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).

Modeling and illustrating requirement prioritization in public e-service development from a value-based perspective

A major problem in e-service development is the prioritization of the requirements of different stakeholders. The main stakeholders are governments and their citizens, all of whom have different and sometimes conflicting requirements. In this paper, the prioritization problem is addressed by combining a value-based approach with an illustration technique. This paper examines the following research question: How can multiple stakeholder requirements be illustrated from a value-based perspective in order to be prioritizable? We used an e-service development case taken from a Swedish municipality to elaborate on our approach. Our contributions are: 1) a model of the relevant domains for requirement prioritization for government, citizens, technology, finances and laws and regulations; and 2) a requirement fulfillment analysis tool (RFA) that consists of a requirement-goal-value matrix (RGV), and a calculation and illustration module (CIM). The model reduces cognitive load, helps developers to focus on value fulfillment in e-service development and supports them in the formulation of requirements. It also offers an input to public policy makers, should they aim to target values in the design of e-services.

Gestão pública orientada para resultados: avaliando o caso de Minas Gerais

This research analyses the model of management for results from Minas Gerais State. The theoretical research begins with the origin of the management for results, then analyses its influences and tools. A case study about Minas Gerais State is presented and the model analysis tool is applied. This tool was developed by the Inter-American Development Bank (IADB). It is being applied in many countries and states. After that, interviews with the main people of Minas Gerais government were carried out to get information about the current model of management. With all this information collected, the model is analysed to verify if it is adequate or not to the standards of the management for results.

Análise de investimento em projetos agroindustriais tipo Greenfield de bioenergia no Brasil

O setor de bioenergia no Brasil segue com um grande potencial de crescimento. Projeta-se um aumento de 71,6% no consumo total de bioenergia de 2011 a 2021 (BRASIL. EPE, 2012b). Consequentemente, novos mercados e oportunidades para novos projetos estão surgindo. Neste contexto, investidores precisarão avaliar projetos Greenfield, ponderando adequadamente riscos e retorno. Entretanto, a avaliação destes projetos não é simples pelas suas diversas particularidades. Deste modo, o objetivo desta dissertação é estabelecer um padrão metodológico para a análise destes investimentos. A partir de uma seleção de metodologias existentes, propõe-se uma série de abordagens alternativas e complementares, de forma a contemplar adequadamente as particularidades destes projetos. Portanto, este trabalho é inédito no que se refere à padronização de metodologias para a análise de investimento especificamente de projetos agroindustriais Greenfield de bioenergia. Para este fim, este trabalho não só propõem um padrão metodológico detalhado de análise, mas também o aplica em um estudo de caso de um projeto de cogeração de energia a partir de eucalipto. O intuito do estudo é ilustrar que a metodologia de análise de investimento proposta é eficaz. Além disso, serve como referência e guia de como aplicar esta ferramenta na análise de quaisquer projetos agroindustriais Greenfield no setor de bioenergia. Desta forma, é possível concluir que o uso do padrão metodológico proposto possibilita uma análise coerente de projetos desta natureza e permite uma tomada de decisão de investimento consciente. A criação desta ferramenta de análise e a exemplificação de seu uso são as principais contribuições deste trabalho.

ISE-SPL: Uma abordagem baseada em linha de produtos de software aplicada à geração automática de sistemas para educação médica na plataforma E-learning

E-learning, which refers to the use of Internet-related technologies to improve knowledge and learning, has emerged as a complementary form of education, bringing advantages such as increased accessibility to information, personalized learning, democratization of education and ease of update, distribution and standardization of the content. In this sense, this paper aims to develop a tool, named ISE-SPL, whose purpose is the automatic generation of E-learning systems for medical education, making use of concepts of Software Product Lines. It consists of an innovative methodology for medical education that aims to assist professors of healthcare in their teaching through the use of educational technologies, all based on computing applied to healthcare (Informatics in Health). The tests performed to validate the ISE-SPL were divided into two stages: the first was made by using a software analysis tool similar to ISE-SPL, called SPLOT and the second was performed through usability questionnaires to healthcare professors who used ISESPL. Both tests showed positive results, proving it to be an efficient tool for generation of E-learning software and useful for professors in healthcare

