Sequence alignment has become a routine procedure in evolutionary biology in looking for evolutionary relationships between primary sequences of DNA, RNA, and protein. Smith Waterman and Needleman Wunsch algorithms are two algorithms respectively for local alignment and global alignment. Both of them are based on dynamic programming and guarantee optimal results. They have been widely used for the past dozens of years. However, time and space requirement increase exponentially with the number of sequences increase. Here I present a novel approach to improve the performance of sequence alignment by using graphics processing unit which is capable of handling large amount of data in parallel.

In the study of pairwise sequence alignment, a clear relationship between the scoring system and assumptions about the occurrence of evolutionary events has been established in [BT86], [TKF91], [TKF92] and [TC95] by proposing an evolutionary model. To align two given sequences, one need estimate some evolutionary parameters through maximum likelihood method, and find an alignment with the maximum probability using the estimated parameters. In this thesis, we extend the above model and the maximum likelihood method to star alignment of three molecular sequences along the same line. We overcome the duplications of star alignments by defining canonical star alignments. Two star alignment algorithms, i.e. sum approach and direct alignment approach, are proposed in this thesis based on two different likelihood functions. A software system, called MLSAS (Maximum Likelihood Star Alignment System), is developed to implement the two algorithms with a friendly graphical user interface. Simulation studies show their behaviors are satisfactory for closely related sequences. A few real examples are also provided. / Thesis / Master of Engineering (ME)

We are able to define architectural members specifically, and create identity of members within a hierarchy. Through appropriate placement with respect to their character and hierarchy, relationships are created that strengthen the individual's traits. This reinforcement creates an effect beyond what the individual elements are able to project toward one another, and influences our participation in their relationships. If we question how element identity, placement and alignment work together to create prepositional relationships, and consciously define members within a physical hierarchy, then we are able to strengthen identity of individual members, and ultimately create a more meaningful and considerate environment. / Master of Architecture

The merging of business and information technology (IT) strategies, effectively becoming a Digital Business Strategy (DBS), is changing the way that organisations have to leverage resources to create differential value. Due to the DBS being such a novice idea, there is no clear understanding of what the DBS is, what its characteristics and boundaries are, how it impacts alignment between business and IT, and how it impacts organisational performance. Without this understanding, organisations leveraging a DBS run the risk of launching technological initiatives or making organisational changes that are disjointed from their strategic direction. These misaligned efforts may result in unrealised strategy and unsatisfactory organisational performance. The purpose of this study was to define the boundaries and characteristics of the DBS, provide a definition of a DBS and to establish if the DBS has a positive effect on organisational performance. To examine the DBS, it was observed in its natural habitat, through a single case study approach, focusing on an organisation that has been leveraging a DBS as part of their digital journey. The organisation is a South African based financial services provider and is a subsidiary of a larger financial services provider. In this study, the DBS was observed from an intellectual, operational, social and cultural alignment perspective, using a combination of the Strategic Alignment Model (SAM) and the Complex Adaptive System (CAS) frameworks. This study subscribed to a mixed-method approach which included both qualitative and quantitative research techniques. Staff providing input into this study included senior, middle, junior and non-management employees. The study was conducted over a period of thirteen months. The findings from both the qualitative and quantitative data suggest that to leverage a DBS the organisation must be concerned with more than just leveraging digital resources. For instance, organisations must focus on customer and staff empowerment, use customer and industry-related information to create opportunistic and competitive decision-making opportunities, and create a change-ready culture where bold experimentation and failing forward is embraced. Researchers and practitioners alike can use the findings of this case study as lessons on how to leverage organisational resources in the context of the DBS.

