Genome-wide Association (GWA) studies have become a widely used method for analyzing genetic data. It is useful in detecting associations that may exist between particular alleles and diseases of interest. This thesis investigates the dataset provided from problem 1 of the Genetic Analysis Workshop 16 (GAW 16). The dataset consists of GWA data from the North American Rheumatoid Arthritis Consortium (NARAC). The thesis attempts to determine a set of single nucleotide polymorphisms (SNP) that are associated significantly with rheumatoid arthritis. Moreover, this thesis also attempts to address the question of whether the one-sided alternative hypothesis that the minor allele is positively associated with the disease or the two-sided alternative hypothesis that the genotypes at a locus are associated with the disease is appropriate, or put another way, the question of whether examining both alternative hypotheses yield more information.

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Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-02-28Bitstream added on 2014-06-13T18:29:27Z : No. of bitstreams: 1 fernandes_afa_me_jabo.pdf: 322816 bytes, checksum: d60d045e58509fb91c9a8dc47345094d (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / No Brasil, são escassos os estudos referentes ao escore de condição corporal (ECC) de vacas de corte que, quando associado ao peso, têm impacto na produção de bezerros e na reprodução, pois reflete o balanço energético do corpo animal. Assim, o objetivo deste trabalho foi associar ECC com a prenhez de vacas Nelore e com o desempenho de seus produtos a desmama, bem como verificar se esta característica pode ser incluída nos critérios de seleção da raça Nelore. O ECC das vacas foi atribuído no diagnóstico de gestação ou no desmame, variando de 1 a 5. Por regressão logística, utilizando o método de seleção Stepwise, foram analisados os seguintes efeitos sobre o ECC: grupo de contemporâneos a desmama, peso e altura de garupa da vaca, ordem de parto, diagnóstico de gestação, histórico reprodutivo anterior à coleta do ECC, presença de bezerro ao pé e escores de C e P dos produtos a desmama. Na análise genética, elaborada usando-se inferência baeysiana, foram incluídos os mesmos efeitos anteriores, com peso e altura de garupa da vaca como co-variáveis, e acrescidos do efeito genético aditivo da vaca. Os resultados mostraram que vacas com ECC elevado emprenharam mais do que as de pior ECC, porém o desempenho dos seus bezerros foi inferior. Vacas multíparas foram mais pesadas e de escores mais magros (ECC 1 e 2). As correlações de Spearman entre ECC e suas fontes de variação foram, em sua maioria, de baixa magnitude. Os efeitos que mais explicaram a variação do ECC foram peso, grupo de contemporâneos e altura da garupa. A estimativa de herdabilidade do ECC foi igual a 0,22, com intervalo de credibilidade entre 0,13 e 0,31, valor de magnitude moderada, demonstrando a presença de ação gênica aditiva na determinação do ECC e que este pode ser utilizado como critério de seleção de vacas / In Brazil few studies have been done on the body condition score (BCS) of beef cows. The knowledge of this score associated with body weight can produce an impact on calf production and cow´s reproduction, because it reflects the energy balance of the animal body. The objective of this study was to associate BSC with pregnancy of cows and the performance of their calves at weaning, and to verify if this trait could be included as selection criteria. The BCS was recorded on pregnancy diagnosis or at weaning and ranged from 1 to 5. Applying logistic regression, using the Stepwise selection method, we analyzed the following effects on BSC: contemporary group at weaning, classes of weight and hip height of the cow, number of calvings, pregnancy diagnosis, reproductive history prior to collection BSC, the presence of calf and C and P score of calves at weaning. For the genetic analysis, performed using Baesyan inference, the same effects were considered, with weight and hip height as covariate, and also the genetic direct effect of the cow. The results showed that cows with higher BCS had better pregnancy rate than those with lower BSC, but the performance of their calves was worse. Multiparous cows were heavier and had leaner scores (BCS 1 and 2) than the primiparous ones. The Spearman rank correlation between BSC and their sources of variation were generally of low magnitude. Contemporary group, body weight and height of the cow were the effects that accounted for most of the variation of BSC. The heritability estimate of BCS was equal to 0.22 with credible interval ranging from 0.13 to 0.31, a moderate magnitude value that indicates the presence of additive genetic variation and that BSC can be used as selection criterion for cows

