New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Burgoyne Centre for Entrepreneurship fonds

An Entrepreneurship Centre was established at Brock University in 1988 as a joint venture between the University and the City of St. Catharines. In Januaray 1989, a generous donation was made to the Centre by the Burgoyne family, proprietors of the St. Catharines Standard. The Centre subsequently became known as the Burgoyne Centre for Entrepreneurship (BCE). The Centre’s mission was to “promote excellence in research, education and training for entrepreneur development and new venture creation”. To achieve this objective, it was necessary for the BCE to become a community focal point and serve as a link between academic, private and government sectors in the Niagara Region that were involved in entrepreneurial activities. This was primarily done with the provision of educational programs offered through cooperating organizations. Funding for the Centre came from multiple sources, including fees for services and contract research, endowments and grants, as well as Brock University. An Advisory Council, composed of local prominent businesspeople and chaired by Henry Burgoyne, assisted the Centre with promotion and fundraising. The partnerships established by the BCE with other community bodies such as the Lincoln County Board of Education and the Niagara Region Development Corporation resulted in important collaborative community initiatives such as the Niagara Enterprise Agency and the New Enterprise Store. Such collaborations increased the Centre’s profile without duplicating or competing with services offered by existing agencies. The BCE was also instrumental in establishing an entrepreneurship curriculum for secondary school students, and collaborated with the Faculty of Education at Brock University to offer an Ontario Secondary School Entrepreneurship Specialist Teaching Certificate Program to teachers. As the BCE became more prolific in the community, and the iniatives it fostered in the community began to thrive, the Centre’s leadership required the authority to make instantaneous decisions. This was at odds with the hierarchical structure of the University, to which the BCE was accountable. Ultimately, this situation led to the demise of the Centre. The university focused its efforts on academic research and undergraduate courses, while the community partners took responsibility for any joint programs.

The synthesis of a-Tocohexaenol, a new fluorescent analogue of a-Tocopherol

Since its discovery in 1922, vitamin E has been widely investigated for its role as a powerful, chain-breaking antioxidant that is required for human health. However, some basic issues still remain unclear, such as the mechanism and dynamics of the intracellular trafficking of a-tocopherol. To better understand tocopherol's biological activity at the cellular level, fluorescence spectroscopy and microscopy have been found to be valuable tools. This thesis reports the synthesis of a new fluorescent analogue of a-tocopherol, atocohexaenol, an intrinsically fluorescent analogue of a-tocopherol. Different methodologies of preparation have been attempted and a strategy using a preformed chromanol head plus ClO and Cs portion of the polyene side chain finally provided us the desired a-tocohexaenol. a-Tocohexaenol shows a strong fluorescence in both ethanol and hexanes with maximum Aab = 368 nm and maximum /...em = 521 nm. This compound is stable for a couple of weeks in ethanol or hexane solution if stored at 0 °C and protected form light. It decomposes slowly at room temperature and light will accelerate its decomposition (within 5 hours). Thus, a-Tocohexaenol may be a useful fluorescent probe to study the biochemistry and cell biology of vitamin E.

Analyzing the learning of the taking personal and social responsibility model within a new physical education undergraduate degree program in El Salvador

EI Salvador presents an unfortunate history that includes a military regime and a civil war that together created a legacy of violence in which the country still struggle nowadays. Salud Escolar Integral (SEI) was created in 2005 as a program to combat youth violence throughout the re-formulation of physical education (PE) classes in public schools, promoting life skills learning that supports the resolution of conflicts with nonviolent ways. In 2007, SEI supported the creation of a physical e~ucation teacher education (PETE) degree at the Universidad Pedag6gica de EI Salvador (UPES), having the goal to assist pre-service teachers with a better understanding of humanistic principles. The present research analyzed if after attending all three years ofUPES PETE program, students presented high self-perception levels of competence and confidence related to attitude, skills and knowledge to teach PE within humanistic principles. Taking Personal and Social Responsibility (TPSR) was the theoretical framework used to analyze the development of humanistic principles. The study had a mixed-method longitudinal design that included questionnaires, reflection templates and interviews. In conclusion, although it is suggested that UPES should provide better support for the development of the teaching principles of empowering students and transfer learning, most of the humanistic principles were highly promoted by the program. At last, it is suggested that future research should track teachers' progress while teaching in schools, in order to analyze if the theory of promoting humanistic principles have also become a daily practice.

