VictorJuiz/thesis huggingface dataset:
Genome-wide Distribution and Regulation of DNA Methylation and Hydroxymethylation in Prostate Cancer

Prostate cancer (PCa) is the most common malignancy in men. Epigenetic alterations, including DNA methylation, significantly influence disease pathogenesis. Aberrant methylation of the cytosine base (5mC) transcriptionally regulates several genes associated with PCa development. Recent discovery that 5mC marks are converted to DNA hydroxymethylation (5hmC) marks by ten-eleven translocation (TET) proteins has opened avenues for epigenome regulation. The intent of my MSc research was to define the genome-wide DNA methylation and hydroxymethylation patterns in prostate cell lines, benign and cancerous, using next-generation sequencing technology and bioinformatics analysis. I defined regions of differential methylation between normal and cancer, and suggest novel biomarkers for the disease. Additionally, this is the first study to discover the landscape of DNA hydroxymethylation in PCa, which suggests enrichment in specific genomic regions. Furthermore, I revealed pathways potentially regulated by 5mC and 5hmC marks to expand our knowledge of aberrant epigenetic processes in PCa pathogenesis.

Keywords: DNA hydroxymethylation
DNA methylation
Epigenetics
Next-generation sequencing
Prostate cancer
TET proteins
Advisor: Bapat, Bharati
Charames, George
The Effects of Implementing Student-centred Learning on At-risk Students' Self-efficacy

This study examined the effects of implementing student-centred learning (SCL) in a college at-risk mathematical classroom, and how this teaching strategy affected students’ self-efficacy. A triangulation of methods and data was used to examine these effects in two cohorts of students at a large urban college’s Academic Upgrading program. The evidence from the study suggests implementing SCL in classrooms for at-risk students is beneficial. The major findings were as followed: (1) both students and teachers experience some level of resistance when SCL is initially implemented; (2) increased levels of self-efficacy lead to better mathematical performance; (3) SCL did not appear to raise achievement; (4) SCL activities improved students’ confidence levels.

Keywords: Math
Self-Efficacy
Student-Centred Learning
Advisor: McDougall, Doug
State and Ideology: Youth Public Policy in Ontario

As global youth unemployment and youth led social movements become increasingly widespread, states have begun to consider youth a policy concern. In this thesis, I ask how youth experience being a policy concern. Ontario is the site of analysis, where the provincial government has recently released numerous public policies that draw on contemporary trends in youth research. Through policy analysis and semi-structured interviews, I connect the experience of Ontario’s young people to the theoretical principles of the state's policy approach. I focus on the tension between the individual and the social: between the idea of youth as described in public policy, and the actual social conditions of the youth who participated in this program. The experiences of individual youth, whose lives are socially coordinated by state policy initiatives, are a window into understanding the consciousness and learning that arises for a generation brought up in economic instability and austerity.

Keywords: Consciousness
Crisis
Ideology
Public Policy
State
Youth
Advisor: Mojab, Shahrzad
Modeling Ca2+-dependent Regulation of KCC2 Phosphorylation as a Mechanism for Inhibitory Synaptic Plasticity

Inhibitory synaptic transmission in the mammalian central nervous system is chiefly mediated by the neurotransmitter γ-aminobutryic acid (GABA), which binds the Cl−-permeable ionotropic GABAA receptor. In mature neurons, low intracellular Cl− is maintained by the K+-Cl− cotransporter KCC2, allowing Cl− influx and hence hyperpolarization of the cell upon GABA binding. Repetitive coincident activation (within ±20 ms) of pre- and postsynaptic neurons at inhibitory synapses leads to a depolarizing shift in the GABA reversal potential (EGABA), diminishing the strength of inhibition. It has been hypothesized that this is due to Ca2+-dependent dephosphorylation of KCC2 mediated by T-type voltage gated Ca2+ channels (VGCCs). We simulated this proposed mechanism using a kinetic model of KCC2 phosphorylation. Simulations showed that Ca2+ entry via T-type VGCCs could produce spike timing-dependent changes in KCC2 phosphorylation leading to removal from the membrane, hence intracellular Cl− accumulation and reduced strength of inhibition.

Keywords: Cl- regulation
Inhibitory transmission
Modeling
Phosphorylation
Synaptic Plasticity
Advisor: Richards, Blake A
Woodin, Melanie A
Faster Camera Sightfield Sensing using Computational Lightpainting

This thesis studies faster estimation of the sightﬁeld (ﬁeld of view) of an arbitrary camera. Beyond faster veillance ﬁeld estimation, this work also presents the visualizing and localizing of this ability through “Abakography” ( computational lightpainting for 3D Augmented Reality) using an array of addressable lights (known as the “bugbroom” method ). These visualizations can be seen through augmented reality (AR) glasses. “Veillometrics” as a ﬁeld of research was developed by Ryan Janzen and Steve Mann, and “Abakography” was invented by Steve Mann in the 1970s which later formed the basis for gesture-based wearable computing. In this work diﬀerent methods of veillance ﬁeld detection using a bugbroom are proposed and their performance is tested against the current existing solution. These are visualized and modelled using computational abakography . Moreover, computer vision is used in conjunction with an abakographic user-interface to construct 3D models of time-varying light sources moved through space.

Keywords: Augmented Reality
Computational lightpainting
Sightfield
Tracking
User interface
Veillance
Advisor: Mann, Steve
Multi-objective Energy-noise Wind farm Layout Optimization under Land Use Constraints

Recently the environmental impact of onshore wind farms is receiving major attention from both governments and wind farm designers. As land is more extensively exploited for wind farms, it is more likely for wind turbines to be in proximity with human dwellings, infrastructure, and natural habitats. This proximity makes significant portions of land unusable for the designers, introducing a set of land-use constraints. In this study, we perform a constrained multi-objective wind farm layout optimization considering energy and noise as objective functions, and considering land use constraints. A stochastic evolutionary algorithm (NSGA-II) solves the optimization problem, while the land-use constraints are handled with penalty functions and a novel hybrid constraint handling approach based on Constraint Programming. Results of this study illustrate the effect of constraint severity on the energy-noise trade-off. In addition, the potential of the new constraint handling approach to outperform existing constraint handling approaches is investigated.

Keywords: Constraint Programming
Land use constraints
Multi-objective optimization
Penalty functions
Wind farm layout
Wind farm noise
Advisor: Amon, Cristina H
The Role of the Dopamine D5 Receptor and D1-D2 Receptor Heterooligomer Signalling in Rodent Prefrontal Cortex and Cognition

The dopamine D5 receptor is highly expressed in rodent prefrontal cortex (PFC) a region involved in cognition. We have previously shown that acute activation of the Gq-coupled dopamine D5 and D1-D2 receptor heteromer by the agonist SKF 83959 inhibited glycogen synthase kinase- 3 (GSK-3) activity in PFC, a protein that mediates cognitive performance in this region. Specifically, the dopamine D5 receptor suppressed GSK-3 activity through a mechanism dependent on brain-derived neurotrophic factor (BDNF) signaling, whereas inhibition of GSK-3 activity by D1-D2 heteromer appears to be independent of BDNF signaling in the PFC. We have demonstrated that SKF83959 improved cognitive performance in male rats using the egocentric learning task in the small Morris water maze. These studies potentially offer a novel therapeutic drug target to treat cognitive deficits in Alzheimer's disease and schizophrenia through activation of the dopamine D5 receptor signaling pathway involving increased BDNF signaling and inhibition of GSK-3 activity.

Keywords: Akt
BDNF
Cognition
Dopamine Receptor
GSK3β
Prefrontal Cortex
Advisor: George, Susan R
Differentiating Reading Comprehension Skill Mastery Patterns of Immigrant and Domestic Students of Various Home Language Environment

The present study compared reading comprehension skill mastery profiles (SMPs) among 1600 grade-6 students with different immigration status and home language environments (HLEs) in Ontario schools in Canada. Immigrant students of five or more years of residence had significantly higher scores relative to domestic students. Inferencing was most predictive of total reading comprehension for both groups of students, followed by explicit comprehension and vocabulary skills. Students who mostly speak English at home while exposed to multilingual home language environments were significantly more likely to master both vocabulary and inferencing. According to the interactive compensatory model (Stanovich, 1980), various skills develop in support of one another in strengthen their total competency in skilled readers. The study result highlights the importance of examining students’ home language environments for tracking and supporting the development of reading comprehension skills, especially of higher order processing skills.

Keywords: home language environment
immigrant
multilingualism
Reading comprehension skills
Advisor: Jang, Eunice E
The Relationship between Action Execution, Imagination, and Perception in Children

Action simulation has been proposed as a unifying mechanism for imagination, perception and execution of action. In children, there has been considerable focus on the development of action imagination, although these findings have not been related to other processes that may share similar mechanisms. The purpose of the research reported in this thesis was to examine action imagination and perception (action possibility judgements) from late childhood to adolescence. Accordingly, imagined and perceived movement times (MTs) were compared to actual MTs in a continuous pointing task as a function of age. The critical finding was that differences between actual and imagined MTs remained relatively stable across the age groups, whereas perceived MTs approached actual MTs as a function of age. These findings suggest that although action simulation may be developed in early childhood, action possibility judgements may rely on additional processes that continue to develop in late childhood and adolescence.

Keywords: Action Imagination
Action Perception
Development
Fitts' Law
Motor Imagery
Simulation
Advisor: Welsh, Timothy N
Establishment of a Working Model for the Study of HEB Transcription Factor Activity and Elucidation of the Function of the Alternative Domain of HEBAlt

T cell development in the thymus occurs in a series of tightly regulated stages and is controlled by a complex network of transcription factors. E proteins, part of the class I basic-helix-loop-helix (bHLH) transcription factors, have been shown to be critical for T cell specification and commitment, as E protein deficiencies leads to major breaches in the T cell developmental program. There are three members of the E protein family: HEB, E2A and E2-2. HEBAlt, the shorter alternative isoform of HEB, has a unique and highly conserved alternative domain, the function of which still remains elusive. I was able to show that HEBAlt is also able to positively regulate the RORγt promoter in the context of 293T cells, and that the alternative domain is only partially responsible for this function. Further research is needed to elucidate the role of HEBAlt in T lymphopoiesis and its interactions with other factors.

Keywords: E proteins
HEBAlt
HEBCan
HEB factors
T cell development
transcription factor
Advisor: Anderson, Michele K
Study of Hoist Performance during Peak Hours for Tall Building Construction

The increasing height of urban buildings creates challenges in the vertical delivery of essential resources during construction phase, which makes the efficient use of construction hoists crucial in building construction. The inappropriate arrangement of temporary hoists can result in a loss of productivity, especially during peak-hours when a large number of specialty trades requires hoists simultaneously. To address this challenge, this paper introduces a discrete-event simulation model that can assist in examining the impact of different lifting strategies on workers’ delay during peak-hours. The application of the proposed model in high-rise building projects shows a potential for minimizing workers’ idle time and increase labour productivity.

Keywords: Construction efficiency
Hoist planning
Advisor: McCabe, Brenda
Pressnail, Kim
Oral Antioxidants for Radioprotection during Medical Imaging Examinations

The oncogenic effect of ionizing radiation (IR) is clearly established and occurs in response to DNA damage. Many diagnostic imaging exams make use of IR and the oncogenic risk of IR-based imaging has been calculated. We hypothesized that the DNA damage sustained from IR exposure during medical imaging exams could be reduced by pre-medicating patients with antioxidants. First, we tested and validated a method for measuring DNA double-strand breaks (DSBs) in peripheral blood mononuclear cells (PBMCs) exposed to low doses of ionizing radiation. Afterwards, we conducted a pilot clinical study in which we administered oral antioxidants to patients undergoing bone scans, prior to radiotracer injection. We showed that oral antioxidant pre-medication reduced the number of DSBs in PBMCs induced by radiotracer injection. Our study shows proof-of-principle for this simple and inexpensive approach to radioprotection in the clinical setting.

Keywords: antioxidants
DNA damage
radiation protection
Advisor: Mikulis, David J
Fracture Resistance Behaviour of γ-Irradiation Sterilized Cortical Bone Protected with a Ribose Pre-Treatment

Structural bone allograft reconstructions are often implemented to repair large skeletal defects. To ensure the biological safety of the patient, allograft material is routinely sterilized with γ-irradiation prior to implantation. The sterilization process damages the tissue, specifically the collagen protein network, leading to severe losses in the mechanical properties of the bone. Our lab has begun developing a ribose pre-treatment that can protect bone from these harmful effects. The goals of the present study were to develop a method to measure the fracture toughness of bone, an important clinical failure mode, and implement it to determine the effectiveness of the ribose pre-treatment on fracture toughness. We have shown that the ribose pre-treatment is successful at protecting some of the original fracture toughness of sterilized bone, and that the connectivity of the collagen network is an important contributor to the fracture resistance of bone.

Keywords: bone
collagen
fracture
fracture resistance curves
ribose
γ-irradiation sterilization
Advisor: Willett, Thomas L
Polymyxin B-modified Glass Beads: an Alternative Approach to Reduce Lipopolysaccharide Toxicity in Blood

Being one of the leading causes of death globally and especially in intensive care units, sepsis is a medical condition of overwhelming inflammatory response due to infection. Bacterial endotoxin, also known as lipopolysaccharide (LPS), plays a major role in the initiation of such response. Thus, removal of endotoxin from patient blood is a critical treatment to minimize mortality. However, problematic detection of LPS in blood leads to difficulties in preparing therapy targeting LPS and monitoring patient condition. In fact, there is no medicine currently available in the North Americas. Here in, a new approach to reduce endotoxin concentration in blood with the use of polymyxin B (PMB)-modified glass beads is presented. An alternative mechanism of LPS-PMB interaction as opposed to the generally accepted mechanism was presented in this manuscript. The LPS-PMB interaction is characterized and evaluated by gas chromatography and enzyme-linked immunosorbent assay (ELISA).

Keywords: Bead Chemistry
Endotoxemia
Endotoxin
Lipopolysaccharide (LPS)
Polymyxin B (PMB)
Sepsis
Advisor: Thompson, Michael
Combustion Analysis For Flame Stability Predictions at Ground Level and Altitude in Aviation Gas Turbine Engines with Low Emissions Combustors

Low emissions combustors operating with low fuel/air ratios may have challenges with flame stability. As combustion is made leaner in the primary zone, the flame can lose its stability, resulting in operability problems such as relight, flameout or cold starting. This thesis analyzes combustion processes for the prediction of flame stability in low emissions combustors. A detailed review of the literature on flame stability was conducted and main approaches in flame stability modelling were indicated. Three flame stability models were proposed (Characteristic Time, Loading Parameter, and Combustion Efficiency models) and developed into a unique Preliminary Multi-Disciplinary Design Optimization (PMDO) tool. Results were validated with a database of experimental combustor test data and showed that flame stability can be predicted for an arbitrary shape of combustors running at any operational conditions including ground and altitude situations with various jet fuels and nozzles. In conclusion, flame stability can be predicted for newly designed low emission combustors.

Advisor: Sampath, Sam
Massive Questionnaire Analysis and Sleep Apnea

Massive data analysis is a new and growing field in applied mathematics. Questionnaire datasets are ubiquitous in many different fields and they usually contain massive structures. This study surveys prominent supervised and unsupervised massive data analysis techniques for classification and clustering, including k-means clustering, spectral clustering, hierarchical clustering, support vector machine, and random forest. It also explores a novel new approach to questionnaire data analysis developed by Professor Ronald Coifman that incorporates the dual geometry metric. All of these techniques are then applied to an easily obtainable and noninvasive questionnaire dataset in order to predict the severity of a patient's obstructive sleep apnea. The resulting analysis is found to have significant predicative power for female patients.

