A genetic catalogue was generated from expressed sequence tags (ESTs) from the pathogenic filamentous fungus Ophiostoma novo-ulmi. Rather than full sequencing of the entire genome, fragments of each gene being actively expressed at a specific point in time were catalogued and annotated for identity and function. This catalogue represents a resource of considerable depth for the purposes of gene discovery, genetic regulation, protein expression, pathogenicity, and growth state studies. An online database was generated to serve as a powerful tool for downstream applications, facilitating and enhancing future research in all of these important areas of fungal biology. The ascomycetous fungus Ophiostoma novo-ulmi represents an excellent model organism for genetic experimentation. A diversity of physiological functions, including dimorphism, pathogenicity, melanin biosynthesis, and glycoprotein secretion at high levels mean that principles elucidated from this fungus are likely of broad application. Ophiostoma novo-ulmi has been identified as the causative agent of Dutch elm disease, which has become an economic and horticultural pandemic in North America. As a result, the mechanisms of host-pathogen interaction of this fungus are of particular interest. Initial attempts at disruption of pathogenicity, most commonly by disruption of single genes identified as potential pathogenicity factors, have met with little success. As our understanding of the complexity and co-ordination of proteins involved with host-pathogen interaction deepens, the discovery of a single dominant pathogenicity gene is becoming increasingly unlikely. As such, a broader genomics approach was employed to work towards identification of groups, or networks of genes that operate in a concerted manner, regulating pathogenicity or parasitic fitness. A low redundancy library was constructed from Ophiostoma nova-ulmi complementary DNA, producing a total of 4386 readable expressed sequence tags (ESTs) from 5760 clones. Of these, 2093 sequences matched with sequences found in public databases while 2293 represented orphan sequences. Of the sequences in the former group, 1761 sequences matched with known proteins while 332 sequences matched with hypothetical/predicted proteins. Sequences matching known proteins included 880 singletons, corresponding to 49.97 % of the ESTs in this category. Extrapolating this proportion to the sequences matching hypothetical proteins estimated the number of singletons in this category to be 166. Similarly, 1835 orphan sequences were estimated to contain 917 unique sequences. Singletons matching entries in public databases (n=880) were manually annotated into functional categories as established by the Munich Information Centre for Protein Sequences (MIPS). Metabolism (21%), Protein Synthesis (10%), Subcellular Localization (10%), Biogenesis of Cell Components (8%), and Transcription (8%) categories were the most highly represented.

Singly-periodic (SP) and doubly-periodic (DP) graphs arc infinite graphs which have translational symmetries in one and two dimensions, respectively. The problem of counting the number of connected components in such graphs is investigated. A method for determining whether or not an SP graph is k-colourable for a given positive integer k is given, and the question of deciding k-colourability of DP graphs is discussed. Colourings of SP and DP graphs can themselves be either periodic or aperiodic, and properties which determine the symmetries of their colourings arc also explored.

This study investigated the developing identities of first generation Canadian female adolescent women. Using qualitative methodology, it seeks to illuminate the intersectionalities of race, gender and sexuality in its analysis. Transnational feminist frameworks are used as theoretical lenses from which to critically examine the ways in which identity development research has been portrayed in psychology, child and youth care, and related disciplines. This analysis was used as a means to complicate objective, hierarchical models of identity development as they apply (or do not apply) to the stories of first generation Canadian women. Five women between the ages of 19-26 of Chinese, Latin American, Vietnamese and Indian decent participated in this study. Semi-structured interviews were conducted, covering family background and traditions, gender role negotiation, sexuality and identity development. Findings support transnational feminist notions of multiplicity, hybridity and fluidity in identity development. They provided context and storied analysis to issues of identity development that are often silenced in traditional psychology literature. The stories of first generation Canadian women are important contributions to identity development research. They highlight the need for situated knowledges and the need for anti-racist research frameworks in psychology, child and youth care, and social science disciplines.

