Records of abundance of salmon that return to their natal spawning stream (escapements) are important indices that can assist with monitoring, conservation, and management of a salmon population over time. On their own, however these data reveal very little about the habitat, ecosystem and human communities that salmon encounter on their journey from freshwater to sea and back again. This research examines monitoring protocols for Goldstream River salmon stocks (coho, chinook and chum Pacific salmon). It includes and reaches beyond biostatistics from stream surveys to gauge First Nations’ artisanal fishing activities at Goldstream River and Saanich Inlet as well as their commercial chum fishing endeavours in Saanich Inlet on south Vancouver Island, British Columbia. Methods included summations of major themes from interviews on traditional ecological knowledge (TEK) shared by local Saanich First Nation fishers whose families have lived in the communities around Goldstream River and Saanich Inlet for more than 200 years. Analyses of Goldstream salmon escapements for the period 1932 to 2004 and native harvest statistics of chum caught from Saanich Inlet between 1982 and 2004 are integrated with results from analysis of TEK research undertaken for this project. Key recommendations arising from the results of this research are: stream habitat restoration in response to loss and degradation of salmon-bearing streams; modification of stream survey procedures to measure for morphological and physiological attributes including indicators of the health of Goldstream salmon; monitoring and eliminating sources of pollution to Saanich Inlet waters; implementing precautionary measures to ensure that overfishing of Goldstream salmon and shrimp in Saanich Inlet does not recur; and safeguarding naturally abundant Goldstream chum populations at the river. Under current management of the Goldstream chum fishery, the maximum carrying capacity (K) or target escapement of chum that the Goldstream River spawning grounds sustain is 15,000. Based on population assessments as well as physiography and ecosystem dynamics, I infer that Goldstream River’s K for its natural chum population is between ~16,000 and 18,000; ~1,500 for the mixed stocks of natural and hatchery enhanced coho; and ~50 for chinook (based on the river’s naturally occurring populations between 1932 and 1973) or ~385 enhanced chinook (based on the returning population from 1975 to 2002 since hatchery enhancement took place). A co-management relationship exists between Fisheries and Oceans Canada (DFO) resource managers and the Saanich First Nations bands (Saanich Tribal Fisheries councilors). Improvements to communication, collaboration and information sharing between DFO resource managers, Goldstream hatchery operators and Saanich First Nations with regards to decisions made about Goldstream salmon stocks are, however, necessary. In this thesis, I propose a model with recommendations for compatible fisheries management goals and techniques including adaptive management and ecosystem-based management to address this problem.

Research into the phenomenon of youth suicide is typically guided by quantitative methodologies focused on young people who have attempted or died by suicide. Questions related to epidemiology, etiology, and the development of actuarial measures of risk are often the drivers of these particular kinds of research. Similarly, research into school-based youth suicide prevention curricula is predominantly focused on quantitative measures of the degree to which young people acquire knowledge or change attitudes about suicide, after exposure to a delivered program. Grounded in post-structural ideas, the purpose of this thesis is to expand upon these mainstream inquiries into youth suicide prevention education through close exploration and analysis of how “suicide” is discursively produced within the context of a classroom delivered curriculum. This study will pay particular attention to the discursive productions of suicide in the curriculum, as well as how these productions result in the constitution of particular objects, concepts, and subjectivities. Transcripts of “naturally occurring classroom talk” will serve as the site of analysis. Troubling contemporary “truth regimes” about suicide and its prevention through close analysis of the discursive frames by which they are produced offers up the potential of re-imagining new possibilities for thinking about and delivering youth suicide prevention education.

The successful execution of goal-directed movement requires the evaluation of many levels of errors. On one hand, the motor system needs to be able to evaluate ‘high-level’ errors indicating the success or failure of a given movement. On the other hand, as a movement is executed the motor system also has to be able to correct for ‘low-level’ errors - an error in the initial motor command or change in the motor command necessary to compensate for an unexpected change in the movement environment. The goal of the present research was to provide electroencephalographic evidence that error processing during motor control is evaluated hierarchically. The present research demonstrated that high-level motor errors indicating the failure of a system goal elicited the error-related negativity, a component of the event-related brain potential (ERP) evoked by incorrect responses and error feedback. The present research also demonstrated that low-level motor errors are associated with parietally distributed ERP component related to the focusing of visuo-spatial attention and context-updating. Finally, the present research includes a viable neural model for hierarchical error processing during motor control.