Reflection Reframed: The Process of Photography as Strategy for Teachers' Reflective Practice

Teacher reflective practice is described as an effective method for engaging teachers in improving their own professional learning. Yet, some teachers do not understand how to effectively engage in the reflective processes, or prefer not to formalize the process through writing a reflective journal as taught in most teacher education programs. Developing reflective skills through the process of photography was investigated in this study as a strategy to allow enhanced teacher reflection for professional and personal growth. The process of photography is understood as the mindful act of photographing rather than focusing on the final product-the image. For this study, 3 practicing educators engaged in photographic exercises as a reflective process. Data sources included transcribed interviews, participant journal reflections, and sketchbook artifacts, as well as the researcher's personal journal notes. Findings indicated that, through the photographic process, (a) teacher participants developed new and individual strategies for professional leaming; and (b) teacher participants experienced shifts in the way they conceptualized their personal worldviews.

New Building Blocks for Dual-Property Molecule-Based Magnets

Two classes of compounds have been prepared and characterized as building blocks for chiral magnets and ferromagnetic conductors. In the fIrst project, the organic framework of a pentadentate, (N302) macro cycle has been synthetically modifIed to introduce phenyl substituents into its organic framework and the synthesis of four new [Fe(In(N302)(CN)2] complexes (I) - (IV) is presented. [Molecular diagram availble in pdf] This work represents the fIrst structural and magnetic studies of a family of spin crossover macrocycles that comprise of both structural and stereo-isomers. Magnetic susceptibility and Mossbauer data for the R,R-complex (I) is consistent with both a thermal and a light induced spin crossover transition. The X-ray data supports a change in geometry accompanying the thermal spin transition, from a high spin (HS) 7 -coordinate complex at room temperature to a low spin (LS) 5-coordinate complex at 100 K. The crystal structure ofthe racemic complex (III) reveals a HS, 7-coordinate complex at 200 K that undergoes no signifIcant structural changes on cooling. In contrast, the magnetic - susceptibility and Mossbauer data collected on a powder sample of the racemic complex are consistent with a LS complex. Finally, the meso complex (IV) was prepared and its structure and magnetic properties are consistent with a 5-coordinate LS complex that remains low spin, but undergoes conformational changes on cooling in solution. The chiral [Fe(H)(N302)(CN)2] macro cycle (I), together with its Mn(H) and Fe(H) derivatives have also been exploited as building blocks for the self-assembly of chiral magnets. In the second project, a synthetic route for the preparation of tetrathiafulvalene (TTF) donors covalently attached to a diisopropyl verdazyl radical via a cross conjugated pyridyl linker IS presented. Following this strategy, four new TTF-py- (diisopropyl)verdazyl radicals have been prepared and characterized (V) - (VIII) . [Molecular diagram available in pdf] The first (2:1) charge transfer complex ofa TTF-py-(diisopropyl)verdazyl radical donor and a TCNQ acceptor has been prepared and structurally characterized. The crystal packing shows that the donor and acceptor molecules are organized in a mixed stacking arrangement consistent with its insulating behaviour. EPR and magnetic susceptibility data support intramolecular ferromagnetic interactions between the TTF and the verdazyl radicals and antiferromagnetic interactions between TTF donors within a stack. In an attempt to increase the intramolecular exchange interaction between the two radicals, a TTF-x-(diisopropyl)verdazyl radical (IX) was prepared, where the two radicals are connected ia a conjugated divinylene linker. The neutral radical donors stack in a more favourable head-to-head arrangement but the bulky isopropyl groups prevent the donor radicals from stacking close enough together to facilitate good orbital overlap. [Molecular diagram available in pdf].

The neoliberalization of street vending policy in Lima, Peru: the politics of citizenship. property and public space in the production of a new urban marginality

Neoliberalism is having a significant and global impact on political, social and economic life across spaces. This work illustrates how neoliberalism is attempting to change the ways in which the urban poor - particularly those that participate in street vending - use urban spaces in Lima, Peru. Using municipal policies, newspaper articles and local academic texts I argue that there is a changing marginality in Lima that is being experienced by street vendors, and currently in los canas of Lima. In particular, I discuss formalization, a neoliberal strategy in street vending policy, which is used with eradication and social assistance strategies in attempts to re-regulate street vendors.