The central focus of this thesis is an exploration of how mothers in prison construct a sense of self as mothers according to motherhood ideologies and reconstruct this sense of self as a result of imprisonment. The study, informed by feminist poststructuralism, shows how relations of power/knowledge shape the experiences of women in prison leading to marginalization. The notion of the constitution of subjectivities through discourses offers `other' ways to see the lives of imprisoned mothers, destabilizing assumptions and constructed truths and challenging fixed frameworks of meaning and truth surrounding motherhood. The research methodology employed was a qualitative approach based on `interpretive interactionism'. The premise of this approach was to make visible and accessible to the reader, the problematic lived experiences of the participants through their stories. The research methods involved interviews with six imprisoned women who shared stories of their experiences being mothers. The analysis involved an interpretation of the meanings participants applied to mothering in prison, expressed by their feelings, thoughts and practice of mothering. The participants' position as mothers within a prison institution was met with daily challenges as they sought out ways to have relationships with their children and maintain a sense of self as mothers. The research showed that even in a restricted prison environment of limited choices participants were able to be agents of choice and possibilities. The study shows that the participants resisted dominant ideologies of motherhood and maintained a sense of being mothers through connections with their children, with each other, as well as through self-reflection and harbouring hopes and dreams for the future. Feminist poststructuralism provided the tools for revealing the possibilities of alternative ways of mothering in prison that did not hinge on being either `good' or `bad' mothers.

In preparation for the ATLAS experiment at the LHC at CERN. the high pseudorapidity region (|n| > 2.5) of the ATLAS end-cap liquid argon calorimeters underwent particle beam testing in 2004. One of the main goals of these tests is to study energy reconstruction in the complex interface region between the electromagnetic. hadronic, and forward calorimeters at. 1 - 3.2. These detectors were exposed to beams of electrons and pions with energies ranging from 6 GeV to 200 GeV. Three methods of calibration in the electromagnetic end-cap calorimeter (EMEC) are studied and compared to the results of a previous beam test. of the EMEC. The electromagnetic scale factor (aEM) is computed and compared to the previous beam test value. Studies of the energy response and resolution of the high pseudorapidity region of the three end-cap calorimeters to the particle beam position scans are given.

Transport in nanostructures and on-chip detection using nanohole arrays are investigated using a combination of analytical, numerical and experimental techniques. The first half of the thesis describes a fundamental theoretical contribution to the study of nanofluidic species transport. The second half of the thesis describes an applied experimental application of nanostructure-based species detection in a microfluidic framework. A continuum based analytical solution and numerical model are developed to quantify ionic dispersion of charged and neutral species in nanochannels and identify fundamental dispersion mechanisms unique to nanoscale flows. Ionic dispersion for circular cross-section nanochannels is quantified as a function of a valance parameter. the relative electrical double layer thickness. and the form of the velocity profile. Two unique mechanisms governing ionic dispersion in both pressure- and electrokinetically driven flows are identified. The results of the analytical solution are supported and extended by the results of the numerical model. Collectively, these results indicate that dispersion of ionic species in nanoscale channels is markedly charge dependent and substantially deviates from that of neutral solutes in the same flow. A microfluidic device with a set of embedded nanohole array surface plasmon resonance sensors is developed and successfully demonstrated experimentally as a chemical/biological sensor. The device takes advantage of the unique optical properties. the surface-based sensitivity, the transmission mode operation. relatively small footprint, and repeatability characteristic of nanohole arrays. Proof-of-concept measurements are performed on-chip to detect changes in liquid refractive index at the array surface. proportional to change in near wall concentration or indicative of a surface binding event. Employing a cross-stream array of nanohole arrays. the device is applied to detect microfluidic concentration gradients as well as to detect surface binding in the assembly process of a cysteamine monolayer-biotin-streptavidin system.

