This thesis describes an optimising compiler for translating from SMV to CLP(B). The optimisation is aimed at reducing the number of required variables in order to decrease the size of the resulting BDDs. Also a partitioning of the transition relation is performed. The compiler uses an internal representation of a FSM that is built up from the SMV description. A number of rewrite steps are performed on the problem description such as encoding to a Boolean domain and performing the optimisations. The variable reduction heuristic is based on finding sub-circuits that are suitable for reduction and a state space search is performed on those groups. An evaluation of the results shows that in some cases the compiler is able to greatly reduce the size of the resulting BDDs.

Magister Scientiae - MSc / Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIVÂ’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions; suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents. / South Africa

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Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-07-12T13:26:23Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) SergioBarzaDissertation.pdf: 2147656 bytes, checksum: 5c75fe2262be1d224538c1ad6a575ebb (MD5) / Made available in DSpace on 2017-07-12T13:26:23Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) SergioBarzaDissertation.pdf: 2147656 bytes, checksum: 5c75fe2262be1d224538c1ad6a575ebb (MD5) Previous issue date: 2016-02-25 / Software Maintainability (SM) has been studied since it became one of the key componentes of the software quality model accepted around the world. Such models support researchers and practitioners to evaluate the quality level of his systems. Therefore, many researchers have proposed a lot of metrics to be used as SM indicators. On the other hand, there is a suspicious that using SM metrics on industry is different from the academic context. In this case, practitioners do not adopt the metrics proposed/used by academia. Consequently, the goal of this research is to investigate the SM metrics adoption and applicability scenario on the Brazilian industrial context. This study will allow confirming if the practitioners use the SM metrics proposed by academics around the globe or if they propose their own metrics for SM measurement. As empirical method for data assessment, we used survey, divided in two steps. The first one was focused in gathering information that allowed us to design a specific scenario about the use and applicability of SM metrics. To achieve this goal, it was chosen, as research instrument, semi-structured interviews. The next step focused in a more general scenario, compassing the Brazillian software production industrial context. An online questionnaire was used as research instrument. Practitioners with different positions in several companies participated of this work. Data from requirements engineers, quality analysts, testers, developers and project managers were collected. 7 software companies participated in the first part of the study and 68 valid answers were collected on the second moment, resulting in 31 SM metrics listed. The results showed us that about 90% of the companies perform maintenance on their software products. However, only 60% confirms using maintainability metrics, resulting in a discrepancy regarding software maintenance vs SM metrics. Nearly half of the companies researched have used well-defined processes to collect these metrics. Nevertheless, there are those that do not have any formal methodology. Instead of it, they have used SM metrics that best fit to the needs of a specific project. The conclusions of this study point to an issue that is nothing new in the academic researchers around the world. Many of the academics results conducting, mainly, in the universities, are not coming to the software industries and this fact is also a truth when the subject is software maintenance. The results of this research may lead to discussions on how SM metrics are being proposals nowadays. / Manutenibilidade de Software (MS) é estudada desde que se tornou um dos componente de modelos de qualidade aceitos globalmente. Tais modelos auxiliam pesquisadores e profissionais do mercado na avaliação do nível de qualidade dos seus sistemas. Como consequência, muitos pesquisadores vêm propondo métricas que podem ser utilizadas como indicadores de MS. Por outro lado, existe uma suspeita que o uso de métricas de MS ocorre de maneira diferente da academia. Neste caso, as empresas não estão adotando as métricas que estão sendo propostas no ambiente acadêmico. O objetivo desta pesquisa é investigar o cenário de adoção e aplicação de métricas de manutenibilidade de software sob o contexto industrial brasileiro. Este estudo permitirá afirmar se estas empresas utilizam atributos de MS propostos por acadêmicos ao redor do mundo ou se elas propõem suas próprias métricas para medição de MS. Para ter acesso aos dados desta pesquisa, foi utilizado o método empírico survey, dividido em duas etapas. A primeira etapa objetivou levantar informações que permitissem um panorama mais específico sobre a utilização e aplicação de tais métricas. Para isto, foi escolhido, como instrumento de pesquisa, entrevistas semi-estruturadas. A segunda etapa apresenta um enfoque mais amplo, englobando todo o cenário industrial de produção de software brasileira. Um questionário online foi utilizado como instrumento de pesquisa. Profissionais de diferentes posições em várias empresas participaram desta pesquisa. Foram coletados dados de engenheiros de requisitos, analista de qualidade, testadores, desenvolvedores, gerente de projetos, entre outros. Sete empresas participaram da primeira etapa da pesquisa e 68 respostas válidas foram levantadas no segundo momento. Com isto, 31 métricas de MS foram identificadas. Os resultados mostram que cerca de 90% das empresas realizam manutenção em seus produtos de software. Porém somente 60% (aproximadamente) afirmaram fazer uso de métricas de MS, resultando em uma discrepância com relação à manutenção de software vs. uso de métricas. Quase metade das empresas possuem processos bem definidos para coletar estas métricas. Entretanto, muitas delas ainda não apresentam tais processos formais de coleta. Neste último caso, elas utilizam aqueles atributos que melhor se adaptam às necessidades de um projeto específico. As conclusões deste estudo apontam para problemas que não é novidade nas pesquisas acadêmicas ao redor do mundo. Pela amostra investigada neste trabalho, reforça-se a suspeita de que muitos dos resultados das pesquisas científicas realizadas nas universidades não estão chegando na indústria e este fato se reflete quando o assunto é manutenção de software. Os resultados deste estudo apresentam dados que poderão ocasionar discussões sobre a forma como as métricas de manutenibilidade são propostas atualmente.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20256号 / 医博第4215号 / 新制||医||1020(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 生田 宏一, 教授 三森 経世, 教授 前川 平 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21635号 / 医博第4441号 / 新制||医||1034(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 椛島 健治, 教授 岩田 想, 教授 山田 亮 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DGAM

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