Objective: The Six Elements Task (SET; Shallice and Burgess, 1991; Burgess et al., 1996) measures examinees’ ability to plan and organize their behaviour, form strategies for novel problem solving, and self-monitor. The task has adequate specificity (Wilson et al., 1996), but questionable sensitivity to mild impairments in executive function (Jelicic, et al., 2001). The SET is vulnerable to practice effects. There is a limited range in possible scores, and ceiling effects are observed. This dissertation sought to evaluate the validity and clinical utility of a modification of the SET by increasing the difficulty of the test, and expanding the range of possible scores in order to make it more suitable for serial assessments. Participants and Methods: The sample included 26 individuals with mixed acquired brain injury, and 26 healthy matched controls (20 – 65 years). Participants completed a battery of neuropsychological tests on two occasions eight weeks apart. To control for confounding variables in executive function test performance, measures of memory, working memory, intelligence, substance abuse, pain, mood and personality were included. Self and informant reports of executive dysfunction were also completed. The two groups’ performances on the various measures were compared, and the external validity of the 12ET was examined. In addition, normative data and information for reliable change calculations were tabulated. Results: The ABI group exhibited very mild executive function deficits on established measures. The matched control group attempted more tasks on the 12ET, but the difference was non significant. Neither group tended to break the rule of the task. The 12ET showed convergent validity with significant correlations with measures of cognitive flexibility (Trailmaking B and Ruff Figural Fluency), and a measure of planning (Tower of London). The 12ET and published measures were also significantly correlated with intelligence in the brain-injured group. The 12ET did not show divergent validity with a test of visual scanning speed (Trailmaking A). No demographic variables were found to be significant predictors of 12ET performance at Time 2 over and above performance at Time 1, and both participant groups obtained the same benefit from practice. The 12ET did not suffer from ceiling effects on the second administration, and the test-retest reliability of the 12ET variables ranged from low (r = .22 for Rule Breaks in the brain-injured group) to high (r = .78 for Number of Tasks Attempted in the control group). Conclusions: Despite their (often severe) brain injuries, this sample of brain injured participants did not demonstrate executive impairments on many published tests and their scores were not significantly different from the control group’s scores. Therefore, it was not possible to determine if the 12ET was a more sensitive measure of mild executive deficits than the SET. However, the increase in range did reduce the tendency for participants to perform at ceiling levels. The 12ET showed a number of significant correlations with other executive measures, particularly for the brain-injured group, though these correlations may have been moderated by general intelligence. Two variables of the 12ET, deviation from the optimal amount of time per task and Number of Tasks Completed, showed promise as measures of reliable change in this sample over an 8-week interval.

Plasticity in spinal networks has been proposed as a means to permit motor skill learning and recovery after central nervous system disorders. This plasticity is significantly driven by input from the periphery (Wolpaw & Carp, 2006). For instance, attenuation of soleus Hoffmann (H) reflex can last beyond the period of different types of conditioning via putative presynaptic inhibition (Brooke et al., 1997). Interestingly, rhythmic arm cycling can also attenuate soleus H-reflex via interlimb connections and presynaptic pathways (Frigon, Collins, & Zehr, 2004). However, it remains to be studied if this attenuation is maintained beyond the period of arm cycling. In this study, we hypothesized that excitability of H-reflex pathway would remain suppressed after cessation of arm cycling. Subjects were seated with their trunk and feet fixed at a neutral position. Using an arm ergometer, they cycled at 1Hz for 30min. H-reflexes were evoked via stimulation of the tibial nerve in the popliteal fossa at 5 minute intervals. These intervals began prior to the cycling and continued during cycling and up to 30 minutes iv after termination of cycling (n=12). Besides soleus muscle, electromyography was recorded from tibialis anterior, vastus lateralis and biceps femoris. Stimulation was set to evoke an M-wave which evoked an H-reflex on the ascending limb of the recruitment curve (size was 75% Hmax) obtained prior to cycling. The M-wave amplitude was maintained throughout all trials by monitoring and adjusting the level of stimulation intensity. All H-reflex and M-wave data were normalized to the averaged Mmax to reduce inter –subject variability. The main result was that the suppression of H-reflex amplitude persisted beyond the period of arm cycling. H-reflex amplitudes were significantly (p<0.05) smaller up to 20 min after arm cycling had stopped. This suggests that arm cycling can induce plastic adaptation in the soleus H-reflex pathway that persists well beyond the period of conditioning. Also, in an additional experiment (n=8), the prolonged effect of arm cycling combined with superficial radial (SR) nerve stimulation was investigated. Interestingly, this cutaneous nerve stimulation cancelled out the prolonged suppression of H-reflex amplitude induced by arm cycling. Since SR nerve stimulation facilitates soleus H-reflex via reductions in the level of Ia presynaptic inhibition (Zehr, Hoogenboom, Frigon, & Collins, 2004), persistence in presynaptic inhibitory pathways is suggested as an underlying neural mechanism. These results have relevance for optimizing rehabilitation techniques in the treatment of spasticity which is known to be related to the H-reflex size (Levin & Hui-Chan, 1993).

