Orientador: Marco Aurelio Amaral Henriques / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Eletrica e de Computação / Made available in DSpace on 2018-08-06T23:04:47Z (GMT). No. of bitstreams: 1 Herai_RobertoHirochi_M.pdf: 4053882 bytes, checksum: c48bdb80fdf9c0bbdb2249a62b3a2345 (MD5) Previous issue date: 2005 / Resumo: A predição de desempenho é um importante mecanismo para avaliar a utilização de recursos e estimar o tempo de execução de aplicações em sistemas paralelos. Este trabalho apresenta uma ferramenta que permite criar modelos que representam características da aplicação e dos computadores utilizados para processá-la. Tais modelos são combinados para gerar um modelo de desempenho mais abrangente, cuja análise permite obter estimativas de tempo de execução que contemplem fatores de atraso tais como operações aritméticas sobre diferentes tipos de dados e efeitos de contenção, causados por concorrência. As estimativas podem ser geradas em poucos segundos e permitem analisar o impacto causado na aplicação pela utilização de diferentes configurações do sistema de processamento paralelo. A ferramenta foi implementada para um sistema de processamento paralelo baseado em Java, chamado JoiN, e ela mostrou ser possível obter estimativas satisfatórias de tempos de execução para diversos tipos de aplicações paralelas / Abstract: Performance prediction is an important mechanism to evaluate the use of resources and predict the execution time of applications in parallel systems. This work presents a tool for the creation of models that represent applications and computers characteristics. Such models are combined to generate a performance model, whose analysis derives execution time estimates that include delay factors, such as arithmetic operations on different data types and contention effects caused by process concurrence. The estimates can be generated in a few seconds and allow the analysis of the impact caused in the application by changes in the parallel system configuration. The tool was implemented for a Java based parallel processing system called JoiN and it showed that satisfactory execution time estimates can be obtained for several types of parallel applications / Mestrado / Engenharia de Computação / Mestre em Engenharia Elétrica

Orientador: Michel Eduardo Beleza Yamagishi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-15T17:21:19Z (GMT). No. of bitstreams: 1 Herai_RobertoHirochi_D.pdf: 3625854 bytes, checksum: 3f19d10a9b0bb7f77091197cd302f66e (MD5) Previous issue date: 2010 / Resumo: A grande quantidade de dados biológicos gerados recentemente permitiu verificar que os genomas são repletos de seqüências repetitivas (SR), como microsatélites e elementos genéticos móveis, altamente improváveis de ocorrer estatisticamente se os genomas fossem gerados a partir de uma distribuição aleatória de nucleotídeos. Tal comprovação motivou a classificação de tais seqüências e também a construção de diversas ferramentas de bioinformática, além de mecanismos de armazenamento baseados em sistemas de gerenciamento de bancos de dados (SGBD) para permitir localizá-las e armazená-las para posterior estudo. Entretanto, foi com a comprovação biológica da importância das SR, como no mecanismo de interferência por RNAi (SR reversa complementar), que as SR despertaram maior interesse por parte da comunidade científica. Atualmente, já há fortes evidências que associam as SR com fenômenos biológicos bastante interessantes, como o processamento de RNA por cis-splicing e a formação de transcritos quiméricos, freqüentes em organismos inferiores e muito raro em organismos superiores. Tais tipos de transcritos podem ser gerados a partir de trans-splicing ou, como conjecturamos nesse trabalho, pela transposição de elementos genéticos móveis (como por exemplo transposons ou retrotransposons). Em virtude disso, este projeto propõe a construção de metodologias de Bioinformática, disponibilizadas na WEB, para detectar transcritos quiméricos em genomas de organismos, tanto em versões draft ou em alta qualidade, e também estudar as SR que ocorrem no locus gênico dos transcritos envolvidos na formação de uma seqüência quimérica. As ferramentas propostas permitiram identificar, a partir de bibliotecas de transcritos de full-length cDNA, tanto de humanos quanto de bovinos, novos transcritos quiméricos provenientes de células de tecidos normais, e que não seguem splice-sites canônicos na região de fusão dos transcritos envolvidos. Além disso, as seqüências encontradas apresentam uma elevada taxa de concentração de pares de SR do tipo reverso complementar no locus gênico dos dois transcritos que formam a seqüência quimérica. As ferramentas propostas podem ser utilizadas para outros organismos e direcionar trabalhos experimentais para tentar comprovar em bancada novos transcritos quiméricos, tanto em organismos inferiores quanto em superiores / Abstract: The recent availability of a huge amount of biological data allowed to know about the high concentration of repetitive sequences (SR) like microsatellites and genetic mobile elements in different genomes. Repetitive sequences are improbable to occur statistically if genome data were generated by a random distribution of nucleotides. Such observation motivated the classification of repetitive sequences, and the construction of several bioinformatics tools. Furthermore, several mechanisms to store repetitive sequences, which are based on data base management systems (DBMS) were proposed and created. They can be used to search for specific sequences to make a posteriori study. However, it was with the biological confirmation of the importance of repetitive sequences, like by the RNA interference (reverse complement, or inverted repeat) mechanism, that the scientific community gained more interest by such sequences. Actually, there is strong evidence that associates the repetitive sequences with some interesting biological phenomena, like in RNA processing by cis-splicing, and in chimeric transcript formation mechanism. This last one is very frequently in inferior organism, but rare in superior organisms. Such types of transcripts can be generated by trans-splicing, or like conjectured in this work, by the retrotransposition of mobile genetic elements (like transposons or retrotransposons). In this way, this work proposed the construction of several Bioinformatics methodologies, available in the WEB, to detect new evidences of chimeric transcripts in genomes of different organisms, both in draft genome and in high quality genome assemblage. We also studied repetitive sequences in gene loci of the involved transcripts in a chimeric sequence formation. The proposed tools allowed us to identify, using a full-length cDNA databank, new chimeric transcript candidates in human and in bovine genome. They are from cells of normal tissues, and do not follow canonical splice-sites in the fusion region of the involved transcripts. Moreover, it was possible to show that the detected sequences have high concentration pairs of reverse complement type of repetitive sequences in gene loci of the two involved transcripts, which originated a new chimeric transcript candidate. The created bioinformatics tools can be used in other organisms in addition to the one used in this work, leading to the proposition of new experimental work to try to prove in vivo new chimeric transcripts, both in superior organism and in inferior organism / Doutorado / Bioinformatica / Doutor em Genetica e Biologia Molecular