Reflexões e contribuições para o ensino de gravitação clássica no nível médio

The subject of Classic Gravitation is part of the actual curriculum for High School in Brazil, and it is taught in the first year of that education level. This master thesis presents a research regarding the subject Classic Gravitation in High School. This research was based in two complementary guidelines of research and action. The first guideline was the analysis of 21 didactic books of physics which are the more frequently used in High School, in the city of Natal/RN. The second guideline, worked after being verified the most common deficiencies presents in the didactic books, was the elaboration, followed by a practical application, of a course suggesting how to approach that subject in the classroom. The Parâmetros Curriculares Nacionais para o Ensino Médio (National Curricular Parameters for High School PCNEM) defend that Classic Gravitation is very important in the student s formation and that its study helps the comprehension of many nature s phenomena. Because of this vision of that subject by the PCNEM, the 21 analyzed books were separated in two groups: the first one, containing 10 books, was edited before the spreading of PCNEM, and the second, with 11 books, after that spreading. Whatever the group to which the didactic books belonged, the great majority of them let that subject in a second plan; two of them even suggesting, in the teacher s orientations, that the subject Gravitation can be suppressed in case of insufficient time . These analyses points that the PCNEM had produced no changes in the conception of the authors that wrote books regarding that subject. To analyze the didactic books, we elaborated a script which was used as an analysis tool, in which we put in evidence the relative importance of the historic and philosophic contextualization of the subject, the quotidian experience of the students and the interdisciplinary approach, among other aspects. It became evident that the didactic books give very little emphasis to historic aspects of the knowledge construction, to the relations with the day-by-day questions and to the interdisciplinary character of the subject Gravitation. It calls attention the non concordance among the authors opinions regarding the necessary previous knowledge or prerequisites the students should fulfill in order to begin to study Gravitation. The course we elaborated was given to a group of teachers as well as to students. In those courses we treated theoretical and practical aspects and emphasized historical questions and the ones which are related to people s daily life. The course for teachers was realized as an extra-mural activity of the UFRN and was given by the author of this thesis at the Escola Estadual Francisco Ivo Cavalcanti (a state public school in Natal/RN). There were 23 teachers present, from several public schools and several fields of knowledge. The thesis supervisor and the master degree s colleagues of the author acted as collaborators , reporting the participants opinions and speeches. The course to the students, on the other hand, had the participation of 300 regular students who belonged to 6 different 1st year classes of the High School Escola Marista de Natal (RN), in which the author acts as a physics teacher. The student s course was realized as part of the regular curriculum activities, in which three classes stood under the responsibility of the author and other three classes in charge of another Marista s teacher, who participated as a collaborator . The teacher s course as well as the students one were given in two stages, with five hours each. The first stage was divided in two moments, the first one focused on the survey of the spontaneous conceptions about gravitation, in which we worked basically with experiments of free throwing and pendulum, and the second one focused in theoretical presentations and quarrels about universe s models. In the second stage of the course we improved the study of Kepler s laws and the Newton s Universal Gravitation law, and we used as motivating tools some practices involving the construction of the solar system in scale. As instruments for evaluating both courses we used questionnaires and reported the speeches with participants opinions, beyond usual written evaluations in the course for the students. The teachers who participated in the course showed very good wills in realizing interdisciplinary practices; nevertheless, according their own speeches, they frequently came across the difficulty of how to do . From the experience we had in both courses, we conclude that the approach we propose hear to the teaching of the subject Classic Gravitation , supported on the tripod theory, practice and historical and philosophical aspects, is viable and effective. One hopes that this research may contribute in the formation of a opinion, among the teachers, concerning how to approach the subject of Classic Gravitation, and may offer suggestions in order those who want to apply that approach may develop classroom practices aiming to improve the teaching of that subject, which has a singular importance in the formation of High School students

Caracterizando os fluxos excepcionais em linhas de produto de software: um estudo exploratório

The Exception Handling (EH) is a widely used mechanism for building robust systems. In Software Product Line (SPL) context it is not different. As EH mechanisms are embedded in most of mainstream programming languages (like Java, C# and C++), we can find exception signalers and handlers spread over code assets associated to common and variable SPL features. When exception signalers and handlers are added to an SPL in an unplanned way, one of the possible consequences is the generation of faulty family instances (i.e., instances on which common or variable features signal exceptions that are mistakenly caught inside the system). In this context, some questions arise: How exceptions flow between the optional and alternative features an LPS? Aiming at providing answers to these questions, this master thesis conducted an exploratory study, based on code inspection and static analysis code, whose goal was to categorize the main ways which exceptions flow in LPSs. To support the study, we developed an static analysis tool called PLEA (Product Line Exception Analyzer) that calculates the exceptional flows of LPSs, and categorize these flows according to the features associated with handlers and signalers. Preliminary results showed that some types of exceptional flows have more potential to yield failures in exceptional behavior of SLPs

