Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-19T15:28:50Z No. of bitstreams: 1 igorlucasdesouzarusso.pdf: 2265113 bytes, checksum: 0eb7e55f7354359d8fb9419e6e6da17f (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-20T12:28:17Z (GMT) No. of bitstreams: 1 igorlucasdesouzarusso.pdf: 2265113 bytes, checksum: 0eb7e55f7354359d8fb9419e6e6da17f (MD5) / Made available in DSpace on 2017-04-20T12:28:17Z (GMT). No. of bitstreams: 1 igorlucasdesouzarusso.pdf: 2265113 bytes, checksum: 0eb7e55f7354359d8fb9419e6e6da17f (MD5) Previous issue date: 2017-01-26 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A área de Otimização envolve o estudo e emprego de métodos para determinação dos parâmetros que levam à obtenção de soluções ótimas, de acordo com critérios denominados objetivos. Um problema é classificado como multiobjetivo quando apresenta objetivos múltiplos e conflitantes, que devem ser otimizados simultaneamente. Recentemente tem crescido o interesse dos pesquisadores pela análise de pós-otimalidade, que consiste na busca por propriedades intrínsecas às soluções ótimas de problemas de otimização e que podem lançar uma nova luz à compreensão dos mesmos. Innovization (inovação através de otimização, do inglês innovation through optmization) é um processo de descoberta de conhecimento a partir de problemas de otimização na forma de relações matemáticas entre variáveis, objetivos, restrições e parâmetros. Dentre as técnicas de busca que podem ser utilizadas neste processo está a Programação Genética (PG), uma meta heurística bioinspirada capaz de evoluir programas de forma automatizada. Além de numericamente válidos, os modelos encontrados devem utilizar corretamente as variáveis de decisão em relação às unidades envolvidas, de forma a apresentar significado físico coerente. Neste trabalho é proposta uma alternativa para tratamento das unidades através de operações protegidas que ignoram os termos inválidos. Além disso, propõe-se aqui uma estratégia para evitar a obtenção de soluções triviais que não agregam conhecimento sobre o problema. Visando aumentar a diversidade dos modelos obtidos, propõe-se também a utilização de um arquivo externo para armazenar as soluções de interesse ao longo da busca. Experimentos computacionais são apresentados utilizando cinco estudos de caso em engenharia para verificar a influência das ideias propostas. Os problemas tratados aqui envolvem os projetos de: uma treliça de 2 barras, uma viga soldada, do corte de uma peça metálica, de engrenagens compostas e de uma treliça de 10 barras, sendo este último ainda não explorado na literatura de descoberta de conhecimento. Finalmente, o conhecimento inferido no estudo de caso da estrutura de 10 barras é utilizado para reduzir a dimensionalidade do problema. / The area of optimization involves the study and the use of methods to determine the parameters that lead to optimal solutions, according to criteria called objectives. A problem is classified as multiobjective when it presents multiple and conflicting objectives which must be simultaneously optimized. Recently, the interest of the researchers has grown in the analysis of post-optimality, which consists in the search for intrinsic properties of the optimal solutions of optimization problems. This can shed a new light on the understanding of the optimization problems. Innovization (from innovation through optimization) is a process of knowledge discovery from optimization problems in the form of mathematical relationships between variables, objectives, constraints, and parameters. Genetic Programming (GP), a search technique that can be used in this process, is a bio-inspired metaheuristic capable of evolving programs automatically. In addition to be numerically valid, the models found must correctly use the decision variables with respect to the units involved, in order to present coherent physical meaning. In this work, a method is proposed to handle the units through protected operations which ignore invalid terms. Also, a strategy is proposed here to avoid trivial solutions that do not add knowledge about the problem. In order to increase the diversity of the models obtained, it is also proposed the use of an external file to store the solutions of interest found during the search. Computational experiments are presented using five case studies in engineering to verify the influence of the proposed ideas. The problems dealt with here are the designs of: a 2-bar truss, a welded beam, the cutting of a metal part, composite gears, and a 10-bar truss. The latter was not previously explored in the knowledge discovery literature. Finally, the inferred knowledge in the case study of the 10-bar truss structure is used to reduce the dimensionality of that problem.