VictorJuiz/thesis huggingface dataset:
Milk Fat Content, Vitamin D, and Andiposity in Early Childhood

Background: Vitamin D is fat soluble and cow's milk is the main dietary source of vitamin D in North America. I hypothesized higher fat milk would be associated with higher 25-hydroxyvitamin D and decreased BMI in children. Methods: Multivariable linear regression and bivariate regression models were used to test the associations between percent fat content of milk and 25(OH)D, and both 25(OH)D and BMI z-scores (zBMI) in children 12-72 months. Results: Higher fat milk had a positive effect on 25(OH)D, but a negative effect on zBMI. Children who drank whole milk had 25(OH)D 5.4 nmol/L (95% CI 4.3 to 6.5) higher than children who drank 1% milk, but a 0.72 (95% CI 0.68 to 0.76) lower zBMI. Volume of milk modified the relationship between percent fat content of milk and 25(OH)D (p=0.003), but not zBMI (p=0.77). Conclusion: Consumption of lowfat milk may compromise both 25(OH)D and adiposity in children.

Keywords: adiposity
dairy
fat
milk
vitamin D
zbmi
Advisor: Maguire, Jonathon
Frequency of Abnormal Electroencephalogram in Asymptomatic Relatives of Patients with Epilepsy: A Systematic Review and Meta-analaysis

Objective: To systematically review studies of asymptomatic relatives of patients with Juvenile Myoclonic (JME), Childhood Absence (CAE) and Benign Rolandic (RE) Epilepsy who had an abnormal electroencephalogram (EEG) recording and determine the frequency of these waves through meta-analysis in order to better understand the genetics and mode of inheritance of idiopathic epilepsy. Methods: MEDLINE, EMBASE, CINHAL and Cochrane databases were searched. Two independent reviewers conducted all screening levels, data abstraction, and quality appraisal. A meta-analysis was performed. Results: After screening 10,233 citations and 211 full-text articles, 15 studies were included. A total 3885 asymptomatic relatives were included. The prevalence of all abnormal waves in asymptomatic relatives was 31%. Prevalence for each epilepsy type was 21% for JME, 42% for CAE and 33% for RE. Conclusion: Further investigations are needed to test inheritance patterns to identify "major" genes.

Keywords: Childhood Absence
Epilepsy
Idiopathic
Juvenile Myoclonic
Metaanalysis
Rolandic
Advisor: Minassian, Berge
Informing the Design of a Smartphone-based Telemonitoring System for Multiple Chronic Conditions

People with multiple chronic conditions (MCC) often struggle with managing the diverse facets of their health, which includes monitoring physiological parameters such as blood pressure and weight, maintaining appropriate diet and level of exercise, adhering to medications, keeping updated health records and traveling to multiple healthcare providers. Therefore a user-centric design process was utilized to design a smartphone-based telemonitoring system to support self-care and clinical management of patients with MCC. Semi-structured interviews with fifteen patients and eleven clinicians and an analysis of existing disease-specific smartphone applications provided insight into the requirements and architecture for designing the telemonitoring system for MCC. Utilizing the gathered information, prototypes of smartphone application were created and refined through three rounds of usability testing. Themes and design principles generated in this study highlighted the complexity and challenges for designing interventions for multiple conditions, and could be utilized for informing the design of smartphone based telemonitoring systems for MCC patient populations.

Keywords: mHealth
Multiple Chronic Condtions
Remote Patient Monitoring
Telemonitoring
Advisor: Seto, Emily
Clinical Prediction Models of Patient and Graft Survival in Kidney Transplant Recipients: A Systematic Review and Validation Study

There have been an increasing number of clinical prediction models (CPM) of patient and graft survival in kidney transplant recipients (KTR). The performance of these models in Canadian KTR is unknown. The purpose of this thesis is: To systematically review CPM of patient and graft survival in KTR and externally validate CPM in a cohort of Canadian KTR. CPM were assessed for performance, bias risk and clinical usefulness. Selected CPM were externally validated in a cohort of 1,326 Canadian KTR. The results of this work shows that four of 18 studies that developed CPM were found to have a low risk of bias, were externally validated and clinically usable. CPM showed modest discrimination (c statistics: 0.67 to 0.74) and poor calibration (P values