Squid impact analyser: uma ferramenta para análise de impacto de mudança em linhas de produto de software

Software Products Lines (SPL) is a software engineering approach to developing software system families that share common features and differ in other features according to the requested software systems. The adoption of the SPL approach can promote several benefits such as cost reduction, product quality, productivity, and time to market. On the other hand, the SPL approach brings new challenges to the software evolution that must be considered. Recent research work has explored and proposed automated approaches based on code analysis and traceability techniques for change impact analysis in the context of SPL development. There are existing limitations concerning these approaches such as the customization of the analysis functionalities to address different strategies for change impact analysis, and the change impact analysis of fine-grained variability. This dissertation proposes a change impact analysis tool for SPL development, called Squid Impact Analyzer. The tool allows the implementation of change impact analysis based on information from variability modeling, mapping of variability to code assets, and existing dependency relationships between code assets. An assessment of the tool is conducted through an experiment that compare the change impact analysis results provided by the tool with real changes applied to several evolution releases from a SPL for media management in mobile devices

O triângulo da formação docente: seus jogadores e configurações

O artigo tem por tema a formação dos professores que atuam nos anos iniciais da educação básica, considerando-a como um jogo que assume diferentes configurações em função das relações estabelecidas entre seus jogadores. Essas relações são analisadas por meio de um esquema de triangulação, aqui denominado como triângulo da formação docente. Cada um dos três vértices desse triângulo é ocupado por agentes que, a partir de seus capitais específicos, localizam-se em lugares desiguais no campo da formação docente: os professores e as instâncias que os representam; as universidades, fundações e institutos de pesquisa, com seus especialistas; e o poder público, representado por secretarias de educação e outros órgãos administrativos. Relações privilegiadas entre dois vértices do triângulo da formação docente apontam para diferentes modelos formativos. Explorando esse triângulo como um recurso de análise, o artigo focaliza as configurações assumidas pelo jogo da formação docente na versão brasileira do movimento ora em curso de universitarização do magistério. Atenção especial é conferida ao lugar que os professores atuantes nos anos iniciais da educação básica ocupam nesse jogo, às relações que eles estabelecem com os demais jogadores e, também, às possibilidades que têm de subverter e alterar o jogo em andamento.

Classification of masses in mammographic image using wavelet domain features and polynomial classifier

Breast cancer is the most common cancer among women. In CAD systems, several studies have investigated the use of wavelet transform as a multiresolution analysis tool for texture analysis and could be interpreted as inputs to a classifier. In classification, polynomial classifier has been used due to the advantages of providing only one model for optimal separation of classes and to consider this as the solution of the problem. In this paper, a system is proposed for texture analysis and classification of lesions in mammographic images. Multiresolution analysis features were extracted from the region of interest of a given image. These features were computed based on three different wavelet functions, Daubechies 8, Symlet 8 and bi-orthogonal 3.7. For classification, we used the polynomial classification algorithm to define the mammogram images as normal or abnormal. We also made a comparison with other artificial intelligence algorithms (Decision Tree, SVM, K-NN). A Receiver Operating Characteristics (ROC) curve is used to evaluate the performance of the proposed system. Our system is evaluated using 360 digitized mammograms from DDSM database and the result shows that the algorithm has an area under the ROC curve Az of 0.98 ± 0.03. The performance of the polynomial classifier has proved to be better in comparison to other classification algorithms. © 2013 Elsevier Ltd. All rights reserved.

Ergonomia e avaliação pós-ocupação (APO): a relação entre ambiente, usuário e atividade: uma contribuição da ergonomia aos estudos da Arquitetura

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estabelecimento de um índice de sensibilidade ambiental ao óleo em ambientes fluviais, com o suporte da ferramenta MORPH

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Os limiares das cidades médias: reflexões a partir da cidade de Teófilo Otoni-MG

Pós-graduação em Geografia - FCT

Caracterização de solos sob diferentes usos na região sul do Amazonas

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