Este trabalho tem por objetivo estudar as interações superfíciais de cristais líquidos em uma interface cristal líquido-polímero, com a utilização de filmes poliméricos contendo cadeias laterais com corante azo. Nesse estudo foi utilizado um fotopolímero, onde pode se promover o ordenamento dos grupos laterais ao longo de uma direção preferencial através de um processo de isomerização trans-cis. Através da irradiação do filme de polímero com luz polarizada é possível promover a formação de uma anisotropia óptica no filme. A intensidade deste efeito pode ser controlada através da energia incidente e da concentração dos grupos laterais corante azo presentes no polímero. Neste trabalho foi realizado um estudo sistemático da orientação induzida ao cristal líquido nemático por um filme contendo corante azo no grupo lateral. Os aspectos investigados são: a estabilidade térmica e temporal do alinhamento induzido ao cristal líquido; a competição entre dois efeitos de orientação induzidos ao cristal líquido, o esfregamento e o fotoalinhamento; a influência da cncentração dos grupos laterais e da energia de irradiação. Para caracterizar as interações entre o cristal líquido e o filme polimérico foram empregadas técnicas ópticas que permitiram a determinação das intensidades de ancoramento azimutal e zenital em função da concentração de grupos laterais e da energia de irradiação. Mostramos ser possível um ancoramento azimutal que pode ter sua intensidade controlada pela concentração dos grupos laterais, pelo tempo de irradiação com luz polarizada, ou ainda pela potência do laser de excitação, e um ancoramento zenital bastante fraco, que praticamente não é afetado pelo processo de foto-isomerização. / The aim of this work is to study the superficial interactions of liquid crystals in an interface liquid Crystal-polymer, with the use of polymer films containing azo-dyes groups as side chain. In this study a photopolymer was used, where the ordering of the side group can be promoted along a preferential direction through a trans-cis isomerization process. Through the irradiation of the polymeric film with polarized light it is possible to promote the formation of an optical anisotropy in the film. The intensity of this effect can be controlled through the incident energy and the concentration of the azo-dye side groups presents in the polymer. In this work a systematic study of the orientation induced to the nematic liquid crystal by a polymeric film containing azo-dye groups in the side group was performed. The investigated aspects are: -The thermal and temporary stability of the alignment induced to the liquid crystal; -The competition among two orientation effects induced to the liquid crystal, the rubbing and the photo alignment; -The influence of the concentration of the side groups and of the irradiation energy. To characterize the interactions between the liquid crystal and the polymeric film we used optical techniques that allowed the determination of the azimuthal and zenithal anchoring strengths as a function of the concentration of side groups and of the irradiation energy. We showed to be possible an azimuthal anchoring that can have its intensity controlled by the concentration of the side groups, and the irradiation time with polarized light, or still for the power of the excitation laser, and a zenithal anchoring quite weak, that practically is not affected by the process of photo isomerization.

This research investigates the role of strategic alignment in the success of data warehouse implementation. Data warehouse technology is inherently complex, requires significant capital investment and development time. Many organizations fail to realize the full benefits from it. While failure to realize benefits has been attributed to numerous causes, ranging from technical to organizational reasons, the underlying strategic alignment issues have not been studied. This research confirms, through two case studies, that the successful adoption of the data warehouse depends on its alignment to the business plans and strategy. The research found that the factors that are critical to the alignment of data warehouses to business strategy and plans are (a) joint responsibility between data warehouse and business managers, (b) alignment between data warehouse plan and business plan, (c) business user satisfaction, (d) flexibility in data warehouse planning and (e) technical integration of the data warehouse. In the case studies, the impact of strategic alignment was visible both at implementation and use levels. The key findings from the case studies are that a) Senior management commitment and involvement are necessary for the initiation of the data warehouse project. The awareness and involvement of data warehouse managers in corporate strategies and a high level of joint responsibility between business and data warehouse managers is critical to strategic alignment and successful adoption of the data warehouse. b) Communication of the strategic direction between the business and data warehouse managers is important for the strategic alignment of the data warehouse. Significant knowledge sharing among the stakeholders and frequent communication between the iv data warehouse managers and users facilitates better understanding of the data warehouse and its successful adoption. c) User participation in the data warehouse project, perceived usefulness of the data warehouse, ease of use and data quality (accuracy, consistency, reliability and timelines) were significant factors in strategic alignment of the data warehouse. d) Technology selection based on its ability to address business and user requirements, and the skills and response of the data warehousing team led to better alignment of the data warehouse to business plans and strategies. e) The flexibility to respond to changes in business needs and flexibility in data warehouse planning is critical to strategic alignment and successful adoption of the data warehouse. Alignment is seen as a process requiring continuous adaptation and coordination of plans and goals. This research provides a pathway for facilitating successful adoption of data warehouse. The model developed in this research allows data warehouse professionals to ensure that their project when implemented, achieve the strategic goals and business objectives of the organization.

