Gene-fusions are a prevalent class of genetic variants that are often employed as cancer biomarkers and therapeutic targets. In recent years, high-throughput sequencing of the cellular genome and transcriptome have emerged as a promising approach for the investigation of gene-fusions at the DNA and RNA level. Although, large volumes of sequencing data and complexity of gene-fusion structures presents unique computational challenges. This dissertation describes research that first addresses the bioinformatics challenges associated with the analysis of the massive volumes of sequencing data by developing bioinformatics pipeline and more applied integrated computational workflows. Application of high-throughput sequencing and the proposed bioinformatics approaches for the breast and ovarian cancer study reveals unexpected complex structures of gene-fusions and their functional significance in the onset and progression of cancer. Integrative analysis of gene-fusions at DNA and RNA level shows the key importance of the regulation of gene-fusion at the transcription level in cancer.

The mechanisms by which hydrates deposit in a petroleum production-line are likely to be related to pipeline surface properties, e.g. pipeline material, surface energy and roughness. In this work, the wettability alteration of pipeline surfaces from contact with oil, as well as the adhesion energy between water and solid in the presence of oil is investigated. Contact angles are determined as a function of solid material and oil composition, for both model oils and crude oils. Although contact angles in oil/brine/solid systems have been extensively reported in the literature, the variety of solids that may mimic a pipeline is limited. In this study, we include various metal surfaces in addition to glass and a coating. Initial results from using near infrared imaging for collecting contact angle data in non-translucent systems are also presented.

The pipeline industry has conducted a vast amount of research on the subject of mechanical damage. Mechanical damage makes up a large portion of the total amount of pipeline failures that occur each year. The current methods rely on engineering judgment and experience rather than scientific theory. The method for the assessment of mechanical damage introduced in this study uses a material property called critical strain to predict the onset of cracking within the pipe wall. The critical strain is compared to the strain within a dent using a ductile failure damage indicator (DFDI). To investigate the use of the DFDI to indicate the onset of cracking within a dent, the study attempted to accomplish three tasks. The first was to investigate the use of various techniques to locate the critical strain from the stress-strain curve. Five samples taken from the pipe material was used to generate both engineering and true stress-strain curves. A sensitivity analysis was conducted to show the effects of different variables on the critical strain value. The DFDI compares the critical strain value to the calculated strain at the deepest depth location within a dent. The strain calculations use the curvature of the dent and thus require a dent profile. A high resolution laser scanner was used to extract dent profiles from a pipe. The second task of the study was to investigate the reliability of the laser scanner equipment used for this study. The results from the investigation showed that the laser scanner could be used to scan the inside of the pipe despite its design for external scanning. The results also showed that the scans should be 1 mm in length along the axis of the pipe at a resolution of 0.5 mm and 360 degrees around the pipe. The final task was to conduct the denting test. The test used a spherical indenter to dent the pipe at increments of 3% of the outside diameter. The results from the test showed that a visible crack did not form on the inside pipe surface as expected from the DFDI method. This does not mean a crack did not form. During the denting test distinct popping sounds were observed possibly indicating cracks forming within the pipe wall.

<p><font face="Times New Roman"><font face="Times New Roman"> <p align="left">As a case study, the paper analyzes the Bank&rsquo / s role in the Chad-Cameroon Petroleum Development and Oil Pipeline project (the project) in which the Bank has been involved since the year 2000. The paper presents the lessons, challenges and implications from this protection of human rights.</p> </font></font></p>

This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.