<p>Proteins have such structural features that they may interact with different types of surfaces by all possible forces, i.e., electrostatic, hydrogen bonding, hydrophobic. In this thesis two different types of coatings for fused silica capillaries aimed to eliminate such interactions have been studied. The first is a covalent, electroosmosis-free coating with polyacrylamide (PAA) and the second involves a non-covalent coating with the quaternary ammonium compound N, N-didodecyl –N, N- dimethylammonium bromide (DDAB) with a strong anodic electroosmosis. Optimal conditions regarding efficiency and resolution were established by variations of the composition and ionic strengths of buffers at pH below the isoelectric point of the proteins. To achieve high efficiency and resolution the choice of buffer constituents was extremely important. </p><p>The PAA coating was very stable at neutral and acidic conditions. Ammonium acetate (0.12 M) and ammonium hydroxyacetate (0.15 M) both at pH 4 provided the best separations with plate numbers up to 1 700 000 plate/m that is among the highest reported in the literature. Capillaries coated with DDAB were stable enough to, without recoating, permit consecutive separations of the proteins up to 9 hours (90 injections). High apparent efficiencies (over 1 million plates/m) were achieved with ammonium acetate (0.07 M), ammonium hydroxyacetate (0.08 M) and sodium phosphate (0.1 M) at pH 4. </p><p>Zone broadening was studied by determination of the variance contributions from all main parameters. Significant variances were contributions from longitudinal diffusion, capillary curvature, injection plug, detector time response and detector slit width while other variances, e.g., variances for Joule heat and vertical sedimentation were negligible. The remaining undetermined variance may have its origin in all types of relatively slow interactions including adsorption onto the capillary surfaces and protein-buffer component interactions. The results indicate that the latter is the main cause to zone broadening in protein separations.</p>

Proteins have such structural features that they may interact with different types of surfaces by all possible forces, i.e., electrostatic, hydrogen bonding, hydrophobic. In this thesis two different types of coatings for fused silica capillaries aimed to eliminate such interactions have been studied. The first is a covalent, electroosmosis-free coating with polyacrylamide (PAA) and the second involves a non-covalent coating with the quaternary ammonium compound N, N-didodecyl –N, N- dimethylammonium bromide (DDAB) with a strong anodic electroosmosis. Optimal conditions regarding efficiency and resolution were established by variations of the composition and ionic strengths of buffers at pH below the isoelectric point of the proteins. To achieve high efficiency and resolution the choice of buffer constituents was extremely important. The PAA coating was very stable at neutral and acidic conditions. Ammonium acetate (0.12 M) and ammonium hydroxyacetate (0.15 M) both at pH 4 provided the best separations with plate numbers up to 1 700 000 plate/m that is among the highest reported in the literature. Capillaries coated with DDAB were stable enough to, without recoating, permit consecutive separations of the proteins up to 9 hours (90 injections). High apparent efficiencies (over 1 million plates/m) were achieved with ammonium acetate (0.07 M), ammonium hydroxyacetate (0.08 M) and sodium phosphate (0.1 M) at pH 4. Zone broadening was studied by determination of the variance contributions from all main parameters. Significant variances were contributions from longitudinal diffusion, capillary curvature, injection plug, detector time response and detector slit width while other variances, e.g., variances for Joule heat and vertical sedimentation were negligible. The remaining undetermined variance may have its origin in all types of relatively slow interactions including adsorption onto the capillary surfaces and protein-buffer component interactions. The results indicate that the latter is the main cause to zone broadening in protein separations.