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-06-07T14:54:57Z No. of bitstreams: 1 rodrigoferreiramartins.pdf: 1789352 bytes, checksum: 9d2bb55856b7bf33c9dd2abbd5125259 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-06-07T14:57:16Z (GMT) No. of bitstreams: 1 rodrigoferreiramartins.pdf: 1789352 bytes, checksum: 9d2bb55856b7bf33c9dd2abbd5125259 (MD5) / Made available in DSpace on 2017-06-07T14:57:16Z (GMT). No. of bitstreams: 1 rodrigoferreiramartins.pdf: 1789352 bytes, checksum: 9d2bb55856b7bf33c9dd2abbd5125259 (MD5) Previous issue date: 2015-09-10 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Atualmente os tradicionais computadores de mesa e laptops estão perdendo mercado para dispositivos mais pervasivos, como smartphones, tablets e wearables que em sua grande maioria têm limitações de hardware devido às restrições de tamanho, peso e duração da bateria. As aplicações mais populares nos dias de hoje envolvem multimídia e algumas vezes consomem mais recursos do que esses dispositivos são capazes de suportar, por exemplo, realidade aumentada, jogos e o uso de computação para estender a capacidade cognitiva como reconhecimento facial e de fala, processamento de linguagem natural,aprendizagem de máquina, planejamento e tomada de decisão. Nesse contexto, mesmo a já tão popular cloud computing não serve como solução por si só, uma vez que a latência e o jitter criam uma restrição para aplicações interativas. Este trabalho propõe um framework para a construção de aplicações multimídia adaptativas que, no lado cliente, permite explorar recursos dos dispositivos alcançáveis, sejam móveis ou não, a fim de tornar as aplicações mais imersivas. Não apenas os recursos quantitativos, mas também os qualitativos são levados em consideração para distribuir as tarefas. Quanto à nuvem, a proposta apropria-se da ideia de edge cloud computing para aumentar a Qualidade de Serviço (QoS) e permitir que regras de negócio também sejam levadas em consideração durante a distribuição das tarefas, bem como na sintonização do serviço. / Currently traditional desktop computers and laptops are losing market share to more pervasive devices such as smartphones, tablets and wearables that usually have hardware limitations due to restrictions on size, weight, and battery life. The most popular applications today involve multimedia and sometimes consume more resources than these devices are capable of supporting, for example, augmented reality, games, and the use of computing to extend the cognitive ability as facial and speech recognition, natural language processing, machine learning, planning and decision making. In this context, even the widespread cloud computing does not serve as a single-handed solution, since the latency and jitter create a restriction for interactive applications. This work proposes a framework for building adaptive multimedia applications, which, on the client side, allows for exploring resources from reachable devices, whether mobile or not, in order to make applications more immersive. Not only quantitative, but also qualitative resources are considered to distribute tasks. Regarding the cloud side, the proposal appropriates the idea of edge cloud computing to increase Quality of Service (QoS) and allow business rules to be also taken into account during the distribution of tasks and service tuning.

In today’s world of rapid technological development one cannot deny the importance of collaborative writing systems. Besides many advantages of a collaborative writing system the major one is to allow its end users to work in collaboration with each other without having to physically meet. In the past various researches has been carried out for the usability evaluation of collaborative writing systems using the think aloud protocol method however there is no study conducted on the comparison of different usability evaluation methods in the context of collaborative writing systems. In this thesis work the authors have tried to find the limitations and capabilities of think aloud protocol and co-discovery learning methods in the context of a collaborative writing system called ZOHO, as well as the usability evaluation of ZOHO using think aloud protocol and co-discovery learning methods. The authors found various usability errors in ZOHO. Apart from this the authors also observed the two usability evaluation methods when they were used for usability evaluation of ZOHO. The authors found that both the methods have its’ own benefits and drawbacks. While the co-discovery learning method was fast enough, it was expensive in terms of human resource. On the other hand think aloud protocol method was slow to perform but there was less human resource used. Both the usability methods found almost the same usability errors. / In this thesis work the primary objective was to figure out the limitations and capabilities of think aloud protocol and co-discovery learning methods in the context of ZOHO; a collaborative writing system. Apart from this the secondary objective of this thesis was to conduct the usability evaluation of ZOHO and to find out what makes ZOHO ineffective, inefficient and unsatisfactory. The authors carried out usability tests on ZOHO using the think aloud protocol and co-discovery learning methods. After the tests results’ analysis the effectiveness, efficiency and satisfaction level of ZOHO was figured in section 7.2.1, 7.2.2 and 7.2.3 while the usability problems that make ZOHO ineffective, inefficient and unsatisfactory are discussed in section 7.2.4 of this thesis. Apart from the usability of ZOHO, the authors were also able to identify strong and weak points of the think aloud protocol and co-discovery learning methods when used for the usability evaluation of a collaborative writing system. They found that think aloud protocol testing is better if the evaluator is cost cautious or if he is looking for a detailed usability problems but does not cares about the time taken by the test. However if the evaluator cares about the test time and he cares less about the cost in terms of participants required for the test then he should use the co-discovery method for testing a collaborative writing system.