Keywords: Clinical Prediction Models
External Validation
Graft Survival
Kidney Transplantation
Patient Survival
Systematic Review
Advisor: Naimark, David M J
A Voltage Scaling Power Reduction Strategy for Memory-based LDPC Decoders

In baseband digital signal processing, dynamic voltage scaling is an effective method to reduce the power consumption of an SOC. Voltage scaling directly applied to embedded memories can lead to stability issues such as memory read and write errors. This thesis explores the possibility of applying voltage scaling technique to embedded memory that is used in forward error correction circuits (an LDPC decoder), in order to compensate for the error induced by voltage scaling while improving the over energy efficiency of an LDPC decoder. This thesis used an LDPC decoder designed for wireless IEEE802.11ad WiFi standard as a target to quantitatively characterize its inherent tolerance to embedded memory errors. An adaptive voltage scaling control algorithm is then proposed based on the error tolerance model. A hardware aware implementation strategy is also presented with a simulated energy saving potential of up to 20%.

Keywords: Embedded Memory
Error Correction
LDPC
Memory
Power Efficiency
Voltage Scaling
Advisor: Gulak, Patrick Glenn
The Lived Experiences of Transracial Adoptees in the Greater Toronto Area (GTA)

There has been increasing interest in the area of transracial adoption over the past decade, as there has recently been an increase in the number of Caucasian couples parenting non-Caucasian children (Lindsey, 2012). Although much research has been conducted regarding transracial adoption, very few studies have spoken directly with transracial adoptees. The present study addressed this gap in the literature through conducting interviews with eight transracially-adopted individuals. Interviews addressed adoptees' lived experiences, with a focus on the importance of relationships in the adoptees' lives. Data was analyzed using grounded theory and results demonstrated the crucial importance of relationships in transracial adoptees' lives. Additionally, it was found that a sense of understanding is paramount for transracial adoptees in these relationships. The insights gained from this study regarding the importance of open, understanding relationships can eventually be used by mental health professionals to aid adoptees and multicultural individuals.

Keywords: Multiculturalism
Relationships
Transracial Adoption
Advisor: Moodley, Roy
(Re)Making Identities: Negotiating Critical Literacy in an Urban High School

How can teachers meaningfully engage with the students around issues of identity in the classroom? In response to this question, I used my urban Toronto public school classroom as a space to investigate the interactive processes of constructing and deconstructing identity through teacher-student relationships. Using practitioner inquiry, my research asks how critical literacy can encourage high school students to reflect on their identity in relation with my own teaching practice. Through a series of reflective in-class activities I observed the implications of students (and teachers) bringing their whole selves and diverse experiences into the classroom. My findings demonstrate that when given the opportunity, students were eager to explore the many factors that influenced their self-perceptions of who they are and who they want to be. Placing myself at the centre of the research and understanding teaching as a relational act facilitated the analysis of the relationship dynamics through dialogue and reflection. This research resulted in a powerful and transformative experience for everyone involved. The findings are also valuable for educators and administrators interested in using critical and holistic education to engage with youth voices, experiences and ideas that have historically been excluded from public education.

Keywords: critical literacy
culturally relevant pedagogy
practitioner research
transition programs
youth identity
youth voice
Advisor: Simon, Rob
Bickmore, Kathy
The Influence of Socioeconomic Status on Selection of Anticoagulation for Atrial Fibrilation: A Population Based Study

Introduction: Without third-party insurance, access to marketed drugs is limited to those who can afford to pay. We examined this phenomenon in the context of anticoagulation for nonvalvular atrial fibrillation (NVAF). Methods: To determine whether, wealthier patients with NVAF were more likely to switch from warfarin to dabigatran prior to its addition to the provincial formulary, we conducted a population-based retrospective cohort study. Results: We found that higher SES was associated with switching to dabigatran prior to its coverage on the provincial formulary y (p

Keywords: anticoagulation
atrial fibrillation
dabigatran
equity
warfarin
Advisor: Laupacis, Andreas
Role of SPARC in Drosophila Melanogaster basal lamina homeostasis