Les applications de flux de données sont des cibles importantes de l'optimisation de programme en raison de leur haute exigence de calcul et la diversité de leurs domaines d'application: communication, systèmes embarqués, multimédia, etc. L'un des problèmes les plus importants et difficiles dans la conception des langages de programmation destinés à ce genre d'applications est comment les ordonnancer à grain fin à fin d'exploiter les ressources disponibles de la machine.Dans cette thèse on propose un "framework" pour l'ordonnancement à grain fin des applications de flux de données et des boucles imbriquées en général. Premièrement on essaye de paralléliser le nombre maximum de boucles en appliquant le pipeline logiciel. Après on merge le prologue et l'épilogue de chaque boucle (phase) parallélisée pour éviter l'augmentation de la taille du code. Ce processus est un pipeline multidimensionnel, quelques occurrences (ou instructions) sont décalées par des iterations de la boucle interne et d'autres occurrences (instructions) par des iterationsde la boucle externe. Les expériences montrent que l'application de cette technique permet l'amélioration des performances, extraction du parallélisme sans augmenter la taille du code, à la fois dans le cas des applications de flux des donnée et des boucles imbriquées en général.

Carbon capture and storage (CCS) and a point of electricity generation is a promising option for mitigating greenhouse gas emissions. One issue with respect to CCS is the design of carbon dioxide transport, storage and injection system. This dissertation develops a model, OptimaCCS, that combines economic and spatial optimization for the integration of CCS transport, storage and injection infrastructure to minimize costs. The model solves for the lowest-cost set of pipeline routes and storage/injection sites that connect CO2 sources to the storage. It factors in pipeline costs, site-specific storage costs, and pipeline routes considerations involving existing right of ways and land use. It also considers cost reductions resulting from networking the pipelines segment from the plants into trunk lines that lead to the storage sites. OptimaCCS is demonstrated for a system involving carbon capture at 14 Texas coal-fired power plants and three potential deep-saline aquifer sequestration sites. In turn OptimaCCS generates 1) a cost-effective CCS pipeline network for transporting CO2 from all the power plants to the possible storage sites, and 2) an estimate of the costs associated with the CO2 transport and storage. It is used to examine variations in the configuration of the pipeline network depending on differences in storage site-specific injection costs. These results highlight how various levels of cooperation by CO2 emitters and difference in injection costs among possible storage sites can affect the most cost-effective arrangement for deploying CCS infrastructure. This study also analyzes CCS deployment under the features in a piece of legislation the draft of American Power Act (APA) - that was proposed in 2010 which contained a goal of CCS capacity for emissions from 72 Gigawatt (GW) by 2034. A model was developed that simulates CCS deployment while considering different combinations of carbon price trajectories, technology progress, and assumed auction prices. The model shows that the deployment rate of CCS technology under APA is affected by the available bonus allowances, carbon price trajectory, CCS incentive, technological adaptation, and auction process. Furthermore it demonstrates that the 72GW objective can only be achieved in a rapid deployment scenario with quick learning-by-doing and high carbon price starting at 25 dollars in 2013 with a 5 percent annual increase. Furthermore under the slow and moderate deployment scenarios CCS capacity falls short of achieving the 72 GW objective.

Leakage and blockage of oil and gas pipeline systems, water pipelines, pipe-work of process plants and other pipe networks can cause serious environmental, health and economic problems. There are a number of non-destructive testing (NDT) methods for detecting these defects in pipeline systems such as radiographic, ultrasonic, magnetic particle inspection, pressure transient and acoustic wave methods. In this study, the acoustic wave method and a modal frequency technique, which based on a roving mass method, are used. The aim of the thesis is to employ acoustic wave propagation based methods in conjunction with stationary wavelet transform (SWT) to identify leakage and blockage in pipe systems. Moreover, the research is also aimed at using the difference of modal frequencies of fluid-filled pipes with and without defects and a roving mass, and consequently, to develop a roving mass-based defect detection method for pipelines. In the study, the acoustic finite-element analysis (AFEA) method is employed to simulate acoustic wave propagation in small and large air-filled water-filled straight pipe and pipe networks with leakage and blockage but without flow. Computational fluid dynamics (CFD) analysis was also employed to simulate acoustic wave propagation in air-and water-filled pipes with flow, leakage and blockage. In addition, AFEA was used to predict the modal frequencies of air- and water-filled pipes with leakage and blockage in the presence of a roving mass that was traversed along the axis of the pipes. Experimental testing was conducted to validate some of the numerical results. Two major experiments were performed. The first set of experiments consisted of the measurement of acoustic wave propagation in a straight air-filled pipe with leakage and blockage. The second set of experiments concerned the measurement of acoustic wave propagation in an air-filled pipe network comprising straight pipe, elbows and T-piece and flange. The AFEA and CFD analysis of fluid-filled pipe can be used to simulate the acoustic wave propagation and acoustic wave reflectometry of a fluid-filled pipe with leakage and blockage of different sizes down to a small leakage size of 1mm diameter and a blockage depth of 1.2mm in a pipe. Similarly, the AFEA method of a static fluid-filled pipe can be used to simulate acoustic wave modal frequency analysis of a fluid-filled pipe with leakage and blockage of different sizes down to a leakage of 1mm diameter and a blockage depth of 1.2mm. Moreover, the measured signal of acoustic wave propagation in an air-filled can be successfully decomposed and de-noised using the SWT method to identify and locate leakages of different sizes down to 5mm diameter, and small blockage depth of 1.2mm. Also, the SWT approximation coefficient, detail and de-noised detail coefficient curves of an air-filled pipe with leakage and blockage and a roving mass give leakage and blockage indications that can be used to identify, locate and estimate the size of leakage and blockage in a pipe.