Dentro do gênero Rhipicephalus, há o chamado complexo sanguineus formado por várias espécies presentes apenas no Velho Mundo, das quais apenas a espécie Rhipicephalus sanguineus é considerada de ocorrência no Novo Mundo. Como as espécies deste complexo apresentam grande similaridade morfológica, é possível que mais de uma espécie do complexo sanguineus esteja ocorrendo nas Américas. Um trabalho recente relatou parâmetros biológicos e genéticos significativamente diferentes entre uma população de R. sanguineus do Brasil e outra da Argentina, sugerindo que o status biosistemático de R. sanguineus na América do Sul deva ser revisto. Diante disto, e da inquestionável importância medico-veterinária de R. sanguineus na América do Sul, este projeto objetivou realizar uma análise genética de 32 populações de R. sanguineus, sendo 17 do Brasil (englobando 13 estados), 3 do Chile, 2 da Venezuela, 2 da Colômbia e 1 de cada um dos seguintes países: Argentina, Uruguai, Itália, Espanha, África do Sul, Costa Rica, Panamá, México. Uma amostra de Rhipicephalus turanicus da Espanha e uma da África do sul também foram analisadas. Para tal, carrapatos oriundos das diferentes populações foram analisados geneticamente através de seqüências dos genes mitocondriais 16S rDNA. O resultado deste trabalho permitiu inferir sobre a possibilidade da existência no mínimo de dois grupos distintos de carrapatos sob o táxon R. sanguineus na América Latina, um se aproximando dos carrapatos de origem africana e com distribuição na América tropical e subtropical e outro se aproximando das amostras européias e com distribuição temperada do sul da América do Sul / Among the genus Rhipicephalus, there is the sanguineus complex composed by many species of distribution restricted to the Old World. It has been considered that Rhipicephalus sanguineus is the only species from this complex to be present in the New World. Due to the high similarity between the sanguineus complex species, it is possible that more than one species is present in the Americas, as suggested by recent papers. The present study performed a genetic evaluation based on 16S rDNA mitochondrial gene sequences of ticks representative 26 R. sanguineus populations from South America, one from: Italy, Spain, South Africa, Costa Rica, Panama, Mexico. Additionally, Rhipicephalus turanicus ticks from South Africa and Spain were also used. The results confirm the existence of genetically distinct populations of the \"sanguineus\" complex in the Americas

[EN] Domain-specific languages (DSLs) are considered to be a powerful tool for enhancing the efficiency of software developers and bring software development closer to end-users from complex domains. However, the successful development of a DSL for a complex domain is a challenge from the technical point of view and because end-user acceptance is key. Despite this fact, the relevant role of end-users during DSL development has traditionally been neglected. Normally, end-users participate at the beginning to communicate their preferences but they do not participate again until the DSL is completely implemented. As a consequence, if the language to develop reaches a complex domain, the chances that errors appear in the DSL are higher and solving them could involve large modifications that could have been avoided. As a solution, in this PhD thesis, we propose an agile, model-driven method to involve end-users in DSL development. This thesis researches if the combination of best practices from the model-driven development (MDD) discipline and best practices from agile methods is a suitable approach to involve end-users in the DSL development process. In order to validate the proposal, we have selected a highly complex domain such as the genetic analysis domain and we have collaborated with geneticists from three organizations. The proposed method has been used to involve these geneticists in the development of a DSL for the creation of genetic analysis pipelines. Simultaneously, we have carried out an empirical experiment to validate whether end-users and developers were satisfied with the proposal. / [ES] Los lenguajes específicos de dominio (DSLs) son una herramienta muy potente para mejorar la eficiencia de los desarrolladores de software, así como para acercar el desarrollo software a usuarios sin conocimientos informáticos. Sin embargo, su principal problema es que desarrollar un DSL es complejo; no sólo desde el punto de vista técnico, sino especialmente porque la aceptación de dicho lenguaje por parte de los usuarios finales es clave. A pesar de este hecho, los métodos tradicionales de desarrollo de DSLs no enfatizan el importante rol de los usuarios finales durante el