Les progrès technologiques en systèmes de localisation (AIS, radar, GPS, RFID, etc.), de télétransmission (VHF, satellite, GSM, etc.), en systèmes embarqués et leur faible coût de production a permis leur déploiement à une large échelle. Énormément de données sur les déplacements d'objets sont produites par le biais de ces technologies et utilisées dans diverses applications de surveillance temps-réel comme la surveillance du trafic maritime. L'analyse a posteriori des données de déplacement de navires et d'événements à risques peut présenter des perspectives intéressantes pour la compréhension et l'aide à la modélisation des comportements à risques. Dans ce travail de thèse une méthodologie basée sur la fouille de données spatio-temporelle est proposée pour l'extraction de connaissances sur les comportements potentiellement à risques de navires. Un atelier d'aide à l'analyse de comportements de navires fondé sur cette méthodologie est aussi proposé. / The advent of positioning system technologies (AIS, radar, GPS, RFID, etc.), remote transmission (VHF, satellite, GSM, etc.), technological advances in embedded systems and low cost production, has enabled their deployment on a large scale. A huge amount of moving objects data are collected through these technologies and used in various applications such as real time monitoring surveillance of maritime traffic. The post-hoc analysis of data from moving ships and risk events may present interesting opportunities for the understanding and modeling support of risky behaviors. In this work, we propose a methodology based on Spatio-Temporal Data Mining for the knowledge discovery about potentially risky behaviors of ships. Based on this methodology, a workshop to support the analysis of behavior of ships is also proposed.

Most of the modern cities are today facing tremendous traffic congestions, which is a consequence of an increasing usage of private motor vehicles in the cities. Public transport plays a crucial role to reduce this traffic, but to be an attractive alternative to the use of private motor vehicles the public transport needs to provide services that suit the citizens requirements for travelling. A system that can provide transit agencies with rapid feedback about the usage of their transport network is the Automatic Passenger Counting (APC) system, a system that registers the number of passengers boarding and alighting a vehicle. Knowledge about the passengers travel behaviour can be used by transit agencies to adapt and improve their services to satisfy the requirements, but to achieve this knowledge transit agencies needs to know how to use an APC system. This thesis investigates how a transit agency can make use of an APC system. The research has taken place in Melbourne where Yarra Trams, operator of the tram network, now are putting effort in how to utilise the APC system. A theoretical framework based on theories about Knowledge Discovery from Data, System Development, and Human Computer Interaction, is built, tested, and evaluated in a case study at Yarra Trams. The case study resulted in a software system that can process and model Yarra Tram's APC data. The result of the research is a proposal of a framework consistingof different steps and events that can be used as a guide for a transit agency that wants to make use of an APC system.

