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In the past few years we have witnessed an explosion in the viral genomic data available. GenBank alone holds over 80,000 close to complete viral genomes, and numbers are rising fast. For example, since the submission of the first SARS genome in May 2003, over 140 more have been published. With this genomic data at hand we hope to finally be able to improve our understanding of viruses. Several papers have been dedicated to the study of genome annotation and selection on viral genomes, in particular focusing attention on the evolutionary behaviour of overlapping reading frames. This is a feature common to viruses, where due to the three periodicity of the genetic code, up to three genes may be encoded simultaneously in one direction. The constraints placed on a nucleotide involved in such a multiple coding region will naturally have an effect on its mutational behaviour, and as a result the pattern of evolution will be more complex. Additionally, due to their fast evolution time, we observe changes in gene structure between viruses of the same family. Finally, as a result of this high divergence, alignments between two genomes will tend to be unreliable, thus complicating the issue of comparative analysis further. Our goal is to present methods which may deal with the above mentioned complications. We first introduce an ab initio pairwise comparative annotation method, which not only accounts for the presence of overlapping reading frames in genomes, but also for differences in gene structure between the two compared sequences. Secondly, we develop a hidden Markov model for the annotation of selection strengths across a viral genome accommodating for inter- as well as intragenic differences in selection. Thirdly, we investigate the effect of using a fixed alignment on the inference of selection by incorporating statistical alignment into our selection analysis. All three methods presented here improve on their respective equivalents in the field. We investigate the nature of selection in overlapping regions in several studies, in particular on the genomes of Hepatitis B and HIV2. We provide a full annotation of selection strengths on a nucleotide level for both viral sequences, highlighting fast evolving regions such as the gp120 protein. We also analyse the mutational behaviour of overlapping regions in both genomes and find that in Hepatitis B selection seems to be of equal strength for single and double coding regions. In HIV2, however, single coding regions appear to be under twice as stringent selection as double coding regions, with a tendency for a fast evolving region to overlap a slow evolving one. Each chapter of our work relates to one of our publications. We introduce in turn each method, its academic context and its results. We subsequently in chapter 5 discuss for each method its achievements, its shortcomings and future possible extensions and improvements to it.

This thesis investigates a set of non-classical visual receptive field properties observed in the primate brain. Two main phenomena were explored. The first phenomenon was neurons with head-centered visual receptive fields, in which a neuron responds maximally to a visual stimulus in the same head-centered location across all eye positions. The second phenomenon was perisaccadic receptive field dynamics, which involves a range of experimentally observed response behaviours of an eye-centered neuron associated with the advent of a saccade that relocates the neuron's receptive field. For each of these two phenomena, a hypothesis was proposed for how a neural circuit with a suitable initial architecture and synaptic learning rules could, when subjected to visually-guided training, develop the receptive field properties in question. Corresponding neural network models were first trained as hypothesized, and subsequently tested in conditions similar to experimental tasks used to interrogate the physiology of the relevant primate neural circuits. The behaviour of the models was compared to neurophysiological observations as a metric for their explanatory power. In both cases the neural network models were in broad agreement with experimental observations, and the operation of these models was studied to shed light on the neural processing behind these neural phenomena in the brain.

