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).

Mapping of Diepoxybutane Damage in the Cytochrome b Domain of Mitochondrial DNA and the β-globin Domain of Nuclear Chicken DNA Using Quantitative PCR

Diepoxybutane (DEB), a known industrial carcinogen, reacts with DNA primarily at the N7 position of deoxyguanosine residues and creates interstrand cross-links at the sequence 5'-GNC. Since N7-N7 cross-links cause DNA to fragment upon heating, quantative polymerase chain reaction (QPCR) is being used in this experiment to measure the amount of DEB damage (lesion frequency) with three different targets-mitochondrial (unpackaged), open chromatin region, and closed chromatin region. Initial measurements of DEB damage within these three targets were not consistent because the template DNA was not the limiting reagent in the PCR. Follow-up PCR trials using a limiting amount of DNA are still in progress although initial experimentation looks promising. Sequencing of these three targets to confirm the primer targets has only been successfully performed for the closed chromatin target and does not match the sequence from NIH used to design that primer pair. Further sequencing trials need to be conducted on all three targets to assure that a mitochondrial, open chromatin, and closed chromatin region are actually being amplified in this experimental series.

February 2005: ARTstor Adds to Panoply of Databases

http://digitalcommons.winthrop.edu/dacusfocus/1027/thumbnail.jpg

Mapeamento da mídia digital no Brasil

O impacto da digitalização foi sentido antes mesmo de poder ser descrito ou explicado. O projeto Mapping Digital Media (Mapeamento da mídia digital) é uma maneira de atualizar, uma tentativa ambiciosa de descrever e compreender o progresso e os efeitos da digitalização na mídia e nos sistemas de comunicação ao redor do mundo. A publicação de relatórios em mais de cinquenta países oferece um dos levantamentos mais abrangentes sobre as mudanças sofridas pelo jornalismo, pela produção de notícias e pela mídia como resultado da transição do analógico ao digital na radiodifusão e do advento da Internet. Estes relatórios extensos, todos construídos com a mesma estrutura, cobrem questões como: consumo de mídia, sistemas públicos de comunicação, transformações no jornalismo, ativismo digital, novas regulações e modelos de negócio. Foram publicados nove relatórios de países da América Latina: México, Argentina, Colômbia, Peru, Chile, Brasil, Guatemala, Nicarágua e Uruguai. O Brasil tem passado por recentes evoluções no cenário midiático e regulatório, assumindo uma posição regional de destaque, e poucos relatórios geraram tantas expectativas quanto o brasileiro. O excelente texto aqui apresentado é importante para o entendimento da digitalização no Brasil, na América Latina e em um contexto global.

Bibliotecas digitais em Arquitetura e urbanismo: um estudo sobre a arquitetura da informação digital

The goal of this paper was to search the state of the art from the Digital Libraries in Architecture and Urbanism in the Higher Education Institutions (IES) through conceptualizations and showing the importance of Digital Libraries in the disclosure and easing of information transferring. Questions about digital information architecture, usability, digital preservation and accessibility were approached. The research was made in the websites of Brazilian Universities, firstly to identify the institutions which offered the Architecture and Urbanism course, focusing on postgraduate education. After identifying the offering, the research was done by analyzing the contents, storage and dissemination and access to information, these libraries. It was found that the digital libraries are increasingly and taking part of organizations and educational institutions focusing on the knowledge dissemination releasing digitally information that may be needed for institution or the individual. A monitoring was done over of the physical and computational restructuring of the Board of Studies and Research in Architecture and Urbanism (Câmara de Estudos e Pesquisa em Arquitetura e Urbanismo, CEPAU), from the Architecture and Urbanism Course of the Federal University of Rio Grande do Norte (UFRN), showing the need of installing a Digital Library to integrate the databases of PPGAU s research groups, which today remain independent, with no interface among themselves. The research chosen area was Architecture and Urbanism, because there is a gap and little documentation about digital libraries in this area

Classificação numérica e modelo digital de elevação na caracterização espacial de atributos dos solos