The overall theme of this dissertation is the genomic analysis of poxviruses using bioinformatics. The first analysis presented in this dissertation (Chapter 2) focuses on a new method for predicting which open reading frames (ORFs) in poxviruses are likely to be expressed. A measure that takes into account the amino acid and purine content of all predicted open reading frames (ORFs) in the genome was developed and when used on the vaccinia virus (VACV) strain Copenhagen genome (training case), the measure had a success rate of 94%. Using the measure on an extremely adenine and thymine rich entomopoxvirus (test case), 241 ORFs were found to be potentially expressed and 51 ORFs were likely not expressed although further biochemical experiments will be required to confirm this result. The second analysis of this dissertation (Chapter 3) focuses on determining the nature of an interesting background pattern similar to a set of stripes that was observed while analyzing a self-dotplot of the molluscum contagiosum virus genome. These stripe regions were further analyzed and were found to have a nucleotide composition and amino acid usage that was different to the remainder of the genome. Given this differing nucleotide and amino acid usage, the genes contained in these stripe regions are thought to have been recently acquired from the host or another virus, making these regions similar to bacterial pathogenicity islands. The third analysis of this dissertation (Chapter 4) focuses on predicting the function of “unknown” poxvirus proteins by using a hidden Markov model (HMM) comparison search tool to scan all “unknown” proteins in the VACV genome looking for any database matches that may have been missed by conventional approaches (BLASTp and PSI-BLAST). One protein, the VACV G5R protein, in this scan showed a promising hit (96% probability) to an archaeal flap endonuclease (FEN-1) protein. A structural model of the G5R protein was created and subsequently compared to the crystal structure of the human FEN-1 protein and was found to be highly conserved in both secondary and tertiary structure and with three of the five main features of the FEN-1 protein including the active site suggesting that the G5R protein should be classified as a flap endonuclease protein. Related to the analysis in Chapter 4, are the results presented in Chapter 5 of this dissertation that focus on locating a protein encoded by the VACV genome that is similar to proliferating cell nuclear antigen (PCNA). Knowing that the FEN-1 protein requires PCNA as an intermediary to contact DNA, the genome of VACV was scanned using InterProScan in order to identify any potential proteins that were similar to PCNA. One protein (VACV G8R) was identified and subsequently modeled and compared to the crystal structure of the human PCNA protein. The secondary and tertiary structure was highly conserved between the two proteins suggesting that the G8R protein should be classified as a sliding clamp similar to human PCNA.

Abstract This dissertation is a narrative unraveling of a process of human transformation that interrupts the psyche’s propensity for creating the conditions for suffering. The self privileging of ego consciousness is posited as the origin of suffering. Temporary relief from suffering is accomplished by bringing forward the content of the unconscious. The condition that allows the content of the unconscious to come forward is disrupting the boundary separating consciousness and the unconscious. This boundary is established when reprehensible content regarding the self is repressed by an ego consciousness that thereby privileges itself. Disruption of the boundary separating ego consciousness and the unconscious allows for reintroduction of the previously repressed content to consciousness. As the boundary fails and ego consciousness is dethroned, unforeseen yet yearned for knowledge becomes available to consciousness thereby initiating the possibility for transformation and hence the momentary release from suffering. Implicit in this research are assumptions of self-motivation and self-organization that configure a theory of autopoiesis or self-making. Observed and observer selves are continually reshaped through continuous interaction in the psychosocial and physical environment. In this study this interaction is made visible through autobiographical narratives in which participant selves each demonstrate and share the insight of observer and observed. This narrative interaction is the simultaneous accomplishment and display of the process of human transformation. This transformation is always only momentary. It is a single moment in the ongoing expansion and contraction of the human psyche. Each transformative event reduces the potential for being irretrievably caught in continuous suffering. Each temporary release from suffering is a waypoint on the pathway of self-realization. The transformative process as presented in this study goes beyond existing accounts of consciousness change found in the annals of psychological methodologies, although Jungian terminologies are borrowed to describe loosely shared conceptual constructs. The aim in employing autobiographical narrative is to portray this elusive process as it is experienced including all its subtleties and nuances.