SPARC is a multifunctional, evolutionarily conserved, collagen- and growth factor-binding glycoprotein that is required in Drosophila melanogaster for proper larval development and maintenance of fat body homoeostasis. I have engineered a SPARC RNAi knockdown in the larval fat body, with an emphasis on ultrastructural adipocyte morphology and basal lamina integrity, resulting in adipocyte remodeling characterized by cell rounding and accumulation of fibrous matrix material. SPARC deficient larva show increased deposition of collagen IV and other basal lamina components. How collagen IV assembles into an organized network in basal lamina remains unclear. In seeking to elucidate the potential intra- and extracellular functions of SPARC in this context, I generated five mCherry tagged SPARC constructs which failed to rescue SPARC-null mutants. Together, the data compiled by myself and others in the lab indicate that SPARC is required to maintain adipocyte morphology and basal lamina homeostasis during larval development.

Keywords: chaperone
Collagen IV
fat body
SPARC
Advisor: Ringuette, Maurice J
Reduced Pressure Distillation of Wood Derived Pyrolysis Liquid Biofuels and their Emulsion with Diesel Fuel in a Compression Ignition, Indirect Injection Engine

Reduced pressure distillation was used to reduce water content of crude WPLs from 24.81 to 14.51 wt%, named dewatered WPL (dWPL). Five emulsions were produced with 5-25 wt% dWPL, 5 wt% ethanol, 4 wt% surfactant, 0.15 wt% of a fuel additive, and remainder diesel. Emulsions were tested in a C2.2 engine at three conditions. Max engine duration was 5-25 minutes for dWPL emulsions, where key barriers were injector failure and fuel stability. Ignition delay for dWPLs was found to be 10째CA longer than diesel fuels. In a corrosion study, the mass loss rate for specimens submerged in dWPLs was found to be roughly half that of specimens submerged in WPLs. The absolute mass loss rate for dWPLs at high temperatures (50째C) is non-negligible in engine applications. SEM images of specimens show increased surface roughness, which may cause injector failure when dWPLs are used in engines.

Keywords: Biofuels
Compression Ignition Engines
Emulsions
Fast Pyrolysis Liquid Biofuel
Indirect Injection Engines
Pyrolysis Liquids
Advisor: Thomson, Murray J
GABA Cells in the Central Nucleus of the Amygdala Control Cataplexy

Cataplexy is a hallmark of narcolepsy characterized by the sudden onset of muscle weakness or paralysis during wakefulness. It can occur spontaneously but is typically triggered by positive emotions like laughter. Although cataplexy was identified over 130 years ago, its neural mechanism remains unclear. Here, we show that a newly identified GABA circuit within the central nucleus of the amygdala (CeA) may play a causal role in promoting cataplexy. We found that, in narcoleptic mice, chemogenetic activation of GABA cells within the CeA triggered a 253% increase in the number of cataplexy attacks without affecting their duration. We also show that GABA cell activation only promotes cataplexy attacks associated with emotionally rewarding stimuli such as wheel running, without impacting spontaneous attacks. Our results indicate that the CeA plays a pivotal role in controlling cataplexy onset, and that emotionally rewarding stimuli may trigger cataplexy by activating GABA cells in the CeA.

Keywords: Amygdala
Cataplexy
Chemogenetics
Narcolepsy
Advisor: Peever, John
Transforming Bodies: Affect and Collage in Eating Dis/order Recovery

This thesis explores affective experience in the development of eating disorders as well as its influence and potential in the recovery process. Affect is researched within the context of identity and embodied learning. This research also explores the use of creative practices (collage) in eating disorder recovery. Four women between the ages of 18 and 30 who self-identified as having an eating disorder participated in this study. Their participation included two interviews (one individual and one group) and two group collage sessions. This research suggests that eating disorders can be understood as bodily practices (entangled with emotion and thought) that both build and fragment the sense of self. Using Deleuzoguattarian concepts such as “the fold” and “BwO”, I propose a rhizomatic understanding of eating disorder recovery in which the affective body is paramount. I suggest that arts-based practices have the potential to play an important role in the recovery process.