Keywords: Big data
Dual geometry metric
Massive data
Questionnaire
Random forest
Sleep apnea
Advisor: Wu, Hau-tieng
Roles of Extrinsic Forces in Early Mouse Limb Bud Ectoderm Rearrangement

Oriented cell behaviors are recognized as a conserved morphogenetic process that drives tissue shape change. Mouse limb bud ectoderm provides such an example of how cell behaviors are spatially coordinated to generate tissue-scale patterns. To explore the roles of physical forces in ectoderm morphogenesis, this study quantified cell behaviors especially the multicellular rearrangement during early limb bud development. Integrating finite element modelling with in vivo measurement and manipulation of physical forces using atomic force microscopy, laser ablation and time-lapse micropipette aspiration, we revealed that the observed pattern of cellular rearrangement is due to the extrinsic pulling forces generated by the intercalating AER progenitors. In AER defective Fgfr2 mutants, disoriented cell behaviors indicate the loss of tissue-scale forces in the ectoderm but this mutant phenotype can be rescued by an externally applied tension. We also proposed that aPKC polarity underlies the intercalation of AER progenitors and the active pulling forces it generates.

Keywords: cell rearrangement
ectoderm
Limb bud
Micropipette aspiration
tension
tissue morphogenesis
Advisor: Sun, Yu
Hopyan, Sevan
Heart Rate Variability following Concussion in Youth Athletes: An Observational Pilot Study

Background/Rationale: Concussion is of great concern within the pediatric sport population due to its high prevalence and potential impact on neurological development. There is a need for additional inexpensive and objective measures for concussion assessment and management. Heart rate variability (HRV), an objective marker of physiological stress can be used as a measure of stress capacity and may fill this gap. Methods Analyses: Participants included 29 healthy youth athletes (21 females; 8 males). The variables of interest in this thesis are post-concussion symptoms, concussion status, and time and frequency domain HRV measures. Results: There was a main effect of PCS-I on measures of HRV in the mixed model analysis, whereby, increased post-concussion symptoms were associated with higher heart rate variability. Conclusion: Changes in HRV were associated with an increase in post-concussion symptom inventory scores. These preliminary data may guide future research in determining a physiological marker of stress post-concussion.

Keywords: Concussion
Heart Rate Variability
Youth
Advisor: Keightley, Michelle
Reed, Nick
Sinus and Skull Base Surgery Simulator - Development and Validation

The acquisition of surgical skill has evolved dramatically over the last century. There has been a paradigm shift away from an apprenticeship model where learning occurs in the clinical setting on live patients, to a process where basic skills are acquired in a surgical skills center on a spectrum of simulators. The evolution in the rapid prototyping industry has been slowly integrated in to the medical community. Surgical subspecialists have relied on medical modeling to help with surgical planning. A novel sinus-skull base simulator was developed and validated. Objective structured assessment of technical skill was able to show construct and concurrent validity. Face validity was achieved. However, surgical tool kinematics did not show construct validity. The validation of a novel sinus/skull base simulator may be a beneficial, cost controlled tool to allow novice surgeons to gain basic skills in endoscopic sinus/skull base surgery.

Keywords: 3D Printing
Assessment
Simulation
Sinus
Skull Base
Virtual Reality
Advisor: Witterick, Ian
Irish, Jonathan
Examining the Influence of Music Training on Cognitive and Perceptual Transference: A Quantitative Meta-analysis

Two meta-analyses were conducted in order to delineate whether musicians and non-musicians differ on specific cognitive and music processing domains, and determine the magnitude of any differences. Moreover, potential covariates outlined by the literature were included as moderator variables. As predicted, musicians significantly differed from non-musicians on all music processing tasks (melody perception: d=1.18; pitch perception: d=1.00; temporal perception: d=.834). Furthermore, as predicted, musicians significantly differed on the cognitive domains related to musical ability (Motor: d=1.08, and Audition: d=.837). Significant differences were also obtained in General Intelligence (d=.348), Memory (d=.421), Orientation and Attention (d=.283), Perception (d=.190), and Verbal Functions and Language Skills (d=.423). Meta-regression and sub-group analyses of moderating variables indicated that years of music training, age group, and categories (breakdown of groups within domains) had an effect on summary effects, however this impact was not consistent across all domains. The effects of other potential moderating variables are discussed in the context of existing literature.

Keywords: cognitive transfer
meta analysis
music cognition
music processing
music psychology
transfer effects
Advisor: Schmuckler, Mark A
Zakzanis, Konstantine