VictorJuiz/thesis huggingface dataset:
Investigating the Role of Skeletal Muscle Bcl6 in Glucose Homeostasis and Muscle Mass and Function

Skeletal muscle comprises 30% to 40% of human’s body mass, and it is essential for supporting voluntary movement and posture. It also plays a critical role in lipid metabolism, fatty acid oxidation, and serves as the major site of post-prandial glucose disposal to maintain glucose homeostasis. B-cell lymphoma 6 (Bcl6), a transcriptional repressor, was first discovered for its role in the formation of germinal centres in humoral immune responses. Interestingly, Bcl6 is predominantly expressed in human skeletal muscles; however, its essential role in muscle remains unknown. Bcl6 has recently been identified as an emerging critical player in glucose homeostasis, with improved insulin sensitivity when deleted in adipocytes and led to protection against non-alcoholic steatohepatitis (NASH). Moreover, Bcl6 has been shown to transcriptionally regulate growth hormone (GH)/insulin-like growth factor (IGF)-1 pathway, an important signaling cascade in muscle growth. Thus, the purpose of this study is to investigate the essential role of skeletal muscle Bcl6 in glucose homeostasis and muscle function. My project highlights the findings of skeletal muscle Bcl6 knockout (M-Bcl6 KO) on muscle mass, which is significantly reduced compared to control mice. Interestingly, we did not observe any disruptions in global glucose homeostasis in M-Bcl6 KO mice. Moreover, our study reveals impairments in gene markers of muscle development, autophagy, and apoptosis in muscle of M-Bcl6 KO mice. These results shed light on the crucial role of Bcl6 in regulating muscle mass and provide a foundation for further exploration of its involvement in these pathways.

Keywords: Glucose Homeostasis
Metabolism
Muscle development
Muscle Function
Skeletal muscle
Advisor: Winer, Daniel
Woo, Minna
Effect of Sulfidated Nano Zero Valent Iron on Microbial Growth and Dechlorination Efficiency of a Reductive Dechlorinating Microbial Culture (KB-1)

This research investigated the potential of combining carboxymethyl cellulose coated sulfidated nano zerovalent iron (CMC-S-nZVI) and a reductive dechlorinating microbial culture (KB-1) to degrade a mixture of trichloroethylene (TCE) and 1,2- dichloroethane (1,2-DCA). An effective formulation of CMC-S-nZVI was able to degrade TCE but 1,2-DCA was left untreated. However, combined treatment successfully degraded both TCE and 1,2-DCA and compensated for the inhibitory effect of the anaerobic medium while having a mixed effect on microbial growth. Transmission electron microscopy illustrated that CMC-S-nZVI particles were attached to bacteria but did not penetrate bacterial cells. The combined treatment degraded TCE and 1,2-DCA at faster rates and generated lesser amounts of vinyl chloride than the KB-1 only treatment, confirming a biostimulatory effect of CMC-S-nZVI. Results showed that CMC was utilized as a successful carbon and energy source for microbial degradation in the KB-1 only treatment. Degradation pathways for TCE and 1,2-DCA are proposed, based on degradation products formation.

Keywords: 12-dichloroethane
Carboxymethyl cellulose
Dithionite sulfidation
KB-1
S-nZVI
Trichloroethylene
Advisor: Sleep, Brent
Preventing Slips and Falls: AI-Based Prediction of Footwear Slip Resistance Quality on Icy and Oily Surfaces

Slips and falls on icy and oily surfaces contribute to public health concerns and significant injuries worldwide. To mitigate such risks, this thesis focuses on developing predictive models for assessing slip resistance in footwear during the early stages of development. Specifically, deep learning and machine learning techniques were used to develop models that utilized information about footwear outsoles to classify them as having high or low slip resistance on icy and oily surfaces. The proposed models achieved high performance metrics, demonstrating the potential of Artificial Intelligence (AI) in slip resistance prediction. By offering valuable insights to footwear manufacturers, these models hold the potential to prevent fall-related injuries and fatalities, advancing safety in various environments.

