VictorJuiz/thesis huggingface dataset:
Gaussian Process Regression with Heteroscedastic Residuals and Fast MCMC Methods

Gaussian Process (GP) regression models typically assume that residuals are Gaussian and have the same variance for all observations. However, applications with input-dependent noise (heteroscedastic residuals) frequently arise in practice, as do applications in which the residuals do not have a Gaussian distribution. In this thesis, we propose a GP regression model with a latent variable that serves as an additional unobserved covariate for the regression. This model (which we call GPLC) allows for heteroscedasticity since it allows the function to have a changing partial derivative with respect to this unobserved covariate. With a suitable covariance function, our GPLC model can handle (a) Gaussian residuals with input-dependent variance, or (b) non-Gaussian residuals with input-dependent variance, or (c) Gaussian residuals with constant variance. We compare our model, using synthetic datasets, with a model proposed by Goldberg, Williams and Bishop (1998), which we refer to as GPLV, which only deals with case (a), as well as a standard GP model which can handle only case (c). Markov Chain Monte Carlo methods are developed for the GPLC and GPLV models. Experiments show that when the data isheteroscedastic, both GPLC and GPLV give better results (smaller mean squared error and smaller negative log-probability density) than standard GP regression. In addition, if we do not assume Gaussian residuals, our GPLC model (as in case (b) above) is still generally nearly as good as GPLV when the residuals are in fact Gaussian. When the residuals are non-Gaussian, our GPLC model is better than GPLV.Evaluating the posterior probability density function is the most costly operation when Markov Chain Monte Carlo (MCMC) is applied to many Bayesian inference problems. For GP models, computing the posterior density involves computing the covariance matrix, and then inverting the covariance matrix. The computation time for computingthe covariance matrix is proportional to pn2, and for the inversion is proportional to n3, where p is the number of covariates and n is the number of training cases. We introduce MCMC methods based on the "temporary mapping and caching" framework (Neal, 2006), using a fast approximation, *, as the distribution needed to construct thetemporary space. We propose two implementations under this scheme: "mapping to a discretizing chain", and "mapping with tempered transitions", both of which are exactly correct MCMC methods for sampling , even though their transitions are constructed using an approximation. These methods are equivalent when their tuning parameters are set at the simplest values, but differ in general. We compare how well these methods work when using several approximations, nding on synthetic datasets that a * based on the "Subset of Data" (SOD) method is almost always more efficient than standard MCMC using only On some datasets, a more sophisticated * based on the "Nystrom-Cholesky" method works better than SOD.

Keywords: Bayesian Analysis
Gaussian Process
Heteroscedasticity
Markov Chain Monte Carlo
Advisor: Neal, M Radford
Multiculturalism Policies: Identifying the Dialectic of the "Ideal Type" within the Practices of Canadian Nursing

Since Canada's first multiculturalism policy in 1971, there has been an influx of Internationally Educated Nurses (IENs) of colour to Canada. Studies show IENs occupying low-paid menial positions, while being excluded from policy-making leadership positions. Colonial values currently function through the notion of the "ideal type", a term defined as a nurse who is white, middle class and occupying policy-making leadership roles. Within Canadian nursing, there appears to be a dialectic relationship between multiculturalism policies and the ideal type that become camouflaged by the term I have identified as the "hybrid space." The hybrid space consists of public health nurses, clinicians, clinical case coordinators, and unit leaders who are registered nurses that work on the front-line with minimal leadership responsibilities. Although these nurses have comparable qualifications as their Canadian-born counterpart, they are not groomed into policy making leadership roles, but rather remain fixed in the hybrid-space. Through the experiences of IENs, this study shows how the dialectic relationship helps in maintaining Canada's favourable position within the global market. Post colonial theory, antiracist feminism and Black Canadian feminist thought were used as theoretical frameworks to expose issues of racism and inequalities within the hybrid space. In-depth interviews, a qualitative methodology, explored the experiences of these IENs in the hybrid space. Ten IENs of colour who were from the United Kingdom and the ex-British colonies (India and the Caribbean) were recruited using the snowball method. The research uncovered several major themes such as, Non-Recognition, No Leaders of Colour at the Top, Faith and Spirituality and Valuing Their Heritage. The themes were divided into two further categories: 1) Challenges and 2) Resistance. Although the hybrid space was challenging, the IENs used these barriers as spaces of resistance in order to survive.