One of needs of modern agriculture is the prediction of spatial variability of soil properties at more detailed scales for sustainable management and optimization of management practices. The mathematical model associated with knowledge of variability of soil attributes and mapping of relief forms has helped in agricultural planning. In this regard the aim of this study was to characterize the spatial variability of physical and chemical properties of Oxisols and Ultisols using numerical classification and the digital elevation model. Two distinct landforms: convex for the Oxisol (158 ha) and linear for the Ultisol (172 ha). 53 samples from the Oxisol and 57 samples from the Ultisol were taken. Multivariate analysis of clusters of attributes studied from their euclidean distances was performed. This analysis by dendograms along with digital elevation models for different soils characterized was more homogeneous in Ultisol groups, and less homogeneous for the Oxisol in convex landform. These quantitative methods showed that the landforms conditioned the spatial pattern of soil attributes.

Quantitative fractography by digital image processing: NIH Image macro tools for stereo pair analysis and 3-D reconstruction

A set of NIH Image macro programs was developed to make qualitative and quantitative analyses from digital stereo pictures produced by scanning electron microscopes. These tools were designed for image alignment, anaglyph representation, animation, reconstruction of true elevation surfaces, reconstruction of elevation profiles, true-scale elevation mapping and, for the quantitative approach, surface area and roughness calculations. Limitations on time processing, scanning techniques and programming concepts are also discussed.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB (R)/SIMULINK (R)

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB (R)/SINIULINK (R) models to structural VHDL-AMS descriptions. The tool developed, named (MSSV)-S-2, reads a SIMULINK (R) model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the SystemVision (TM). To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB (R)/SIMULINK (R). The VHDL-AMS code generated automatically by (MSSV)-S-2, (MATLAB (R)/SIMULINK (R) to SystemVision (TM)), was then simulated in the SystemVision (TM). The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Imageamento digital de paleocavernas colapsadas com georadar

In this study, the methodological procedures involved in digital imaging of collapsed paleocaves in tufa using GPR are presented. These carbonate deposits occur in the Quixeré region, Ceará State (NE Brazil), on the western border of the Potiguar Basin. Collapsed paleocaves are exposed along a state road, which were selected to this study. We chose a portion of the called Quixeré outcrop for making a photomosaic and caring out a GPR test section to compare and parameterize the karst geometries on the geophysical line. The results were satisfactory and led to the adoption of criteria for the interpretation of others GPR sections acquired in the region of the Quixeré outcrop. Two grids of GPR lines were acquired; the first one was wider and more spaced and guided the location of the second grid, denser and located in the southern part of the outcrop. The radargrams of the second grid reveal satisfactorily the collapsed paleocaves geometries. For each grid has been developed a digital solid model of the Quixeré outcrop. The first model allows the recognition of the general distribution and location of collapsed paleocaves in tufa deposits, while the second more detailed digital model provides not only the 3D individualization of the major paleocaves, but also the estimation of their respective volumes. The digital solid models are presented here as a new frontier in the study of analog outcrops to reservoirs (for groundwater and hydrocarbon), in which the volumetric parameterization and characterization of geological bodies become essential for composing the databases, which together with petrophysical properties information, are used in more realistic computer simulations for sedimentary reservoirs.

Proposta metodológica para o imageamento digital e modelagem virtual 3d de um bloco de rochas travertinas

