, with ROC areas of 0.8611 (95% CI: 0.7660-0.9562), 0.8600 (95% CI: 0.7659-0.9540), and 0.8368 (95% CI: 0.7346-0.9390), respectively, with no statistical significant differences (chi(2)-test; P = 0.8440).Conclusions: A moderate intraobserver agreement was observed in the classification of periodontal bone defects and the 100%, 200% and 400% zoomed digital images presented similar performances in the detection of periodontal bone defects.

An in vitro evaluation of apicoectomies and retropreparations using different methods

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

Evaluation of the RB-RB/LB-LB mnemonic rule for recording optimally projected intraoral images of dental implants: an in vitro study

Objective: The aim of this study was to evaluate a simple mnemonic rule (the RB-RB/LB-LB rule) for recording intra-oral radiographs with optimal projection for the control of dental implants.Methods: 30 third-year dental students received a short lesson in the RB-RB/LB-LB mnemonic rule. The rule is as follows: if right blur then raise beam (RB-RB), i.e. if implant threads are blurred at the right side of the implant, the X-ray beam direction must be raised towards the ceiling to obtain sharp threads on both implant sides; if left blur then lower beam (LB-LB), i.e. if implant threads are blurred at the left side of the implant, the X-ray beam direction must be lowered towards the floor to obtain sharp threads on both implant sides. Intra-oral radiographs of four screw-type implants placed with different inclination in a Frasaco upper or lower jaw dental model (Frasaco GmbH, Tettnang, Germany) were recorded. The students were unaware of the inclination of the implants and were instructed to re-expose each implant, implementing the mnemonic rule, until an image of the implant with acceptable quality (subjectively judged by the instructor) was obtained. Subsequently, each radiograph was blindly assessed with respect to sharpness of the implant threads and assigned to one of four quality categories: (1) perfect, (2) not perfect, but clinically acceptable, (3) not acceptable and (4) hopeless.Results: For all implants, from one non-perfect exposure to the following, a higher score was obtained in 64% of the cases, 28% received the same score and 8% obtained a lower score. Only a small variation was observed among exposures of implants with different inclination. on average, two exposures per implant (range: one to eight exposures) were needed to obtain a clinically acceptable image.Conclusion: The RB-RB/LB-LB mnemonic rule for recording intra-oral radiographs of dental implants with a correct projection was easy to implement by inexperienced examiners. Dentomaxillofacial Radiology (2012) 41, 298-304. doi: 10.1259/dmfr/20861598