abstract: The purpose of this study was to examine compulsory schooling in the United States and its potential to provide an inconsistent avenue to employment for students from neighborhoods of differing socioeconomic status. Specifically, this study asked why do students from privileged neighborhoods typically end up in positions of ownership and management while those from impoverished urban or rural neighborhoods end up in working-class positions or involved in cycles of incarceration and poverty? This research involved the use of qualitative methods, including participant observation and interview, as well as photography, to take a look at a reputable private day school in the southwest. Data was collected over the span of eight weeks and was then analyzed and compared with preexisting data on the schooling experience of students from impoverished urban and rural neighborhoods, particularly data focused on juvenile detention centers. Results showed that compulsory schooling differs in ways that contribute to the preexisting hierarchical class structure. The research suggests that schooling can be detrimental to the future quality of life for students in impoverished neighborhoods, which questions a compulsory school system that exists within the current hierarchical class system. / Dissertation/Thesis / M.A. Social and Philosophical Foundations of Education 2011

Este trabalho propõe a geração de uma arquitetura dedicada a aplicações específicas, baseadas no microcontrolador MCS8051. Por ser utilizado na solução de problemas em indústrias locais, este processador foi escolhido para servir como base em um sistema dedicado. O 8051 dedicado gerado deverá permitir a integração completa do sistema, proporcionando um aumento do valor agregado e, conseqüentemente, a diminuição do custo. Busca-se com a otimização da arquitetura obter um conjunto de instruções reduzido, construído com as instruções mais utilizadas em cada aplicação. O objetivo principal da otimização do conjunto de instruções está relacionado ao fato de que os circuitos decodificadores e geradores de microcódigo da parte de controle ocupam uma área significativa do processador. Uma otimização no sentido de reduzir-se o conjunto de instruções, portanto, resulta numa economia de área, o que vem de encontro com a idéia da integração completa do sistema com o processador. Um processador dedicado a aplicações específicas (ASIP) irá possuir um custo maior do que a sua versão original, devido as otimizações realizadas. Para compensar este custo, uma alternativa a seguir é a integração completa do sistema. Um Sistema Integrado para Aplicações Específicas (SIAE) torna-se desejável, pois aumentando o valor agregado do circuito possibilita-se a redução do custo pela eliminação de conexões da placa, do encapsulamento de outros circuitos, entre outros motivos. Todavia, para que um SIAE possa ser construído com um custo aceitável, é necessário que seja construído em uma área que não exceda muito a área original do processador. Tenta-se fazer isto neste trabalho, através da implementação de aplicações com poucas instruções diferentes. Por ser uma arquitetura comercial, o 8051 possui um grande parque de software desenvolvido e resolvendo problemas. Isto pode ser considerado uma vantagem pois, software básicos como por exemplo, compiladores, já estão desenvolvidos. Outra vantagem é o grande número de engenheiros treinados na sua utilização. Desse modo, torna-se necessária a criação de uma compatibilidade de software, para preservar o que já está desenvolvido. Uma vez que a programação em nível de linguagem montadora tende a constituir-se em uma tarefa cansativa e sujeita a erros, é desejável que se tenha uma compatibilidade em alto nível, ou seja, através de um compilador. Para criar a compatibilidade de SW necessária é realizada a otimização de um compilador C desenvolvido para o 8051. A escolha pela linguagem C deve-se ao fato de sua grande utilização. O compilador C otimizado procura utilizar um conjunto de instruções reduzido para obter a economia de área. Quando uma instrução necessita ser utilizada e não está presente no conjunto de instruções desejado, o compilador tenta substituí-la por outra(s). Um conjunto de instruções é utilizado para cada aplicação, sendo constituído pelas instruções mais