Keywords: hybrid space
Ideal Type
Internationally Educated Nurses of Colour
Multiculturalism discourses
racism
spaces of resistance
Advisor: Magnusson, Jamie-Lynn
Progesterone and its Metabolites: Anticonvulsant and Behavioral Studies

AbstractProgesterone is a well-known anticonvulsant neurosteroid. Progesterone's inhibitory effects in the brain have long been attributed to its secondary metabolite, 3-alpha,5-alpha-tetrahydroprogesterone (THP, also known as allopregnanolone), a powerful positive modulator of GABA-A receptors. Behavioral and electrophysiological studies of progesterone and its metabolites were conducted for this thesis. Behavioral ExperimentsRecent studies in our laboratory suggested that the primary progesterone metabolite 5-alpha-dihydroprogesterone (DHP) might have anticonvulsant effects in amygdala-kindled rats. Simple measures of sedation and ataxia were minimal in kindled rats treated with anticonvulsant doses DHP and THP. We therefore hypothesized that anticonvulsant doses of DHP and THP (5-10 mg/kg) would not cause psychotoxicity.Anticonvulsant doses of DHP and THP were tested in the elevated plus maze, the forced swim test, open field test, and the Morris water maze, models of anxiety, depression, locomotion, and learning and memory, respectively. No psychotoxicity was found the forced swim test, the open field test or the elevated plus maze. Minimal psychotoxicity was observed in the Morris water maze.Electrophysiology ExperimentsPilot studies in our laboratory had also indicated that progesterone might have anticonvulsant effects in mice independent of its metabolites. We hypothesized that progesterone had a non-GABAergic, non-THP-mediated mechanism of anticonvulsant action.We first conducted studies in hippocampal kindled mice using a range of doses of progesterone (10-160 mg/kg), DHP (5, 10 mg/kg), THP (1-30 mg/kg), progesterone (100 mg/kg) with finasteride (50 mg/kg), as well as finasteride alone (50 mg/kg), the anticonvulsant drugs carbamazepine (50 mg/kg) and midazolam (2 mg/kg). DHP was not anticonvulsant, whereas THP was anticonvulsant at sedative doses. Surprisingly, high doses of progesterone were anticonvulsant when metabolism to DHP and THP was inhibited with finasteride. Focal seizures were not prevented, but seizure spread and severity were attenuated. Subsequent studies were done in the entorhinal slice preparation in the presence of 4-aminopyridine and the GABA-A receptor antagonist picrotoxin. We found that progesterone, in the presence and absence of finasteride, was antiepileptiform. This result confirmed that progesterone had, at least in part, a non-GABAergic mechanism of antiepileptiform action independent of progesterone's metabolism to THP. These are novel findings.

Keywords: Behavioral
Electrophysiology
Epilepsy
Kindling
Progesterone
Seizures
Advisor: Burnham, W. McIntyre
The Structure, Function and Evolution of the Extracellular Matrix: A Systems-Level Analysis

The extracellular matrix (ECM) is a three-dimensional meshwork of proteins, proteoglycans and polysaccharides imparting structure and mechanical stability to tissues. ECM dysfunction has been implicated in a number of debilitating conditions including cancer, atherosclerosis, asthma, fibrosis and arthritis. Identifying the components that comprise the ECM and understanding how they are organised within the matrix is key to uncovering its role in health and disease. This study defines a rigorous protocol for the rapid categorization of proteins comprising a biological system. Beginning with over 2000 candidate extracellular proteins, 357 core ECM genes and 524 functionally related (non-ECM) genes are identified. A network of high quality protein-protein interactions constructed from these core genes reveals the ECM is organised into biologically relevant functional modules whose components exhibit a mosaic of expression and conservation patterns. This suggests module innovations were widespread and evolved in parallel to convey tissue specific functionality on otherwise broadly expressed modules. Phylogenetic profiles of ECM proteins highlight components restricted and/or expanded in metazoans, vertebrates and mammals, indicating taxon-specific tissue innovations. Modules enriched for medical subject headings illustrate the potential for systems based analyses to predict new functional and disease associations on the basis of network topology. This study also explores the evolutionary forces that guided the development of the ECM. Analyses of domain conservation patterns in ECM proteins, including the use of a novel framework for identifying non-contiguous, conserved arrangements of domains shows most are of pre-deuterostome origin. Many participate in novel domain arrangements in vertebrates suggesting the sampling of new domain combinations was an important mechanism leading to neofunctionalization of paralogous ECM genes. Distinct types of proteins and/or the biological systems in which they operate may have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins such as the ECM. Finally, overviewing the current state of our knowledge of the ECM, this study addresses important gaps and highlights areas worthy of further investigation.