desarrollo. Normalmente, los usuarios participan al inicio para comunicar sus preferencias, pero no vuelven a participar hasta que el DSL está completamente desarrollado. Si el lenguaje a desarrollar aborda un dominio complejo, la posibilidad de que existan errores en el DSL es mayor, y su solución podría conllevar a modificaciones de gran calibre que podrían haberse evitado. Como solución, en esta tesis proponemos un método de desarrollo de DSLs, ágil, y dirigido por modelos que involucra a los usuarios finales. Esta tesis investiga si la combinación de buenas prácticas del desarrollo dirigido por modelos (MDD) y de buenas prácticas de métodos ágiles es adecuada para involucrar a los usuarios finales en el desarrollo de DSLs. Para validar la idoneidad de la propuesta, se ha seleccionado un dominio complejo como el de los análisis genéticos y se ha colaborado con un conjunto de genetistas procedentes de tres organizaciones. El método propuesto se ha utilizado para involucrar a dichos genetistas en el desarrollo de un DSL para la creación de pipelines para el análisis genético. Conjuntamente, se ha llevado a cabo un experimento empírico para validar si los usuarios finales y los desarrolladores están satisfechos con la propuesta de la presente tesis. En resumen, las contribuciones principales de esta tesis doctoral son el diseño e implementación de un método innovador, ágil y dirigido por modelos para involucrar a los usuarios finales en el desarrollo de DSLs, así como la validación de dicha propuesta en un entorno industrial en un desarrollo real de un DSL. / [CAT] Els llenguatges específics de domini (DSLs) son una ferramenta molt potent per a millorar l'eficiència dels desenvolupadors de programari, així com per a apropar el desenvolupament de programari a usuaris sense coneixements informàtics. El problema es que desenvolupar un DSL es complex, no sols des del punt de vista tècnic, sinó especialment perquè l'acceptació de dit llenguatge per part dels usuaris finals es clau. Malgrat aquest fet, els mètodes tradicionals de desenvolupament de DSLs no emfatitzen l'important rol dels usuaris finals durant el desenvolupament. Normalment, els usuaris participen a l'inici per a comunicar les seues preferències, però no tornen a participar fins que el DSL està completament desenvolupat. Si el llenguatge a desenvolupar aborda un domini complex, la possibilitat de que hi hagen errors en el DSL es major i solucionar-los podria implicar modificacions de gran calibre que podrien haver-se evitat. Com a solució, en aquesta tesis proposem un mètode de desenvolupament de DSLs, àgil i dirigit per models que involucra als usuaris finals. Aquesta tesis investiga si la combinació de bones pràctiques del desenvolupament dirigit per models (MDD) i de bones pràctiques de mètodes àgils es adequada per a involucrar els usuaris finals en el desenvolupament de DSLs. Per a validar la idoneïtat de la proposta, s'ha seleccionat un domini complex com el dels anàlisis genètics i s'ha col·laborat amb un conjunt de genetistes procedents de tres organitzacions. El mètode s'ha utilitzat per a involucrar a dits genetistes en el desenvolupament d'un DSL per a la creació de pipelines per al anàlisis genètic. Al mateix temps, s'ha dut a terme un experiment empíric per a validar si tant els usuaris finals com els desenvolupadors estan satisfets amb la proposta de la present tesis. En resum, les contribucions principals d'aquesta tesis doctoral son el disseny i implementació d'un mètode innovador, àgil i dirigit per models per a involucrar als usuaris finals en el desenvolupament de DSLs, així com la validació de la proposta en un entorn industrial amb un desenvolupament real d'un DSL. / Villanueva Del Pozo, MJ. (2016). An agile model-driven method for involving end-users in DSL development [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/60156 / TESIS

Leguminous plants are able to fix nitrogen by establishing a symbiotic relationship with soil dwelling bacteria, called rhizobia. The model plant Medicago truncatula forms a partnership with Sinorhizobium meliloti whereby the plant gains bioavailable nitrogen and in exchange the bacteria gains carbohydrates. This process occurs within nodules, which are structures produced on the roots of the plants within which nitrogen is fixed. M. truncatula incomplete root elongation (MtIRE) was localized to the infection zone, which is zone II of indeterminate nodules. It was shown to encode a signaling kinase so it was anticipated to play a role in nodulation. Mutants of MtIRE in the R108 background, mutagenized with the Tnt1 retrotransposon, were obtained from reverse screen, and were assessed to determine if a disrupted MtIRE gene was the cause of nitrogen fixation defective nodules. Mutant