utilizadas por esta. Para determinar as instruções mais utilizadas de cada aplicação é realizada uma análise estática sobre um código em linguagem montadora previamente compilado. As instruções implementadas serão sempre parte do conjunto de instruções original do 8051, de modo que novas instruções não serão criadas.Um programa em linguagem montadora gerado com um conjunto de instruções reduzido (RISC) normalmente terá um número maior de instruções do que o seu 10 equivalente com o conjunto de instruções completo (CISC). Isto ocorre porque possivelmente algumas substituições de uma instrução por outras, terão que ser realizadas. Como as instruções que serão utilizadas nas substituições pertencem ao conjunto de instruções original, o programa gerado com o compilador otimizado poderá executar em um tempo maior do que se fosse compilado com o código CISC. Para compensar esse atraso foi implementado um pipeline de instruções para o 8051. Este trabalho apresenta resultados da Síntese Lógica em Standard Cell e FPGA da arquitetura otimizada. Além disso, resultados de programas em linguagem montadora gerados com o compilador otimizado, são também apresentados. / This work discusses a processor for specific applications architecture, based on the MCS8051 microcontroller. This processor is used as a solution for many local industry applications, being the base of dedicated systems. The dedicated 8051 generated should allow complete integration of the system, and with the added value to the chip, reduced costs. The architecture optimization will produce as result a reduced instruction set, made by the often used instructions for each application. The main instruction set optimization goal refers to the instrucions decoders and microcode generators in the control part, because a large area in the processor is needed to implement them. Thus, a reduced instruction set will allow area savings, making possible the complete system integration in a chip. An ASIP architecture will have a higher cost than the original one. An alternative to solve this problem is add value to the chip, creating an Application Specific Integrated System (ASIS). An ASIS can be made with a acceptable cost, if it’s possible to integrate other circuits to the chip without area increase. This can be done in the area saved by using fewer implemented instructions. Because the 8051 is a commercial architecture, there is a large amount of software developed for it. This can be considered an advantage because basic softwares like compilers are available, being not necessary to create them. Another advantage refers to the large number of engineers trained to use the 8051. To preserve the already developed applications it’s necessary to mantain software compatibility. Assembler level programming is very boring an error prone task, being desirable to have software compatibility at higher levels through the use of high level languages. To create the necessary SW compatibility, a C compiler developed for 8051 was optimized. The chose for C language refers to its large utilization. The optimized C compiler tries to use a reduced instruction set, formed with the most important instructions for each application, in order ro save area. When an instruction needs to be used in an application, and it’s not present in the instruction set, the compiler tries to replace it with other instructions. The compiler will not use instructions not present in the original 8051 instruction set. So, new instrucions will be not created. To create an instruction set formed with the most important instructions for each application, a static analysis is made on a precompiled assembler source. An assembler source generated with a reduced instruction set (RISC) will probably have more instructions than the same assembler generated with a full instruction set (CISC). This can be explained because of the replacements instruction. If one instruction is replaced by other two, and these are from the original instruction set, probably the time needed to execute them would be higher. In order to deal with this problem, an instruction pipeline was implemented to the 8051. This work presents Standard Cells and FPGA results of Logic Synthesis of the optimized architecture. Also, assembly programs generated by the optimized compiler are presented.