Keywords: Domain evolution
Extracellular matrix
Functional annotation
Network biology
Protein interactions
Systems biology
Advisor: Parkinson, John
VLSI Thermal Sensing and Management using Low Power Self-calibrated Delay-line Based Temperature Sensors

The power density of microprocessor chips continues to rise due to the growing demand on microprocessor performance and technology scaling. The resulting temperature rise and thermal gradient not only increase cooling cost, leakage current/power consumption and failure rate, but also affect device speed. These thermal induced problems could be alleviated by employing dynamic thermal management (DTM) that reduces thermal emergencies while avoiding performance degradation. To enable an effective DTM, accurate monitoring of the on-chip temperatures at a large number of strategic locations becomes necessary. This thesis proposes a fully-digital self-calibration method that could remove the delay-line based temperature sensors' sensitivities to process and supply voltage variations. The proposed calibration method assigns a unique correction factor, NC to each sensor, making all the sensors have the same calibrated outputs at start-up. Only one calibration block is required to calibrate multiple delay-line based temperature sensors sequentially. For each additional sensor, only additional registers for storing NC are required. The proposed temperature sensors are demonstrated on an Altera Cyclone IV FPGA based VLSI thermal management system. Four microprocessor cores are mapped onto a Cyclone IV FPGA chip to emulate the VLSI load. Each core has a temperature sensor close by. The runtime thermal profiles for the four microprocessor cores with eight different Dynamic Thermal Management (DTM) methods are obtained. Experimental results from different DTM techniques are studied. In comparison to a conventional global DFS approach, a proposed hybrid DTM reduces the amount of time that the MPSoC spends at higher temperatures and larger thermal gradients, by 10 % and 21 %, respectively. In addition, the proposed hybrid DTM offers a 10 % improvement in the average processing rate (instructions per second) when compared with the conventional global DFS approach.

Keywords: delay lines
digital temperature sensor
field programmable gate arrays
power management
self-calibration
thermal management
Advisor: Ng, Wai Tung
Vibration Modeling and Analysis of a Single Conductor With Stockbridge Dampers

The vibration of a single conductor with Stockbridge dampers is examined theoretically and experimentally. Two novel analytical models are presented. In the first model, the conductor is modeled as a beam subjected to an axial load and the Stockbridge damper is reduced to an equivalent discrete mass-spring-mass and viscous damping coefficient. The second model is based on a double-beam concept. The main beam with an axial load is a representation of the conductor and the Stockbridge damper is modeled as an in-span beam with rigid mass at each end. Using Hamilton's principle, the governing equation of motion and boundary conditions are derived. Expressions are presented for the frequency equations, mode shapes, and orthogonality conditions. Experiments are conducted to determine the equivalent damping coefficient of the Stockbridge damper, the self-damping coefficient of the conductor, the natural frequencies and response of the conductor with and without a Stockbridge damper. The experimental data are used to validate the proposed models. With respect to the dynamics of the conductor, the results of both analytical models are found to be in a good agreement with those of the experiments. The first model is simpler and easier to implement with little computation, but gives a very poor prediction of the dynamics of the Stockbridge damper. The second model is more complicated, but gives a good prediction of the dynamics of both conductor and Stockbridge damper. Numerical examples of the free vibration analysis show a significant dependency of the natural frequencies on the mass of the counterweights, length of the rigid link, length of the messenger, and flexural rigidity. The first mode is dominated by the conductor characteristics. The roles of the location of the Stockbridge damper on the system natural frequencies are inconclusive. The forced vibration results indicate that the response of a bare conductor decreases monotonically with increasing vibration frequency. However, for a loaded conductor, the response can increase or decrease with increasing frequency depending on the location of the damper. Optimization is performed to determine the optimal damping arrangement. The results show that asymmetric damping arrangement and the orientation of the heavier counterweight of the Stockbridge damper toward the span ends result in a better damping performance. These findings can be very useful for transmission lines design engineers and structural engineers.

Keywords: aeolian
cable
Conductor
Stockbridge damper
Transmission lines
Vibration
Advisor: Zu, Jean
Household Educational Decision-making in Low-fee Private Primary Schools in Kenya: An Exploratory Mixed Methods Study