line NF1320, having a mutant phenotype, showed typical Mendelian segregation of 3:1 when backcrossed to R108. Experimental results show that MtIRE gene is not the cause of the mutant phenotype, but was linked to the causative locus. MtIRE co-segregated with the mutant phenotype 83%. Southern blot and the first version of the M. truncatula genome (version 3.5) reported a single MtIRE gene and this was shown to be on chromosome 5 but the latest version of the M. truncatula genome (version 4.0) showed a second copy of the gene on chromosome 4. The genome sequence is based on the A17 reference genome. Both genes are 99% identical. Genetic markers that originate from flanking sequence tags (FSTs) on both chromosome 4 and 5 were tested in an attempt to find an FST that co-segregated with the mutant phenotype 100%. An FST derived from a Tnt1 insertion in Medtr4g060930 (24F) co-segregated with the mutant phenotype closely, with 76% co-segregation. Medtr4g060930 (24F) is on chromosome 4, making it likely that the Tnt1 inserted in the MtIRE gene is also on chromosome 4, and thus the defective gene is on chromosome 4.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22854号 / 農博第2437号 / 新制||農||1082(附属図書館) / 学位論文||R2||N5314(農学部図書室) / 京都大学大学院農学研究科地域環境科学専攻 / (主査)教授 本田 与一, 教授 田中 千尋, 准教授 坂本 正弘 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

In recent years a new field of statistics has become of importance in many branches of experimental science. This is the Monte Carlo Method, so called because it is based on simulation of stochastic processes. By stochastic process, it is meant some possible physical process in the real world that has some random or stochastic element in its structure. This is the subject which may appropriately be called the dynamic part of statistics or the statistics of "change," in contrast with the static statistical problems which have so far been the more systematically studied. Many obvious examples of such processes are to be found in various branches of science and technology, for example, the phenomenon of Brownian Motion, the growth of a bacterial colony, the fluctuating numbers of electrons and protons in a cosmic ray shower or the random segregation and assortment of genes (chemical entities responsible for governing physical traits for the plant and animal systems) under linkage condition. Their occurrences are predominant in the fields of medicine, genetics, physics, oceanography, economics, engineering and industry, to name only a few scientific disciplines. The scientists making measurements in his laboratory, the meteriologist attempting to forecast weather, the control systems engineer designing a servomechanism (such as an aircraft or a thermostatic control), the electrical engineer designing a communication system (such as the radio link between entertainer and audience or the apparatus and cables that transmit messages from one point to another), economist studying price fluctuations in business cycles and the neurosurgion studying brain wave records, all are encountering problems to which the theory of stochastic processes may be relevant. Let us consider a few of these processes in a little more detail. In statistical physics many parts of the theory of stochastic processes were developed in correlation with the study of fluctuations and noise in physical systems (Einstein, 1905; Smoluchowski, 1906; and Schottky, 1918). Consequently, the theory of stochastic processes can be regarded as the mathematical foundation of statistical physics. The stochastic models for population growth consider the size and composition of a population which is constantly fluctuating. These are mostly considered by Bailey (1957), Bartlett (1960), and Bharucha-Reid (1960). In communication theory a wide variety of problems involving communication and/or control such as the problem of automatic tracking of moving objects, the reception of radio signals in the presence of natural and artificial disturbances, the reproduction of sound and images, the design of guidance systems, the design of control systems for industrial processes may be regarded as special cases of the following general problem; that is, let T denote a set of points in a time axis such that at each point t in T an observation has been made of a random variable X(t). Given the observations [x(t), t ϵT] and a quantity Z related to the observation, one desires to from in an optimum manner, estimates of, and tests of hypothesis about Z and various functions h(Z).

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第19069号 / 人博第722号 / 新制||人||173(附属図書館) / 26||人博||722(吉田南総合図書館) / 32020 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)准教授 土屋 徹, 教授 宮下 英明, 教授 川本 卓男 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM