VictorJuiz/thesis huggingface dataset:
Physician Attitudes towards use of Digital Health Apps for Chronic Disease Self-management in Clinical Practice

Background: Despite evidence of effectiveness, few primary care providers (PCPs) are recommending digital health apps to support chronic disease management as part of routine practice. Methods: This study explores factors that influence PCP behaviours in recommending digital apps to patients. Study design included interviews with a deductive analysis, grounded in the Theoretical Domains Framework. PCPs were recruited from across Ontario. Results: Interviews from 15 participants resulted in four key themes. While participant’s wanted to use health apps with patients, a lack of knowledge, including knowledge of evidence, the quality of the current evidence and awareness of specific apps limited prescribing. Recommended interventions to increase use including curated lists, integration with the EMR, and peers supports. Conclusions: Our results suggest knowledge gaps are a key barrier to recommending apps, however this could be addressed using targeted interventions. Future work should explore patient attitudes towards the prescribing and use of apps.

Keywords: chronic disease
digital health
health apps
virtual care
Advisor: Bhatia, Sacha
Teacher Experiences of the International Day of Pink in Ontario K-12 Schools

Although the International Day of Pink, an LGBTQ2+ awareness day meant to celebrate gender and sexual diversity, has been taking place in Ontario schools since 2007, there is little published research on this event. Utilizing interviews with 10 teachers who have organized or actively participated in the Day at school, this study provides a first look into teacher experiences of Day of Pink in Ontario K-12 public schools. The experiences explored in this study indicate that while there is little regulated training and varying levels of board and administrative support for Day of Pink, teachers worked hard to make the Day meaningful and empowering for LGBTQ2+ students. These findings point out a need to better support teachers with Day of Pink resources, training, and enhanced administrative support to ensure that they have explicit institutional guidance and shared responsibility in working toward a safer, more affirming school climate for LGBTQ2+ youth.

Keywords: bullying
Day of Pink
LGBTQ
queer youth
Advisor: Flessa, Joseph
Salivary Gland Neoplasms: Application of RNA-sequencing and Surrogate Immunohistochemical Markers to Refine Classification

Salivary gland tumours are diagnostically challenging neoplasms. Molecular analysis is increasingly being employed in tumour diagnosis and classification. The prevalence of gene fusions in salivary gland neoplasms was investigated using a commercially available RNA-sequencing fusion panel. In a cohort of salivary gland tumours enriched for subtypes known to harbour fusion events, 71% of tumours demonstrated gene fusions by RNA-sequencing, which is comparable to techniques such as FISH and RT-PCR. These gene fusions can aid in the diagnosis and classification of salivary gland neoplasms. Immunohistochemical markers on tissue microarrays were evaluated as more practical surrogates for gene fusion detection. The sensitivity and specificity of MYB immunohistochemistry for adenoid cystic carcinoma was 48.4% and 93.6%, respectively. Additionally, the sensitivity of Pan-Trk immunohistochemistry for secretory carcinoma was 58.8%, while the specificity was 89.5%. Although surrogate immunohistochemical markers may be specific for some salivary gland tumours, they are limited by a lack of sensitivity.

Keywords: Gene fusion
Immunohistochemistry
RNA sequencing
Salivary gland tumour
Advisor: Dickson, Brendan
Leong, Iona
Visual Localization for UAVs using Satellite Images

The primary objective of this thesis is to develop a method to generate offline a map containing only Google Earth (GE) rendered images against which an Unmanned Aerial Vehicle (UAV) is able to localize using vision online. This eliminates the need for a manual mapping flight and would allow the UAV to fly in new unseen areas autonomously. The first part of this thesis presents a novel method for localizing live UAV images against a collection of rendered and encoded GE images that is fast and has low storage requirements. The second part implements this new measurement into the existing Visual Teach \ Repeat (VT\) system. This includes writing a script to generate a compatible map, computing the measurement in the VT\ pipeline, and using it in the localization optimization. We demonstrate the performance on a dataset of real UAV collected images at six different times of day.

Keywords: localization
robotics
Advisor: Barfoot, Timothy D
The Effect of SGLT2 Inhibition on Biomarkers of Diabetic Kidney Disease and Cardiovascular Disease

\Diabetes mellitus affects over 463 million adults globally and substantially increases the risk of developing complications such as chronic kidney disease (CKD) and cardiovascular disease (CVD). Until recently, there has been a notable lack of treatment options for patients with diabetes that also effectively protect against progression of kidney disease and CVD, thus highlighting the need for novel therapeutic options in this field. Sodium glucose cotransporter-2 (SGLT2) inhibitors have been found to have unique cardiovascular and kidney protective effects in patients with diabetes. However, the mechanisms responsible for these benefits are incompletely understood, and even less so in patients with CKD where the effects of these drugs may be attenuated due to reduced kidney function. The focus of this thesis is to investigate the mechanisms behind the cardiovascular and kidney protective effects of SGLT2 inhibitors through biomarker analysis. We conducted a post hoc exploratory analysis of the VERTIS RENAL trial which involved participants with type 2 diabetes and stage 3 CKD. Participants were randomized to ertugliflozin (5 or 15 mg/day) or placebo, and measurements were taken at baseline, 26- and 52-weeks post-randomization. Ertugliflozin treatment was associated with markers of hemoconcentration including increased hematocrit and aldosterone, and decreased NT-proBNP. These changes were observed without a concurrent elevation in erythropoietin, suggesting that the increased hematocrit was primarily due to hemoconcentration rather than increased erythropoiesis. Additionally, we found that ertugliflozin was associated with a sustained lowering of the kidney tubular injury marker, KIM-1, regardless of baseline kidney function. In conclusion, these findings suggest that the cardiovascular and kidney protective effects of SGLT2 inhibitors are intact in patients with reduced kidney function.

Keywords: Biomarkers
Cardiovascular Disease
Diabetes
Kidney Disease
SGLT2 inhibitors
Advisor: Cherney, David DC
Electron Microscopy Analysis of the Gap Junctions of the Adult Caenorhabditis elegans

One mode of communication in the nervous system is via the bi-directional flow of charged ions and metabolites through gap junction pores. A confident structural assessment of gap junctions at the connectomics level has always remained technically difficult. Consequently, the prevalence of gap junctions throughout the brain is poorly understood. Our lab has developed a fixation protocol that allows better appearance of gap junctions. From two wildtype adults prepared using this protocol, I completed gap junction annotations of the C. elegans brain and assessed these gap junctions in a mutant where three innexin proteins that form gap junctions are removed. My results show that many gap junctions that reside in wildtype brains are absent from the triple innexin mutant, validating this fixation protocol. My comparison between wildtype gap junction connectomes, along with that of the legacy wildtype connectomes showed that at least some gap junctions are different among wildtype individuals.

Advisor: Zhen, Mei
An Examination of the Moderating Role of Depressive Symptoms in the Relationships Between Negative Affect, Interpersonal Stressors, and Alcohol Consequences in an Emerging Adult Population

Emerging adults (EAs) exhibit the highest prevalence of alcohol consequences compared to other age groups. Negative affect and interpersonal stressors contribute to increased alcohol consequences for EAs and are heightened among those with depression. The present study used baseline and daily diary data from 203 EAs (18 to 24 years; M = 21.15, SD = 1.91) over 30 days to test within-person hypotheses regarding depression, negative affect, interpersonal stressors, and alcohol consequences. Across participants, greater baseline depressive symptoms was associated with an increased likelihood of daily alcohol consequences. A moderation effect was observed such that the daily relationship between negative affect and alcohol consequences was significantly stronger among depressed participants compared to nondepressed participants. These findings highlight the role of depression as a facilitator of alcohol consequences on days when depressed EAs’ negative affect is higher. Interventions tailored to EAs with depression should consider the unique ways that negative affect contributes to problem drinking.

Keywords: alcohol
daily diary
depression
emerging adult
interpersonal stressors
negative affect
Advisor: Goldstein, Abby L
Inhibitory Effects of Streptococcus salivarius LAB813 on Cariogenic Microbial Biofilms

Preliminary results suggest a strain of Streptococcus salivarius, LAB813, inhibits the growth of Streptococcus mutans (MS), a major cariogenic bacterial species. Our purpose was to quantify the inhibitory effects of LAB813 against MS in single and fungal-bacterial biofilms. MS and MS-Candida albicans biofilms were cultivated with glucose or sucrose for 6h or 24h and challenged with LAB813 at low or high cell concentration for 24h. LAB813 was highly effective at killing (>95%) 6h and 24h MS biofilms but not as effective at high cell concentration. In fungal-bacterial biofilms, the killing effect of LAB813 was only observed on mature biofilms. Bacterial extracts of LAB813 were shown to disrupt S. mutans biofilms and allow permeabilization of MS and Micrococcus luteus. LAB813 therefore possesses strong antimicrobial activity, possibly through induction of pore formation in target bacteria. Further work is needed to maximize LAB813 effectiveness against more complex oral polymicrobial biofilms.

Advisor: Gong, Siew-Ging
Lévesque, Céline M
Secret Key Agreement over Gaussian Two-way Wiretap Channel

We consider secret key agreement over the Gaussian two-way wiretap channel (GTWWC), where all the receivers observe the common channel output. We develop a dependence balance bound related upper bound on the secret key capacity. We establish the optimality of Gaussian inputs of secret key upper bound. We then propose an achievability scheme that is based on a variant of Schalwijk-Kailath coding scheme and exploits cooperative jamming and wiretap coding to match the upper bound, thus establishing the secret key capacity. We show the secret key capacity for single-output GTWWC also provides an operational explanation for dependence balance bound.

Keywords: information theory
physical layer security
Advisor: Khisti, Ashish
Pleading with Our Paesan: An Urgent Call to Re-structure Italian-Canadian Allegiance to White Supremacy

This thesis calls on White Italian-Canadians to recognize and re-structure their allegiance to White supremacy. It will draw from Critical Anti-Racist Theory (Dei Lordan 2013; Omi Winant 2002), Italian-Canadian Studies (Alba, 1985; Dickie, 1996; Guglielmo Salerno, 2003) and Critical Whiteness Studies (Morrison, 1992; Dyer, 1997; Frankenbergs, 1993). I will interrogate Italian-Canadian Whiteness and demonstrate the ways in which it has been mediated by varied socio-historical conditions across space and time. By documenting the work of grassroots organization Italian-Canadians for Black Lives (IC4BL), I will demonstrate how White Italian-Canadians are responding to calls for allyship/solidarity against White supremacy in Vaughan, Ontario. I develop these analyses in order to explore the opportunities and challenges presented in anti-racism activism organized around an Italian-Canadian cultural affiliation. I hope that this research can be utilized towards more meaningful relationships of solidarity, which take our responsibilities as citizens, (im)migrants and settlers seriously.

Keywords: Anti-Colonial Solidarity
Anti-Racism
Community Activism
Critical Whiteness
Italian Diaspora
Italian-Canadian
Advisor: Cannon, Martin
Reliability of Two-person Anthropometric Measurement of Young Children with Parent Facilitator

Background: The current gold-standard for anthropometric measurement collection in children in a clinical research setting, set by the World Health Organization (WHO), requires the use of two trained anthropometrists. Objectives(s): To determine the reliability of anthropometric measurements in the primary care setting between anthropometrists working in a pair and one anthropometrist working with a child’s parent/caregiver and 2) to determine the parent’s overall experience. Methods: Children 0 – 5 years old had their anthropometric measurement taken twice by anthropometrists working in a pair and twice by one anthropometrist working with a child’s parent/caregiver. Reliability was calculated using the technical error of measurement (TEM), relative TEM (%TEM) and coefficient of reliability (R). Results: The %TEM values across both age groups for length/height and weight were

Advisor: Birken, Catherine S
Conformational Analysis of Rotationally Restricted Macrocyclic Peptides

Conformation describes the spatial arrangement of atoms in a molecule. The conformation of a macrocyclic peptide is known to be a primary determinant of its biological utility. Chapter 2 describes methodology for biasing the conformation of macrocyclic peptides toward metastable “dark-space” conformations using a synthetic backbone motif known as the dominant rotor. Methodology for describing unusual conformations in macrocyclic peptides is described using modified Ramachandran plots to classify the geometrical properties of the backbone. The peptide conformations that arise in these systems bear an overrepresentation of positive φ-angles, representing non-canonical conformations. Herein we describe how the characteristics of “dark-space” conformations can be tuned by introducing structural modifications to the dominant rotor. Chapter 3 describes the applications of this methodology to medicinal chemistry with the development of macrocyclic inhibitors of the α4β7 integrin/MAdCAM-1 interaction. The effects of non-ground-state peptide conformations on the inhibition of this interaction are discussed herein.

Keywords: Atropisomers
Conformational analysis
Macrocyclic peptides
Ramachandran plots
Advisor: Yudin, Andrei K.
Detecting Patient Position Using Bed-reaction Forces for Pressure Injury Management

Pressure injuries are largely preventable, yet they affect one in four Canadians across all healthcare settings. The best way to prevent and treat pressure injuries is to ensure at-risk individuals are repositioned regularly, but adherence to repositioning is poor. Our team has designed a repositioning prompting system for patients in bed that uses data from load cells under the bed legs. The goal of this project was to improve the accuracy of predicting a patient’s position as left, right, or supine and to determine the value of higher precision prediction (more than three categories). The range of positions that completely offloaded the great trochanters and sacrum were determined. Position detection (left, right, or supine) was improved to 84.2%. The sacrum was only fully offloaded for transverse pelvic angles of -90° and 90°, indicating there was little benefit to predicting with greater precision than with three categories: left, right, and supine.

Keywords: bed sores
healing
machine learning
pressure injuries
prevention
repositioning
Advisor: Dutta, Tilak
Optimization of Thermal Control Schemes for Small Satellite Constellations Utilizing on-Orbit and Test Data

As satellite constellations in Low Earth Orbit (LEO) become widely used for telecommunications, Earth observation, and astronomy by small commercial space companies, a means of reliable, scalable, and rapid thermal design for small constellations is required.This thesis explores the development of an automated stochastic optimization system for the rapid design of thermal optical tape schemes for small satellite constellations utilizing an SFL NEMO platform mission as a test bed for development and finalizing a design which was launched to orbit. The optimization system has been designed to be rapidly applied to arbitrary platform agnostic satellite geometries and limit the amount of manual thermal design and Non-Recurring Engineering (NRE) required for each satellite cluster for which orbital parameters can vary widely. The collective heritage of subsequent satellite clusters, Thermal Vacuum (TVAC) testing, and on-orbit measurements are used to iteratively inform the structural and thermal design of future clusters.

Keywords: Automation
Design
Optimization
Spacecraft
Structure
Thermal
Advisor: Zee, Robert E.
Dramaturgies of Being: Agency, Pedagogy and the Self-focused Performance of Tabletop RPGs

When approached as a performance medium, tabletop role-playing games, or TTRPGs, demonstrate a dramaturgical method that allows for the exploration of an individual player-performer’s agency, as well as the limits thereof. At the same time, the rule frameworks that structure play work to create experimental and pedagogical environments where suppositions about reality can become true within the virtual play-space, and thus allow space for speculative performances of said reality; if the rules say that something is true, what then becomes true by extension? The combination of these elements allows for the construction of ‘dramaturgies of being,’ which facilitate the performance of identity within the speculative framework, and thus the testing of said identities. Avery Alder’s 2018 game Dream Askew presents a dramaturgy of being for queer postapocalyptic identity exploration, community building, negotiation of agency, and teaching through simulated experience.

Keywords: agency
dramaturgies of being
pedagogy
postapocalyptic performance
tabletop role-playing games
Advisor: Cesare Schotzko, T. Nikki
Investigating the Impact of a Peptide Modified Hydrogel on Dermal Fibroblasts and Keratinocytes

Chronic wounds and excessive scarring represent large problems globally. Clinical efforts to facilitate effective wound healing and closure require a moist environment where coordinated process can occur. As a therapeutic for chronic wounds, Q-Peptide has been chemically conjugated to a chitosan-collagen hydrogel to maintain a stable wet healing environment, with demonstrated accelerated keratinocyte migration and immune modulation. Despite the observed functional efficacy of this peptide biomaterial in animal models, the direct effect on adult dermal fibroblasts and epithelial cells have not been investigated. This study has provided important insight into the direct impact of Q-Peptide on fibroblasts and keratinocytes, the main cells responsible for healthy wound healing. Using a deconstructed in vitro model to investigate these cell populations individually, we observed an anti-fibrotic and anti-inflammatory response that is temporally regulated alongside an appropriate early ECM deposition.