Keywords: Affect
Collage
Deleuze
Eating Disorder
Embodiment
Pedagogy
Advisor: Springgay, Stephanie
CCCTC-binding Factor (Ctcf) is Required for Mouse Cardiovascular Development

Disruption of transcriptional programs controlling development of the cardiovascular system can cause congenital cardiovascular disease. These programs are tightly regulated by chromatin regulators that alter gene expression via formation of active or repressive chromatin and by mediating long-range chromatin interactions. However, how the process of long-range chromatin interactions, facilitated by chromatin mediators, regulate cardiovascular development is not understood. One potential highly conserved chromatin regulator of cardiovascular development is the CCCTC-binding factor (CTCF). Through conditional deletion of Ctcf in mouse cardiac and endothelial progenitors, I found that Ctcf is essential for cardiovascular development. Inactivation of Ctcf in cardiac progenitors induces severe cardiac defects by embryonic day 12.5, while inactivation of Ctcf in endothelial progenitors causes extraembryonic vascular defects by E9.5-10.5. Future investigations in the mechanistic involvement of Ctcf in cardiovascular development will help determine how the process of long range chromatin interactions guide developmental transcriptional programs and function of CV systems.

Keywords: Cardiovascular development
Chromatin regulators
CTCF
Long-range chromatin interactions
mouse embryonic development
Advisor: Delgado-Olguin, Paul
Investigating the Use of a Biologically Active Surface Coating for Coronary Stent Devices: A New Approach to Improving Biocompatibility

Coronary artery disease is a major cause of death globally, and has led to the use of medical implants like coronary stents. Unfortunately, re-narrowing of the artery can occur (restenosis) due to an immune response towards the implanted ‘foreign’ device. A new approach to combat restenosis and reduce the stent-induced immune response has been proposed, which involves re- endothelialization of the implanted stent. In our investigation, a novel proof-of-concept stent was applied towards in vitro cell capture. Steel coupons were coated with an organic adlayer, whole antibodies were ‘immobilized’, and human umbilical vein endothelial cells (HUVECs) and human aortic endothelial cells (HAECs or HAoECs) were cultured. On the adlayer-antibody condition, desirable HUVEC morphology was achieved, and significantly more HUVECs were captured compared to the ‘bare’ surface. For HAECS, no significant difference in cell capture was observed. However, HAECs appeared healthier on the adlayer-antibody condition. These results demonstrate successful re-endothelialization of the stent surface.

Advisor: Thompson, Michael
Romaschin, Alexander
Three, Two, One: Three New C–C Bonds, Two C–H Activations, One Pot. A Highly Efficient Palladium-catalyzed Domino Reaction of Aryl Iodides and Aryl Bromides

Palladium-catalyzed C–C bond formation and C–H activation have become emerging methods of choice in the industrial synthesis of pharmaceutical and agrochemical products. The development of a palladium-catalyzed domino reaction of aryl iodides and aryl bromides to form polycyclic dihydrophenanthrene structures selectively and in high yields is discussed in this thesis. The reaction involves two C–H activations and the formation of three new C–C bonds and demonstrates the high efficiency of domino reaction catalysis. A detailed description of the optimization of two reactions is given, one involving a dimerization of aryl iodides and the other featuring a selective coupling of two distinct aryl bromides. Experiments to demonstrate the scope of these reactions show the tolerance of the optimized systems for a variety of common functional groups.

Keywords: Catalysis
C-H activation
Domino reactions
Palladium
Advisor: Lautens, Mark
Does Androgen Deprivation Therapy Impact Subjective Cognitive Function in Men with Non-metastatic Prostate Cancer?

Androgen-deprivation therapy is used to treat almost 50% of current prostate cancer patients. Despite slowing disease progression and prolonging survival, androgen-deprivation therapy is associated with numerous side effects. However, the impact of androgen-deprivation therapy on subjective cognitive function remains uncertain, as the studies published in this area have assessed objective cognitive function and are limited by small sample sizes and inconsistent findings. The primary objective for this thesis was to determine whether there was a change in subjective cognitive scores over a 12-month period in non-metastatic prostate cancer patients receiving ADT compared to controls. The secondary objectives were to examine the relationship between subjective cognitive function and socio-demographic variables, and change in subjective and objective cognitive function over the 12-month period. Change scores between baseline and 12 months analyzed with adjusted multivariable linear regression models showed no significant change in the prostate cancer patients receiving androgen-deprivation therapy compared to the other control groups.