This study examines the experiences of five teachers who lead and participate in adventure biking trips with students. The narrative case study was framed by the author’s autoethnographic writing: her personal narratives about leading adventure education trips, teaching experiences and reflections on the concept of learning. The meaning four other trip leaders made of their adventure biking experiences was investigated through conversational style interviews characterized by open ended questions and a list of issues to be explored. The purpose of the study was two-fold: to discover what meaning teachers make of adventure bike trip experiences and what happens when teachers collectively explore that meaning in relation to their teaching practice. The voices of the participants uncovered four meaningful elements of the trip experience: personal challenge, shifting perceptions of students and student learning, the opportunity to shed the teacher facade and positive collaboration with colleagues. As the participants collectively reflected upon these meanings they began to examine their in-school teaching practices in relation to the trip spaces. Tension between the two spaces opened up a dialogue where the participants began to challenge their teaching identity, enabling them to imagine their classrooms in a different light. The results of this study point to the need for teachers to have opportunities to participate in unique and novel teaching experiences (such as the adventure education trip) that hold within them the potential to initiate change in practice. In order to challenge education experiences, time and space need to be provided for teachers to reflect and develop teacher knowledge that can transfer into the development of positive, effective learning communities with colleagues and in their classrooms.

Raman spectroscopy is a form of vibrational spectroscopy that is capable of probing biological samples at a molecular level. In this work it was used in the analysis of ionizing radiation-induced damage in DNA. Spectra of both simple, short-stranded DNA oligomers (SS-DNA) and the more complicated calf-thymus DNA (CT-DNA) were acquired before and after irradiation to a variety of doses from 0 to ~2000 Gy. In a technique known as ultraviolet resonance Raman spectroscopy (UVRRS), three UV wavelengths of 248, 257 and 264 nm were utilized in order to selectively enhance contributions from different molecular groups within the samples. Assignment of the spectral peaks was aided by the literature, as well as through analysis of UVRR spectra of short strands of the individual DNA bases obtained at each of the three incident UV wavelengths. Difference spectra between the irradiated and unirradiated samples were calculated and the samples exposed to ~2000 Gy showed significant radiation-induced features. Intensity increases of spectral peaks, observed primarily in the CT-DNA, indicated unstacking of the DNA bases and disruption of Watson-Crick hydrogen bonds, while intensity decreases of spectral peaks, observed only in the SS-DNA, indicated both base damage and the loss of structural integrity of the DNA molecule. The high molecular specificity of UVRRS allowed for precise identification of the specific bonds affected by the radiation, and the use of the varying incident wavelengths allowed for the observation of damage to moieties that would otherwise have been excluded. The use of UVRRS shows promise in the study of radiation-induced damage to DNA and would be well suited for extension to the study of more complicated biological systems.

Multidisciplinary Design Optimization (MDO) is an area in engineering design which has been growing rapidly in terms of applications in the last few decades, aircraft design being no exception to that. The application of MDO to aircraft and more specifically, wing design, presents many challenges, since disciplines like aerodynamics and structures have to be combined and interact. The level to which this interaction is implemented depends only on how much one is willing to pay in terms of computational cost. The objective of the current work is therefore to develop a simplified MDO tool, suitable for the preliminary design of aircraft wings. At the same time, versatility in the definition of optimization problems (in terms of design variables, constraints and objective function) is given great attention. At the same time, modularity will ensure that this framework is upgradeable with higher-fidelity and/or more capable modules. The disciplines that were chosen for interaction were aerodynamics and structures/ aeroelasticity, though more data can be extracted from their results in order to perform other types of analyses. The aerodynamics module employs a Vortex Lattice code developed specifically for the current implementation of the tool. The structural module is based on Equivalent Plate model theory. The fluid structure interaction is simply one-way, wherein the aerodynamics loads are passed on to the structural analyzer for computation of the static deformation. Semi-empirical relations are then used to estimate the flutter speed. The optimizer, which controls the activity of the other modules, makes use of a gradient based algorithm (Sequential Quadratic Programming) to search for a local minimum of a user defined objective function. Among the myriad of MDO strategies available, two are chosen to exemplify the modularity of the tool developed: Multidiscipline Feasible (MDF) and Sequential Optimization (SO), and their results are compared. Several case studies are analyzed to cover a broad spectrum of the capabilities of the framework. Because user interaction is of prime concern in design optimization, a graphical interface (GUI) of the tool is presented. Its advantages in terms of the set up of optimization problems and post-processing of results are made clear. In conclusion, some topics for future work regarding the expansion and improvement of the features of the application are noted.