Keywords: Biomaterial
Fibroblast
Keratinocytes
Peptide
Q-Peptide
Wound Healing
Advisor: Radisic, Milica
The Characterization of Context-dependent Olfactory Memory and Neuropathology in 1.5 Months and 4 Months Old 5xFAD Mouse Model of Alzheimer’s Disease

Alzheimer’s disease (AD) is one of the most prominent neurodegenerative disorders that significantly affects our society. In attempt to develop an earlier diagnostic tool for AD, this study aims to integrate olfactory and spatial contextual components into behavioral tests to characterize the early emergence of olfactory impairments in 1.5 and 4 months old 5xFAD mice and examine amyloid beta (Aβ) plaque deposition in central olfactory regions. Our findings showed that both 1.5month old wildtype and AD mice displayed no neuropathological phenotypes and olfactory memory impairments. Both 4month old wildtype and AD mice did not perform well in all three olfactory behavioral tests, and 4month old AD mice showed Aβ deposition in the anterior olfactory nucleus and ventral hippocampal regions. Our observations are limited by the small sample size in the 4m WT mice cohort and the difference of odor source used. Subsequent experiments would be done to address such limitations.

Keywords: 5xFAD
Alzheimer's Disease
Early
Memory
Mice
Olfaction
Advisor: Kim, JunChul
Practical Implementation of Multi-UAV Flocking Path Planning

The primary objective of this thesis is to implement a flocking path planning algorithm in the three-dimensional dense environment to take into account the aerodynamics downwash effect. A method to model the downwash force generated by the quadrotor unmanned aerial vehicle (UAV) and its effect on the neighboring UAVs is developed. A novel adaptive UAV model is proposed to optimize the path planning while minimizing the downwash impact by adjusting the UAV model zone size. The virtual zone around an UAV for collision-free path planning is modified from a standard spherical body to a proposed adaptive cylinder then to an adaptive cuboid. The cylinder height and the cuboid size vary based on the UAV circumstance and the predicted downwash impact. The flocking algorithm is modified for the adaptive model. The models are simulated and compared via Python and the Gazebo and Robot Operating System (ROS) simulation platform.

Advisor: Liu, Hugh HHTL
Naltrexone use Among Patients Diagnosed with Alcohol use Disorder in Ontario

Naltrexone, a medication used to manage alcohol use disorder (AUD), was added to the Ontario Drug Benefit (ODB) program in 2018. This retrospective population-based cohort study among Ontario public drug beneficiaries who initiated publicly funded naltrexone from June 2018 to September 2019 aimed to determine the duration of naltrexone use in Ontario, as well as assessing the relationship between prescription setting and time to discontinuation of naltrexone. Among 2531 patients with AUD , the median (IQR) duration of naltrexone use was 31 (29-100) days, with  394 (15.6%) continuing naltrexone for 6 month or longer. Overall, there was no strong association between setting of initiation and duration of use, although, compared to those starting in physicians’ office, individuals initiating after an ED visit were less likely to be dispensed a second prescription. Future research can further elucidate the barriers encountered by patients with AUD, that lead to poor treatment retention.

Keywords: alcohol abuse
alcohol use disorder
AUD medication
naltrexone
Ontario
Advisor: Gomes, Tara
Studies on the Effect of Lewis Acids on Fmoc Deprotection in Solution and Solid-phase

New conditions for Fmoc-deprotection in peptide and organic synthesis using solution andsolid-phase conditions have been developed. Classical conditions for Fmoc-deprotections require 20% piperidine as a base, with dimethylformamide as a solvent. While these conditions have enjoyed widespread utility, they are not appropriate for all cases and have practical disadvantages. For example, DMF is known to degrade leaving traces in the deprotected product, requiring additional purification alongside its high boiling-point and teratogenic properties. Piperidine, although efficient leads to side product formation. When used in organic solvents such as dichloromethane, piperidine is also not ideal since an amine salt precipitates after a brief standing. Herein, we report that diethylamine, an inexpensive alternative to piperidine, in CH2Cl2 can be used for removal of a Fmoc-protecting group from the N-termini of amino-acids and peptides in the presence of Lewis-acids. Studies on the optimization of the reaction-conditions/ advantages/limitations using various Lewis-acids will be presented.

Advisor: batey, robert