In this paper we present the methodological procedures involved in the digital imaging in mesoscale of a block of travertines rock of quaternary age, originating from the city of Acquasanta, located in the Apennines, Italy. This rocky block, called T-Block, was stored in the courtyard of the Laboratório Experimental Petróleo "Kelsen Valente" (LabPetro), of Universidade Estadual de Campinas (UNICAMP), so that from it were performed Scientific studies, mainly for research groups universities and research centers working in brazilian areas of reservoir characterization and 3D digital imaging. The purpose of this work is the development of a Model Solid Digital, from the use of non-invasive techniques of digital 3D imaging of internal and external surfaces of the T-Block. For the imaging of the external surfaces technology has been used LIDAR (Light Detection and Range) and the imaging surface Interior was done using Ground Penetrating Radar (GPR), moreover, profiles were obtained with a Gamma Ray Gamae-spectômetro laptop. The goal of 3D digital imaging involved the identification and parameterization of surface geological and sedimentary facies that could represent heterogeneities depositional mesoscale, based on study of a block rocky with dimensions of approximately 1.60 m x 1.60 m x 2.70 m. The data acquired by means of terrestrial laser scanner made available georeferenced spatial information of the surface of the block (X, Y, Z), and varying the intensity values of the return laser beam and high resolution RGB data (3 mm x 3 mm), total points acquired 28,505,106. This information was used as an aid in the interpretation of radargrams and are ready to be displayed in rooms virtual reality. With the GPR was obtained 15 profiles of 2.3 m and 2 3D grids, each with 24 sections horizontal of 1.3 and 14 m vertical sections of 2.3 m, both the Antenna 900 MHz to about 2600 MHz antenna. Finally, the use of GPR associated with Laser Scanner enabled the identification and 3D mapping of 3 different radarfácies which were correlated with three sedimentary facies as had been defined at the outset. The 6 profiles showed gamma a low amplitude variation in the values of radioactivity. This is likely due to the fact of the sedimentary layers profiled have the same mineralogical composition, being composed by carbonate sediments, with no clay in siliciclastic pellitic layers or other mineral carrier elements radioactive

Semi-automatic modeling of buildings from digital surface models

Semi-automatic building detection and extraction is a topic of growing interest due to its potential application in such areas as cadastral information systems, cartographic revision, and GIS. One of the existing strategies for building extraction is to use a digital surface model (DSM) represented by a cloud of known points on a visible surface, and comprising features such as trees or buildings. Conventional surface modeling using stereo-matching techniques has its drawbacks, the most obvious being the effect of building height on perspective, shadows, and occlusions. The laser scanner, a recently developed technological tool, can collect accurate DSMs with high spatial frequency. This paper presents a methodology for semi-automatic modeling of buildings which combines a region-growing algorithm with line-detection methods applied over the DSM.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB®/SIMULINK®

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB®/SIMULINK® models to structural VHDL-AMS descriptions. The tool developed, named MS 2SV, reads a SIMULINK® model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the System Vision™. To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB®/ SIMULINK®. The VHDL-AMS code generated automatically by MS 2SV, (MATLAB®/SIMULINK® to System Vision™), was then simulated in the System Vision™. The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Is characterizing the digital forensic facial reconstruction with hair necessary? A familiar assessors' analysis

Background: In the international scientific literature, there are few studies that emphasize the presence or absence of hair in forensic facial reconstructions. There are neither Brazilian studies concerning digital facial reconstructions without hair, nor research comparing recognition tests between digital facial reconstructions with hair and without hair. The miscegenation of Brazilian people is considerable. Brazilian people, and, in particular, Brazilian women, even if considered as Caucasoid, may present the hair in very different ways: curly, wavy or straight, blonde, red, brown or black, long or short, etc. For this reason, it is difficult to find a correct type of hair for facial reconstruction (unless, in real cases, some hair is recovered with the skeletal remains). Aims and methods: This study focuses on the performance of three different digital forensic facial reconstructions, without hair, of a Brazilian female subject (based on one international database and two Brazilian databases for soft facial-tissue thickness) and evaluates the digital forensic facial reconstructions comparing them to photographs of the target individual and nine other subjects, employing the recognition method. A total of 22 assessors participated in the recognition process; all of them were familiar with the 10 individuals who composed the face pool. Results and conclusions: The target subject was correctly recognized by 41% of the 22 examiners in the International Pattern, by 32% in the Brazilian Magnetic Resonance Pattern and by 32% in the Brazilian Fresh Cadavers Pattern. The facial reconstructions without hair were correctly recognized using the three databases of facial soft-tissue thickness. The observed results were higher than the results obtained using facial reconstructions with hair, from the same skull, which can indicate that it is better to not use hair, at least when there is no information concerning its characteristics. © 2013 Elsevier B.V. All rights reserved.

Desenvolvimento de uma Plataforma de Software para a Modelagem Digital de Terrenos baseada em TIN

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

As multiplicidades espaciais na comunicação midiática digital

Pós-graduação em Comunicação - FAAC