The rapid growth of digital video content in recent years has imposed the need for the development of technologies with the capability to produce condensed but semantically rich versions of the input video stream in an effective manner. Consequently, the topic of Video Summarisation is becoming increasingly popular in multimedia community and numerous video abstraction approaches have been proposed accordingly. These recommended techniques can be divided into two major categories of automatic and semi-automatic in accordance with the required level of human intervention in summarisation process. The fully-automated methods mainly adopt the low-level visual, aural and textual features alongside the mathematical and statistical algorithms in furtherance to extract the most significant segments of original video. However, the effectiveness of this type of techniques is restricted by a number of factors such as domain-dependency, computational expenses and the inability to understand the semantics of videos from low-level features. The second category of techniques however, attempts to alleviate the quality of summaries by involving humans in the abstraction process to bridge the semantic gap. Nonetheless, a single user’s subjectivity and other external contributing factors such as distraction will potentially deteriorate the performance of this group of approaches. Accordingly, in this thesis we have focused on the development of three user-centred effective video summarisation techniques that could be applied to different video categories and generate satisfactory results. According to our first proposed approach, a novel mechanism for a user-centred video summarisation has been presented for the scenarios in which multiple actors are employed in the video summarisation process in order to minimise the negative effects of sole user adoption. Based on our recommended algorithm, the video frames were initially scored by a group of video annotators ‘on the fly’. This was followed by averaging these assigned scores in order to generate a singular saliency score for each video frame and, finally, the highest scored video frames alongside the corresponding audio and textual contents were extracted to be included into the final summary. The effectiveness of our approach has been assessed by comparing the video summaries generated based on our approach against the results obtained from three existing automatic summarisation tools that adopt different modalities for abstraction purposes. The experimental results indicated that our proposed method is capable of delivering remarkable outcomes in terms of Overall Satisfaction and Precision with an acceptable Recall rate, indicating the usefulness of involving user input in the video summarisation process. In an attempt to provide a better user experience, we have proposed our personalised video summarisation method with an ability to customise the generated summaries in accordance with the viewers’ preferences. Accordingly, the end-user’s priority levels towards different video scenes were captured and utilised for updating the average scores previously assigned by the video annotators. Finally, our earlier proposed summarisation method was adopted to extract the most significant audio-visual content of the video. Experimental results indicated the capability of this approach to deliver superior outcomes compared with our previously proposed method and the three other automatic summarisation tools. Finally, we have attempted to reduce the required level of audience involvement for personalisation purposes by proposing a new method for producing personalised video summaries. Accordingly, SIFT visual features were adopted to identify the video scenes’ semantic categories. Fusing this retrieved data with pre-built users’ profiles, personalised video abstracts can be created. Experimental results showed the effectiveness of this method in delivering superior outcomes comparing to our previously recommended algorithm and the three other automatic summarisation techniques.

Faculty of Science; School of Chemistry; PhD Thesis / The synthesis of nitrogen containing ring systems has been one of the interests of this research group at the University of the Witwatersrand for a long time. These systems form part of a group of compounds called alkaloids, whose structural diversity is rivalled only by their distribution in nature. A small sub-set of the alkaloids is the fused 5 and 6 membered bicyclic frames with nitrogen at one bridgehead. Having developed a unique method of synthesising these indolizidine alkaloids, we examined various aspects of this methodology and there remained one crucial question – what is the best way to control the stereochemical outcome of the ring-forming steps? This project looks at this question from the view of a model natural product, the indolizidine alkaloids (+)- and (–)-tashiromine. The synthesis of tashiromine and related compounds was examined using chiral auxiliaries such as the Oppolzer sultam and the Evans oxazolidinone, as well as the use of chirally modified reductants. The efficacies of the chiral auxiliaries were studied using molecular modelling techniques, and certain modifications were suggested from these results.

Esta Dissertação de Mestrado trata da pesquisa e do estudo das esquadrias de alumínio para a construção civil de edifícios, nas diversas categorias de uso. Considera os aspectos referentes ao histórico do metal, aos processos de produção do alumínio e dos perfis para fabricação de esquadrias, à especificação técnica das esquadrias com suas diferentes tipologias, multiplicidade de usos e aplicações e desempenho técnico-construtivo do material. O objetivo deste trabalho é desenvolver literatura didática a respeito do sistema de vãos janelas de alumínio, de modo a orientar os profissionais da construção civil, particularmente os arquitetos, no emprego do material, aliando adequação técnica, estética e demais pormenores, além de promover a otimização de custos numa relação de custo-benefício. O produto resultante da pesquisa inserida nesta Dissertação poderá contribuir e auxiliar na elaboração do projeto e na especificação técnica das esquadrias de alumínio nos edifícios, sempre de maneira responsável e consciente. / This Masters Degree Dissertation is about the research and the study of the aluminum building products for doors and windows, considering the following aspects: the metals historic; the production process of aluminum and profiles for the windows fabrication; the technical specification of the windows, its typologies, its multiplicity of uses and applications and the performance technical constructive of the material. The objective of this job is to develop teaching literature about space systems aluminum windows, in order to orientate the professionals of civil construction, particularly the architects, to use material with the best possible way, allying technical adaptation, aesthetics, and others details, and to promote the cost optimization. The resulting of the research inside this Dissertation could contribute and helps in the technical specification, responsible and conscious, of the aluminum windows and doors for buildings.