Mycobacterium tuberculosis (Mtb), a deadly pathogen, has scourged mankind for many centuries and has remained a major threat to global world health. Tuberculosis, the disease caused by this bacterium, is a major cause of death in developing nations and there is potential for its re-emergence in developed countries. An alarming rise in cases of multidrug-resistant and extremely-drug resistant tuberculosis (MDR-TB and XDR-TB) that do not respond to the customary first-line antibiotics necessitates the urgent need for development of new anti-TB drugs. Mtb becomes engulfed in human macrophages post infection of the host, but persists in the harsh environment of the human lungs by utilization of host cholesterol as a carbon source. The P450s CYP125A1, CYP142A1 and CYP124A1 are responsible for catalysing the side-chain degradation of cholesterol, which is critical for cholesterol to be used in the Mtb β-oxidation pathway for energy production. This PhD thesis focuses on understanding the structure/mechanism of the Mtb cholesterol 27-oxidases with the aim of facilitating the development of novel inhibitors of these P450s, which are crucial for Mtb to infect the host and to sustain infection. CYP142A1 and CYP124A1 were purified through three chromatographic steps with contaminating proteins successfully removed to give highly pure forms of these enzymes following the final purification step. Spectrophotometric titrations indicate that CYP142A1 and CYP124A1 bind tightly to cholesterol and cholestenone (and also to branched-chain methyl lipids for CYP124A1), highlighting their physiological roles in sterol and fatty acid metabolism, respectively. Binding analyses with a range of azole antibiotics revealed tight binding to bifonazole, clotrimazole, miconazole and econazole, and weak binding to fluconazole. Studies with compounds from a fragment screening library revealed weak binding to fragment hits for the cholesterol oxidases, but much tighter binding to these enzymes was found for ‘elaborated’ hits from a previous fragment screen on the Mtb cyclodipeptide oxidase CYP121A1, indicative of improved ligand potency achieved via ‘fragment merging’ strategies, and of structural similarities between these diverse Mtb P450s. Light scattering data indicate that CYP142A1 exists in dimeric form in solution, but becomes monomeric when treated with DTT; while CYP124A1 is completely monomeric. Crystal structures of CYP142A1 and CYP124A1 in complex with cholestenone, econazole and fragment library hits were determined. CYP142A1 crystal structures with econazole and fragment hits revealed heme coordination via the heterocyclic nitrogen in an azole group, and provide important data towards design of superior inhibitor drugs. The binding of cholestenone within the active site channels of CYP124A1 and CYP142A1 revealed an alignment favourable for C27 hydroxylation of the cholestenone side chain, which supports the physiological roles of CYP142A1 and CYP124A1 (as well as CYP125A1) in host cholesterol catabolism.

Les travaux de recherche présentés dans ce mémoire s'inscrivent dans la lignée des approches de modélisation hydrologiques prédictives dirigées par les données. Nous avons particulièrement développé leur application sur le contexte difficile des phénomènes de crue éclairs caractéristiques des bassins versants de la région Caraïbe qui pose un dé fi sé.curi taire. En envisageant le problème de la prévision de crues comme un problème d'optimisation combinatoire difficile nous proposons d'utiliser la notion de métaneuristiques, à travers les algorithmes évolutionnaire notamment pour leur capacité à parcourir efficacement de grands espaces de recherche et fi fournir des solutions de bOlIDe qualité en des temps d'exécution raisonnables. Nous avons présenté l'approche de prédiction AV2D : Aggregate Variable Data Driven dom le concept central est la notion de variable agrégée. L'idée sous-jacente à ce concept est de considérer le pouvoir prédictif de nouvelles variables définies comme le résultat de fonctions tatistiques, dites d'agrégation calculées sur de donnée' correspondant à des périodes de temps précédent uo événem nt à prédire. Ces variable sont caractérisées par des ensembles de paramètres correspondant a leur pJ:opriétés. Nous avons imroduitle variables agrégées hydrométéorologiques permettant de répondre au problème de la classification d événements hydrologiques. La complexité du parcours de l'espace de recherche engendré par les paramètres définissant ces variables a été prise en compte grâce à la njse en oeuvre d'un algorithme évolutionnaire particulier dont les composants ont été spécifiquement définis pour ce problème. Nous avons montré, à travers une étude comparative avec d'autres approches de modélisation dirigées par les données, menée sur deux cas d'études de bassins versant caribéens, que l'approche AV2D est particulièrement bien adaptée à leur contexte. Nous étudions par la suite les bénéfices offerts par les approches de modélisation hydrologiques modulaires dirigées par les données, en définissant un procédé de division en sous-processus prenant en compte les caractéristiques paniculières des bassins versants auxquels nous nous intéressons. Nou avons proposé une extension des travaux précédents à travers la définition d'une approche de modélisation modulaire M2D: Spatial Modular Data Driven, consistant à considérer des sous-processus en divisant l'ensemble des exemples à classifier en sous-ensembles correspondant à des comportements hydrologiques homogènes. Nous avons montré à travers une étude comparative avec d autres approches dU'igées par les données mises en oeuvre sur les mêmes sous-ensembles de données que celte approche permet d améliorer les résultats de prédiction particulièrement à coun Lenne. Nous avons enfin proposé la modélisation d un outil de pi / The work presented in this thesis is in the area of data-driven hydrological modeling approaches. We particularly investigared their application on the difficult problem of flash flood phenomena typically observed in Caribbean watersheds. By considering the problem of flood prediction as a combinatorial optimization problem, we propose to use the notion of Oleraheuristics, through evolutionary algorithms, especially for their capacity ta visit effjciently large search space and to provide good solutions in reasonable execution times. We proposed the hydrological prediction approach AV2D: Aggregate Variable Data Driven which central concept is the notion of aggregate variable. The underlying idea of this [concept is to consider the predictive power of new variables defined as the results of statistical functions, called aggregation functions, computed on data corresponding ta time periods before an event ta predict. These variables are characterized by sets of parameters corresponding ta their specifications. We introduced hydro-meteorological aggregate variables allowing ta address the classification problem of hydrological events. We showed through a comparative study on two typical caribbean watersheds, using several common data driven modelling techniques that the AV2D approach is panicul.rly weil fitted ta the studied context. We also study the benefits offered by modulaI' approaches through the definition of the SM2D: Spatial Modular DataDriven approach, consisting in considering sub-processes partly defined by spatial criteria. We showed that the results obtained by the AV2D on these sub-processes allows to increase the performances particularly for short term prediction. Finally we proposed the modelization of a generic control tool for hydro-meteorological prediction systems, H2FCT: Hydro-meteorological Flood Forecasting Control 1'001

No description available.