Video compression technology aims at compressing large amount of video data for efficient transmission and storage without significant loss of quality. Most video compression techniques rely on removing temporal data redundancy between frames using motion estimation and motion compensation techniques which are generally very computationally expensive. The objective of the research done in this thesis is to develop new efficient motion estimation techniques that reduce the computational complexity of motion estimation. The thesis presents a new prediction technique referred to as weighted sum block matching (WSBM) which dynamically reduces the computational complexity by limiting the search to a small subset of the search area. Simulation results have shown that adding WSBM to some well-known search algorithms reduces their computational complexity by 6-1.5 without affecting the visual quality of the reconstructed video frames. The thesis also presents two new algorithms based on the simplex optimization method. the simplex based block matching algorithm (SMPLX) and the flexible triangle search (FTS). Both techniques use a triangle that moves inside the search area and checks only positions that lie at its vertices. As a result the computational complexity of the search is reduced since it depends directly on the number of positions checked. The techniques can change the size and orientation of the search triangle during the search. The changes make the search highly flexible and efficient and reduce the number of search positions to be checked compared to those in other search algorithms. The SMPLX uses equations based on the simplex optimization method to compute the new triangle size and orientation. The FTS, on the other hand, was implemented to be more suitable for a digital search grid by using look-up tables and integer computations. The two algorithms were implemented as part of the H.263 and H.264 encoders. Both algorithms were compared to the state of the art motion search algorithms. Experimental results showed that both algorithms can reach sub-optimal solutions while checking fewer search positions compared to other algorithms which results in lower computational complexity as a consequence. Additional research was done to analyze and further improve FTS performance. As a result, various extensions of the FTS have been developed such as the enhanced FTS (EFTS), the half-pixel FTS (HP-FTS). and the predictive FTS (PETS). These extensions were also implemented as part of the H.263 and H.264 encoders. In the EFTS. repeated computations are reduced by caching intermediate results. In addition. the termination condition is modified to avoid premature exit. These modifications reduce the computational complexity of the FTS by up to 4%%. The HP-FTS extended the FTS so that the search can be done at half-pixel resolution instead of full-pixel resolution. The commonly used approach for half-pixel search is based on two separate stages. i.e., full-pixel search followed by half-pixel search. By combining the two stages in HP-FTS. the overall computational complexity can be reduced by an average of 13% without affecting the produced quality or compression ratio. The PETS uses prediction to select the direction of the starting search triangle. Analysis results show that the proper selection of the starting search triangle has great effect on the performance of the FTS. Simulation results show that the PFTS can reduce the computational complexity of the FTS by 7-13%. Finally, hardware designs for the FTS and the full search (FS) algorithms are proposed. The FS was chosen due to its regularity, low control overhead, and suitability for hardware implementation. It uses a high degree of parallelism and pipelining in order to improve the computational efficiency. The FTS requires less computation and thus provides high processing rates. Both designs were implemented, simulated, and verified using VHDL and then synthesized with Xilinx FPGAs. Simulation results have shown that both hard-ware implementations are more efficient than other existing implementations in terms of performance and hardware usage.

A new nanostructure for enhancing transmission and local field intensity in thin metal films is presented. The novel double-hole array design was numerically modelled using a finite-difference time-domain technique. Simulations were performed for different array periodicities and hole spacing to optimize the structure for maximum enhancement capabilities. An optimum double-hole array was able to produce simultaneous increase in transmission and near-field intensity. The local field enhancement was found to be 4 orders of magnitude greater than the incident field and strongly localized to a nanoscale area which is promising for a variety of applications. Arrays of the double-hole design were fabricated using a focussed-ion beam on a thin gold film. Linear measurements through the milled arrays showed the predicted enhancement in transmission for the optimum double-hole configuration. Finite-difference time-domain calculations were also done to study an isolated rectangular aperture to show the dependence of transmission on polarization of the incident beam and width of the aperture. Fabry-Perot resonances were shown to exist for different film thicknesses and the phase of reflection was calculated from the transmission results. A microfluidic device with an embedded surface plasmon sensor was developed and its sensitivity to changes in refractive index was shown.