Comparative analysis of genomic data investigates the relationship of genome structure and function across different biological species to shed light on their similarities and differences. In this dissertation, we study two important problems in comparative genomics, namely comparative sequence analysis and comparative network analysis. In the comparative sequence analysis, we study the multiple sequence alignment of protein and DNA sequences as well as the structural alignment of multiple RNA sequences. For closely related sequences, multiple sequence alignment can be efficiently performed through progressive techniques. However, for divergent sequences it is very challenging to predict an accurate alignment. Here, we introduce PicXAA, an efficient non-progressive technique for multiple protein and DNA sequence alignment. We also further extend PicXAA to PicXAA-R for structural alignment of RNA sequences. PicXAA and PicXAA-R greedily build up the alignment from sequence regions with high local similarity, thereby yielding an accurate global alignment that effectively captures local similarities among sequences. As another important research area in comparative genomics, we also investigate the comparative network analysis problem. Translation of increasing number of large-scale biological networks into meaningful biological insights requires efficient computational techniques. One such example is network querying, which aims to identify subnetwork regions in a large target network that are similar to a given query network. Here, we introduce an efficient algorithm for querying large-scale biological networks, called RESQUE. RESQUE adopts a semi-Markov random walk model to probabilistically estimate the correspondence scores between nodes that belong to different networks. The target network is iteratively reduced based on the estimated correspondence scores until the best matching subnetwork emerges. The proposed network querying scheme is computationally efficient, can handle any network query with an arbitrary topology, and yields accurate querying results. We also extend the idea used in RESQUE to develop an efficient algorithm for alignment of multiple large-scale biological networks, called SMETANA. SMETANA outperforms state-of- the-art network alignment techniques, in terms of both computational efficiency and alignment accuracy. The accomplished studies have enabled us to provide a coherent framework for probabilistic approach to comparative analysis of biological sequences and networks. Such a probabilistic framework helps us employ rigorous mathematical schemes to find accurate and efficient solutions to these problems.

Currently, much attention is paid to magnetoreception, a sense which allows an organism to detect a magnetic field of the earth. Now, this discovery is related to positional behaviour of animals (magnetic alignment) in the magnetic field and the world phenomenon of "magnetic cows". The magnetic alignment is a spontaneous (congenital) behaviour, when the animal puts its body axis into the positions of north - south or east - west. Most studies have demonstrated the north - south direction preference. This work contributes to clarify positional behaviour of cattle during the daily cycle. This study is based on a different data collection and is targeted at individuals in the herd. Individuals were photographed in a given direction, at hourly intervals. The magnetic alignment was determined in 26 individuals from three different cattle herds, mainly east or west. Statistically significant results during daily cycles in individual intervals also confirmed the north - south direction preference. There were also discussed the environmental conditions that may affect the final result. For inconclusive results, the individuals were probably motivated by temporarily more important local incentives.

Este trabalho tem por objetivo estudar as interações superfíciais de cristais líquidos em uma interface cristal líquido-polímero, com a utilização de filmes poliméricos contendo cadeias laterais com corante azo. Nesse estudo foi utilizado um fotopolímero, onde pode se promover o ordenamento dos grupos laterais ao longo de uma direção preferencial através de um processo de isomerização trans-cis. Através da irradiação do filme de polímero com luz polarizada é possível promover a formação de uma anisotropia óptica no filme. A intensidade deste efeito pode ser controlada através da energia incidente e da concentração dos grupos laterais corante azo presentes no polímero. Neste trabalho foi realizado um estudo sistemático da orientação induzida ao cristal líquido nemático por um filme contendo corante azo no grupo lateral. Os aspectos investigados são: a estabilidade térmica e temporal do alinhamento induzido ao cristal líquido; a competição entre dois efeitos de orientação induzidos ao cristal líquido, o esfregamento e o fotoalinhamento; a influência da cncentração dos grupos laterais e da energia de irradiação. Para caracterizar as interações entre o cristal líquido e o filme polimérico foram empregadas técnicas ópticas que permitiram a determinação das intensidades de ancoramento azimutal e zenital em função da concentração de grupos laterais e da energia de irradiação. Mostramos ser possível um ancoramento azimutal que pode ter sua intensidade controlada pela concentração dos grupos laterais, pelo tempo de irradiação com luz polarizada, ou ainda pela potência do laser de excitação, e um ancoramento zenital bastante fraco, que praticamente não é afetado pelo processo de foto-isomerização. / The aim of this work is to study the superficial interactions of liquid crystals in an interface liquid Crystal-polymer, with the use of polymer films containing azo-dyes groups as side chain. In this study a photopolymer was used, where the ordering of the side group can be promoted along a preferential direction through a trans-cis isomerization process. Through the irradiation of the polymeric film with polarized light it is possible to promote the formation of an optical anisotropy in the film. The intensity of this effect can be controlled through the incident energy and the concentration of the azo-dye side groups presents in the polymer. In this work a systematic study of the orientation induced to the nematic liquid crystal by a polymeric film containing azo-dye groups in the side group was performed. The investigated aspects are: -The thermal and temporary stability of the alignment induced to the liquid crystal; -The competition among two orientation effects induced to the liquid crystal, the rubbing and the photo alignment; -The influence of the concentration of the side groups and of the irradiation energy. To characterize the interactions between the liquid crystal and the polymeric film we used optical techniques that allowed the determination of the azimuthal and zenithal anchoring strengths as a function of the concentration of side groups and of the irradiation energy. We showed to be possible an azimuthal anchoring that can have its intensity controlled by the concentration of the side groups, and the irradiation time with polarized light, or still for the power of the excitation laser, and a zenithal anchoring quite weak, that practically is not affected by the process of photo isomerization.

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