Thesis advisor: Jennie Purnell / In December of 2005, the United States House of Representatives passed the infamous Sensenbrenner-King immigration reform legislation that, if written into law, would have negatively affected the situation of millions of undocumented workers in the United States, mostly originating from Latin America. In response, the Latino community in the U.S. mobilized to organize a wave of rallies across the country during the spring of 2006. This thesis explores the construction of the collective action frame employed by movement organizers to mobilize protesters. It ultimately finds that the rhetoric of assimilation was chosen because of its ability to resonate both with the goal of effecting political change as well as with the identity of the potential audience. It was nevertheless found to be inadequate in addressing the larger issues of injustice affecting immigrants as it served to reinforce and perpetuate the oppression of consciousness that has often left Latinos feeling that their heritage must be rejected in order to be deemed worthy of certain rights in the United States. While movement organizers managed to mobilize millions of people across the country, their influence on legislation has yet to be seen, as no immigration reforms have been written into law as of the writing of this thesis. / Thesis (BA) — Boston College, 2007. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: International Studies. / Discipline: College Honors Program.

Reinforced concrete moment-resisting frames are structural systems that work to resist earthquake ground motions through ductile behavior. Their performance is essential to prevent building collapse and loss of life during a seismic event. Seismic building code provisions outline requirements for three categories of reinforced concrete moment-resisting frames: ordinary moment frames, intermediate moment frames, and special moment frames. Extensive research has been conducted on the performance of special moment-resisting frames for areas of high seismic activity such as California. More research is needed on the performance of intermediate moment frames for areas of moderate seismicity because the current code provisions are based on past observation and experience. Adapting dynamic analysis software and applications developed by the Pacific Earthquake Engineering Research (PEER) Group, a representative concrete intermediate moment frame was designed per code provisions and analyzed for specified ground motions in order to calculate the probability of collapse. A parametric study is used to explore the impact of changes in design characteristics and building code requirements on the seismic response and probability of collapse, namely the effect of additional height and the addition of a strong column-weak beam ratio requirement. The results show that the IMF seismic design provisions in ACI 318-08 provide acceptable seismic performance based on current assessment methodology as gravity design appeared to govern the system. Additional height did not negatively impact seismic performance, while the addition of a strong-column weak-beam ratio did not significantly improve results. It is the goal of this project to add insight into the design provisions for intermediate moment frames and to contribute to the technical base for future criteria.

Esta Dissertação de Mestrado trata da pesquisa e do estudo das esquadrias de alumínio para a construção civil de edifícios, nas diversas categorias de uso. Considera os aspectos referentes ao histórico do metal, aos processos de produção do alumínio e dos perfis para fabricação de esquadrias, à especificação técnica das esquadrias com suas diferentes tipologias, multiplicidade de usos e aplicações e desempenho técnico-construtivo do material. O objetivo deste trabalho é desenvolver literatura didática a respeito do sistema de vãos janelas de alumínio, de modo a orientar os profissionais da construção civil, particularmente os arquitetos, no emprego do material, aliando adequação técnica, estética e demais pormenores, além de promover a otimização de custos numa relação de custo-benefício. O produto resultante da pesquisa inserida nesta Dissertação poderá contribuir e auxiliar na elaboração do projeto e na especificação técnica das esquadrias de alumínio nos edifícios, sempre de maneira responsável e consciente. / This Masters Degree Dissertation is about the research and the study of the aluminum building products for doors and windows, considering the following aspects: the metals historic; the production process of aluminum and profiles for the windows fabrication; the technical specification of the windows, its typologies, its multiplicity of uses and applications and the performance technical constructive of the material. The objective of this job is to develop teaching literature about space systems aluminum windows, in order to orientate the professionals of civil construction, particularly the architects, to use material with the best possible way, allying technical adaptation, aesthetics, and others details, and to promote the cost optimization. The resulting of the research inside this Dissertation could contribute and helps in the technical specification, responsible and conscious, of the aluminum windows and doors for buildings.

The problem was to determine factors Tennessee school leaders consider important to effective leadership. Organizational frames by Bolman and Deal were used. The four organizational frames used in the study were structural, human resource, political, and symbolic approaches to leadership. The frames were examined with regard to their relationship to Tennessee superintendent's leadership and management styles with the perception of his/her style by their superordinates and subordinates. Leadership Orientations, a validated instrument designed by Bolman and Deal, was used to gain insight about school leader perceptions from superintendents and from individuals who work in school administration with the superintendents. Individual school systems, the director of the Tennessee Academy of School Leaders (TASL), the Tennessee Organization of School Superintendents (TOSS), and the Tennessee School Board Association (TSBA) received the data analysis results about leadership perspectives. The research provided school system personnel a method to understand individual, subordinate, and superordinate expectations as they relate to the four organizational frames. Additionally, the findings indicated predictors of management and leadership effectiveness as perceived by the respondents.