Despite the pronouncement of Free Primary Education (FPE) made by the Government of Kenya in 2003, not all households have equally benefitted from its implementation. Children from many poor households, particularly in urban informal settlements, continue to attend fee-charging private schools which have continued to grow exponentially and to figure prominently on Kenya's educational landscape. To address this conundrum as to why poor Kenyan households are using low-fee private schools (LFP) when there is free primary education in the public schools, I apply notions of social capital and habitus to examine household decision-making pathways. Specifically, I ask which households are using low-fee schools, why, and how do these households navigate and negotiate this emerging educational market.In this study I problematize choice processes as a complex interaction between macro-level institutional policy frameworks, meso-level organizational practices, and micro-level decisions. This mixed methods multilevel study was based on a survey of 209 households from one village in Kibera, and involved five target schools, one public and four low-fee schools. Qualitative in-depth interviews at the state level with Ministry of Education officials, donors, and civil society organizations, as well as school level interviews with school proprietors, teachers, pupils and school management committee (SMC) members, and household level interviews with a smaller set of 21 parents were used to triangulate and to complement findings from the household survey. Overall the study found that decision-making for the economically disadvantaged households in this study was differentiated by the social, cultural, and economic capital they own. As households navigate between public and LFP schools, the results suggest that choice is not equitable as not all households are able to fully exercise their right to choose nor, do they have agency. In many cases households are pushed into a decision. Based on these findings, I propose a categorization of households based on their decision-making pathways into two groups: default decision-makers and strategic decision-makers. The analysis also shows that households rely on social networks, and ethnicity considerations in making school decisions. These decisions however, appear to be reinforcing existing boundaries of social class, and exacerbating stratification in the schools.

Keywords: Private Schools
Advisor: Mundy, Karen
Convergent Knowing: Explorations of a Sustained - and 'Sustainable' - Theological Reflection on Science, Environment, and Liberation

Since the last half of the twentieth century, Christian theorists, theologians, biblical scholars, philosophers and ethicists have been struggling, in varying degrees, with the increasingly pressing issues that have arisen from a planetary environmental crisis and a growing inequality and persistent poverty afflicting the majority of human beings. They have tried to reconcile these emergences with discoveries from science about how our world functions, and traditional affirmations of their faith. The struggle has been daunting, marked by a litany of concerned voices that argue that one or more of the issues or facets of the debate require greater attention. In this dissertation, I investigate the writings of four Christian thinkers: Rosemary Radford Ruether, Leonardo Boff, Diarmuid O'Murchu and Thomas Berry. These authors attempt to integrate, to varying extents, environmental concerns, liberation thought, scientific discovery and traditional precepts of their faith. These thinkers, I argue, are greatly facilitated in their integration of all these aspects by the particular epistemic framework they employ when engaging their faith and science in a communal conversation. I label this framework "convergent knowing," characterized by a close and seemingly continuous relationship between these two significant ways of knowing. I suggest that "convergent knowing" could serve as a model for other Christian thinkers who are currently struggling to integrate ecology, justice, science and their faith. Evidence for this is found within the collective work of the four authors I examine, which reveals an emerging ethical vision that seeks liberation for the human and the other-than-human. I further argue that "convergent knowing" adds a new and important dimension to the religion-science debate, one that does not seem to be adequately represented by current leading typologies representing the religion-science nexus. The dissertation concludes by suggesting that there might be a larger civilizational paradigm shift occurring that underlies a growing convergence of Christianity and science. Characterized by relationality, this new paradigm is shaping how scholars currently approach science, ecology, ethics and religion.

Keywords: Christianity
Environment
Epistemology
Liberation
Science
Advisor: Scharper, B Stephen
Neurohormonal Correlates of Altered Eating Behaviour in Depressive Disorders

Depression and obesity are widespread, significant global public health concerns. Weight and appetite disturbances are common symptoms of Major Depressive Disorder that can complicate treatment and prognosis and, similarly, obesity increases vulnerability to depression. Proposed shared etiologies for depression and elevated body weight include altered stress perceptions and eating behaviours, as well as neurohormonal mediation. The latter includes altered hypothalamic-pituitary-adrenal (HPA) axis activity, and changes in hunger and satiety signals, adding further evidence to phenotype overlap. There are few investigations on eating behavior, weight changes, and HPA axis alterations in depression. The aim of this series of interlinked investigation was to examine the influence of stress and of food ingestion on hormones involved in appetite regulation along side HPA axis activity. Cortisol, ghrelin, and leptin secretory response to two physiological challenges, i.e., psychosocial stress, and food, was evaluated in eighteen patients with clinical depression, and seventeen matched healthy controls. Neurocognition, eating behavior, and stress perception measures were obtained. In response to the stress challenge, depressed participants exhibited elevation of leptin levels in comparison to controls. Such elevation was influenced by the chronicity of illness. No differences between patients with depression or controls were found in cortisol or ghrelin response to either set of experiments. However, among the participants, emotional eaters exhibited significantly lower levels of ghrelin in response to food. In addition, significant associations between leptin and cognition were noted. Results suggest possible alteration in appetite regulation in both depressed and emotional eaters. It is suggested that appetite and weight increase often seen in chronic depression may be in part be mediated by HPA axis leptin interactions. Potential alterations in feedback systems regulating appetite may be suggested as leading to increased vulnerability for future weight gain in depression.

Keywords: Cognition
Depression
Emotional Eating
Ghrelin
Leptin
Stress Reactivity
Advisor: Ravindran, V Arun