This thesis aimed to identify the trypanocidal mode of action of non-natural chamuvarinin analogs, and to assess the previously uncharacterized secondary alternative oxidase (AOX2) as a possible drug target of the trypanosomatids. The drugs used to treat infections with Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are highly toxic and are increasingly becoming less effective as the parasites develop resistance, therefore new drugs against the diseases are desperately needed. Non-natural analogs of chamuvarinin were tested for trypanocidal activity to determine the structure activity relationships of the compounds against insect-form T. cruzi and Leishmania spp. This identified several potent and selective analogs, which retained good activity against the medically relevant intracellular forms of the parasites. Photoaffinity labeling was utilized to identify the mode of action and protein target(s) of the chamuvarinin analogs. The analogs were shown to deplete ATP levels and to induce mitochondrial dysmorphia and mitochondrial oxidative stress. Photoaffinity labeling confirmed the mitochondrial localization of the protein target(s) of these compounds, however the exact protein target(s) were unable to be identified by protein pull-down and mass spectrometry. The previously uncharacterized secondary alternative oxidases (AOX2) are conserved throughout the human-infective trypanosomatids and are absent from mammalian cells, thus making an attractive drug target if the protein is essential. The AOX2 of T. brucei, T. cruzi and L. major were expressed in Escherichia coli to characterize the enzymatic activity of the proteins. T. brucei AOX2 was successfully purified and shown to be an ubiquinol oxidase, which contains bound iron (III). The role of AOX2 within the trypanosomatids was determined by biochemical phenotyping and genetic manipulation of T. brucei, T. cruzi and L. major, which indicated that AOX2 is an essential mitochondrial oxidase in the three trypanosomatids, with a putative role in energy production, and therefore is an attractive multi-trypanosomatid drug target.

The vision of the Semantic Web aims at enhancing today's Web in order to provide a more efficient and reliable environment for both providers and consumers of Web resources (i.e. information and services). To deploy the Semantic Web, various technologies have been developed, such as machine understandable description languages, language parsers, goal matchers, and resource composition algorithms. Since the Semantic Web is just emerging, each technology tends to make assumptions about different aspects of the Semantic Web's architecture and use, such as the kind of applications that will be deployed, the resource descriptions, the consumers' and providers' requirements, and the existence and capabilities of other technologies. In order to ensure the deployment of a robust and useful Semantic Web and the applications that will rely on it, several aspects of the technologies must be investigated, such as whether the assumptions made are reasonable, whether the existing technologies allow construction of a usable Semantic Web, and the systematic identification of which technology to use when designing new applications. In this thesis we provide a means of investigating these aspects for service discovery, which is a critical task in the context of the Semantic Web. We propose a simulation and evaluation platform for evaluating current and future Semantic Web technology with different resource sets and consumer and provider requirements. For this purpose we provide a model to represent the Semantic Web, a model of the evaluation platform, an implementation of the evaluation platform as a multi-agent system, and an illustrative use of the platform to evaluate some service discovery technology in a travel scenario. The implementation of the platform shows the feasibility of our evaluation approach. We show how the platform provides a controlled setting to support the systematic identification of bottlenecks and other challenges for new Semantic Web applications. Finally, the evaluation shows that the platform can be used to assess technology with respect to both hardware issues such as the kind and number of computers involved in a discovery scenario, and other issues such as the evaluation of the quality of the service discovery result.