Traumatic brain injury (TBI) damages many regions of the brain but damage to the hippocampus has been particularly linked to functional deficits in memory and wayfinding (i.e., finding one's way in familiar and unfamiliar environments). The current study investigated the nature of these wayfinding problems using a virtual simulation of a Morris water maze, a standard test of hippocampal function in laboratory animals. Eleven TBI survivors and 12 comparison participants, matched for gender, age and education were tested to see if they could find a location in a virtual room marked by a) a visible platform, b) a single object, c) one object of 8 different ones, or d) distal room cues (which requires cognitive mapping). TBI survivors were impaired at finding the location based on room cues but not when the other cues were present. These results indicate that TBI impairs cognitive mapping but not associative processes in wayfinding.

Because of low-cost optical devices and virtually unlimited bandwidth, optical wireless communications (OWC) for indoor wireless local area networks (WLANs) have recently become an attractive alternative to radio frequency systems. Since optical signals cannot penetrate through walls or other opaque barriers, the security of infrared WLANs is very high and there is no interference between rooms. Subsequently, cell planning is simple and easy, and the potential capacity of an optical-based network in a building is extremely high. However, the system link is susceptible to path loss and multipath dispersion. In addition, the average transmit power is constrained by eye-safety regulations and power consumption concerns. Hence, most recent research deals with the physical layer aspects such as modulation, equalization and error-control coding in order to cope with these draw-backs, especially the effects of multipath dispersion. The objective of this thesis is to study practical signaling techniques capable of eliminating the effects of intersymbol interference (ISI). Regarding the drawbacks of OWC, modulation schemes which are power and band-width efficient are considered. Pulse-position modulation (PPM) has been employed for IrDA and IEEE802.11 standards because it offers high power efficiency. However, it re-quires high bandwidth so that its performance is considerably degraded when the channel is more corrupted by ISI. A number of modified PPM techniques have been proposed to improve bandwidth efficiency. This thesis introduces a hybrid between pulse-amplitude modulation (PAM) and differential pulse-position modulation (DPPM), named differential amplitude pulse-position modulation (DAPPM), in order to gain a better compromise be¬tween power and bandwidth efficiency. It yields better bandwidth and/or power efficiency than PAM, PPM and DPPM depending on the number of amplitude levels (A), and the maximum length (L) of a symbol. The channel capacity of PPM, DPPM and DAPPM systems is investigated. Since these modulation schemes over an ISI channel can be represented by a trellis diagram, their channel capacity is determined using a method for calculating the capacity of a Markov process channel. Over a soft-output channel, DAPPM achieves a higher capacity and is less sensitive to multipath dispersion than PPM and DPPM. Moreover, the comparison of hard-decision decoding (HDD) and soft-decision decoding (SDD) for PPM and DPPM systems shows that the performance of SDD is superior to that of HDD, especially when the channel is dispersive. Then, some soft-decision techniques for DPPM system are considered. Although maximum-likelihood sequence detection (MLSD) is the optimal SDD for DPPM system, its complexity is extremely high. This thesis examines SDDs which are less complex than MLSD, but have performance close to that with MLSD. As the DPPM system is a Markov pro¬cess, maximum a posteriori (MAP), Max-Log-MAP and the soft-output Viterbi algorithm (SOVA) are adopted. In addition, a novel very low complexity soft-decision decoding algorithm is introduced. The performance of the proposed algorithm is independent of the knowledge of the channel model, while the performance of the optimal and suboptimal MAP algorithms is impaired when the receiver has no information about the channel. Finally, to achieve lower power requirements, error-control coding in an OWC system is investigated. Because insertion and deletion errors exist in DPPM systems, conventional coding techniques cannot be used. This thesis presents the concatenation of marker and Reed-Solomon codes which is able to correct such errors. The coded systems with HDD and SDD are examined by analysis and simulation.