Keywords: Androgen Deprivation Therapy
Prostate Cancer
Subjective Cognition
Advisor: Alibhai, Shabbir
The Application of the Cyclic Void Growth Model to Assess the Ultra-low-cycle Fatigue Life of Steel Castings

Steel castings have been used increasingly to develop new seismic force resisting systems. Although they have primarily been used as elements which are to remain elastic during seismic events, recent developments have proposed and validated systems that rely on the yielding response of steel castings, taking advantage of their freedom of geometry and chemistry to obtain optimum combinations of strength, stiffness, and ductility. To this end, an understanding of their ultra-low-cycle fatigue life is paramount. To further this understanding, in this thesis, fatigue laws are calibrated for multiple cast steel heats using a fatigue model which has recently been proposed in the literature for rolled steel elements. The calibrated models are used to predict the ductile failure in multiple full-scale experiments. A method is proposed to assess the casting's fatigue life at the foundry and to utilize the model in designing prototype steel castings for ductile applications.

Keywords: Fatigue
Inelastic
Seismic
Steel Castings
Yielding
Advisor: Christopoulos, Constantin
An Extended GASNet API for PGAS Programming on a Zynq SoC Cluster

This work presents a dynamic development flow to integrate FPGA accelerators into software applications for a Zynq SoC cluster. We provide a high-level library, THe\_GASNet Extended API, based on the Partitioned Global Address Space (PGAS) programming model for remote memory operations. The extended API is built using the THe\_GASNet Core API that implements a global address space view of the memory but provides distinction between local and remote data accesses. The extended API provides an expressive way to implement parallel applications on the x86-ARM-FPGA heterogeneous systems. For the benchmark, we implemented the Jacobi iterative method on the cluster. The hardware implementation of the Jacobi method performs 2.78-fold faster than the software implementation on the i5 processor for a 4096x4096 surface. Compared to the core API, the extended API performs slightly worse for all the data sizes. However, the trade-off of the reduced performance is increased ease of programming.

Keywords: FPGA
GASNet
Programming Models
THe_GASNet
Zynq
Advisor: Chow, Paul
Single Particle Electron Cryomicroscopy of the Thermus thermophilus V/A-type Rotary ATPase and Structure of the Membrane-bound a Subunit

Rotary ATPases are membrane-bound protein complexes found ubiquitously in biology that carry out ion transport and ATP synthesis. Despite variation in structure and function, conserved biochemical features dictate the mechanisms of rotary ATPase action. Structural models are available for many subunits in every class of rotary ATPase, but none exist for the membrane-bound ion-transporting a subunit. Here we present the structure of the intact Thermus thermophilus V/A-type rotary ATPase at 6.4 Ă , obtained by single particle electron cryomicroscopy. This map was used in concert with evolutionary covariance analysis and biomolecular modelling to create a model of the a subunit. Models were similarly generated for the Saccharomyces cerevisiae V-ATPase a subunit and Bos taurus F-type ATP synthase a subunit. These models display similar features despite large sequence variation, indicating a conserved path for protons and suggesting a universal mechanism of proton translocation in rotary ATPases.

Keywords: a subunit
ATP synthase
Electron cryomicroscopy
Evolutionary covariance
V/A-ATPase
V-ATPase
Advisor: Rubinstein, John L
Retinal Thickness Irregularities in Preclinical Diabetic Retinopathy

Diabetic retinopathy (DR) is the most common complication of diabetes and the leading cause of vision loss worldwide. Clinical detection relies on the manifestation of sight-threatening microvascular, macrovascular and edematous ocular insults. However, preclinical investigations detected retinal thickness irregularities. We hypothesized that retinal thickness irregularities are localized to specific retinal regions and layers. Training and validation data were collected from participants with diabetes with no/minimal DR and healthy individuals to identify and verify regions of interest. Optical coherence tomography and MATLAB速 computing were the primary tools used to measure retinal thickness in each participant. Linear mixed-effects models identified four significant regions of thickness irregularities from the training data; these were not matched by validation data. Nonetheless, retinal thickness irregularities were localized to specific regions and layers. Recognizing that there are retinal regions susceptible to retinal thickness irregularities during preclinical stages of disease is important for early disease detection.

Keywords: diabetes
diabetic retinopathy
image analysis
optical coherence tomography
retina
type 1 diabetes
Advisor: Westall, Carol