Along with playing an ever-increasing role in the integration of other communication networks and expanding in application diversities, the current Internet suffers from serious overuse and congestion bottlenecks. Efficient congestion control is fundamental to ensure the Internet reliability, satisfy the specified Quality-of-Service (QoS) constraints and achieve desirable performance in response to varying application scenarios. Active Queue Management (AQM) is a promising scheme to support end-to-end Transmission Control Protocol (TCP) congestion control because it enables the sender to react appropriately to the real network situation. Analytical performance models are powerful tools which can be adopted to investigate optimal setting of AQM parameters. Among the existing research efforts in this field, however, there is a current lack of analytical models that can be viewed as a cost-effective performance evaluation tool for AQM in the presence of heterogeneous traffic, generated by various network applications. This thesis aims to provide a generic and extensible analytical framework for analyzing AQM congestion control for various traffic types, such as non-bursty Poisson and bursty Markov-Modulated Poisson Process (MMPP) traffic. Specifically, the Markov analytical models are developed for AQM congestion control scheme coupled with queue thresholds and then are adopted to derive expressions for important QoS metrics. The main contributions of this thesis are listed as follows: • Study the queueing systems for modeling AQM scheme subject to single-class and multiple-classes Poisson traffic, respectively. Analyze the effects of the varying threshold, mean traffic arrival rate, service rate and buffer capacity on the key performance metrics. • Propose an analytical model for AQM scheme with single class bursty traffic and investigate how burstiness and correlations affect the performance metrics. The analytical results reveal that high burstiness and correlation can result in significant degradation of AQM performance, such as increased queueing delay and packet loss probability, and reduced throughput and utlization. • Develop an analytical model for a single server queueing system with AQM in the presence of heterogeneous traffic and evaluate the aggregate and marginal performance subject to different threshold values, burstiness degree and correlation. • Conduct stochastic analysis of a single-server system with single-queue and multiple-queues, respectively, for AQM scheme in the presence of multiple priority traffic classes scheduled by the Priority Resume (PR) policy. • Carry out the performance comparison of AQM with PR and First-In First-Out (FIFO) scheme and compare the performance of AQM with single PR priority queue and multiple priority queues, respectively.

Along with playing an ever-increasing role in the integration of other communication networks and expanding in application diversities, the current Internet suffers from serious overuse and congestion bottlenecks. Efficient congestion control is fundamental to ensure the Internet reliability, satisfy the specified Quality-of-Service (QoS) constraints and achieve desirable performance in response to varying application scenarios. Active Queue Management (AQM) is a promising scheme to support end-to-end Transmission Control Protocol (TCP) congestion control because it enables the sender to react appropriately to the real network situation. Analytical performance models are powerful tools which can be adopted to investigate optimal setting of AQM parameters. Among the existing research efforts in this field, however, there is a current lack of analytical models that can be viewed as a cost-effective performance evaluation tool for AQM in the presence of heterogeneous traffic, generated by various network applications. This thesis aims to provide a generic and extensible analytical framework for analyzing AQM congestion control for various traffic types, such as non-bursty Poisson and bursty Markov-Modulated Poisson Process (MMPP) traffic. Specifically, the Markov analytical models are developed for AQM congestion control scheme coupled with queue thresholds and then are adopted to derive expressions for important QoS metrics. The main contributions of this thesis are listed as follows: iii ¿ Study the queueing systems for modeling AQM scheme subject to single-class and multiple-classes Poisson traffic, respectively. Analyze the effects of the varying threshold, mean traffic arrival rate, service rate and buffer capacity on the key performance metrics. ¿ Propose an analytical model for AQM scheme with single class bursty traffic and investigate how burstiness and correlations affect the performance metrics. The analytical results reveal that high burstiness and correlation can result in significant degradation of AQM performance, such as increased queueing delay and packet loss probability, and reduced throughput and utlization. ¿ Develop an analytical model for a single server queueing system with AQM in the presence of heterogeneous traffic and evaluate the aggregate and marginal performance subject to different threshold values, burstiness degree and correlation. ¿ Conduct stochastic analysis of a single-server system with single-queue and multiple-queues, respectively, for AQM scheme in the presence of multiple priority traffic classes scheduled by the Priority Resume (PR) policy. ¿ Carry out the performance comparison of AQM with PR and First-In First-Out (FIFO) scheme and compare the performance of AQM with single PR priority queue and multiple priority queues, respectively.