Advisor: Roshan Fekr, Atena
Fernie, Geoff
Barriers to Entry for Equity-Deserving Farmers in Ontario

The Canadian Agricultural industry is on the brink of a major transformation. Canadian farmers on average, are aging out, and very few have a succession plan in place. Young people are abandoning their careers in the sector in favour of job security in urban centers. Farmers in general, experience a number of challenges associated with owning and operating a farm. However, structural barriers further complicate the ways in which ‘Equity-deserving’ farmers experience and navigate these challenges. There has been limited formal study interrogating how systemic marginalization has impacted the ability for 2SLGBTQ+, women, young and racialized farmers to participate and thrive in the agricultural industry. This thesis focused on equity-deserving farmers living and working in rural and peri-urban regions in Ontario, Canada. The data gathered from qualitative interviews and a demographic survey reveals four major areas of interest: (1) Training and Education Opportunities, (2) Land Access, (3) Identity, and (4) Strength in Community. This thesis offers policy suggestions and highlights the need for collaboration in order to effectively address these ongoing challenges.

Keywords: environment
equity
farming
justice
land
sustainability
Advisor: Classens, Michael
Plasma Extracellular RNA Facilitates Non-Invasive Detection of Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) lacks sufficient strategies to capture early-stage disease. To this end, liquid biopsies are an emerging modality for cancer screening. Tumour cells release RNAs that are detectable in the plasma by encapsulation in extracellular vesicles (EVs) as part of intercellular communication. To explore this avenue of detection, an optimized protocol was developed to capture extracellular RNAs (exRNAs). exRNAs consisted of intact full-length transcripts encoding a median of 34,975 genes derived from both protein-coding mRNAs and long non-coding RNAs. exRNA profiling correctly identifies 96\% of patients with resectable or metastatic PDA to the correct disease group, and predicts micrometastatic disease. In PDA patients, an enrichment of pancreatic cancer specific genes was found. In addition, PDA patients had upregulated secretion of repetitive elements, which mediates immunosuppressive effects in the tumour microenvironment and activates innate immune responses.

Keywords: Disease Detection
Extracellular RNA
Liquid Biopsy
Pancreatic Cancer
Transcriptomics
Advisor: Notta, Faiyaz
He, Housheng H
Interfacial Polymerization of Silica Nanoparticles to Create Modifiable, Ultra-Thin, Ultrafiltration Membranes

Interfacial polymerization is an industrially scalable technique, most notably used in the fabrication of reverse osmosis membranes, with the ability to create highly crosslinked thin films. This work successfully expands the interfacial polymerization chemistry library by utilizing 1D nanomaterials to create highly crosslinked, modifiable, defect-free nanoparticle membranes. Silica nanoparticles were used as a proof-of-concept due to their straightforward synthesis and chemical modification, exemplifying the feasibility of integrating nanoparticles into this established technique. Careful selection of the crosslinking agent in the interfacial polymerization scheme allowed for film thicknesses between 100 nm and 1.6 μm to be achieved. The nanoparticle layer exhibited poor mechanical stability under pressure and required a low pore size, high strength support membrane for stable operation. Chemical modification of the nanoparticle film with a hydrophobic polymer altered the water contact angle from 26° to 95°, showing ease of control over surface chemistry. This approach could be readily expanded to incorporate other types of nanoparticles and be applied to a wide range of applications beyond ultrafiltration.

Keywords: Membranes
Nanotechnology
Advisor: Werber, Jay
Collective Communication Enabled Transformer Acceleration on Heterogeneous Clusters

Field Programmable Gate Arrays (FPGAs) are becoming increasingly popular in data centers because of their ability to accelerate High-Performance Computing (HPC) and Machine Learning (ML) workloads. There has been extensive research on providing efficient tools such as Message Passing Interface (MPI) and ML model libraries that target FPGA platforms to developers and customers, due to the power efficiency, low latency, and flexibility provided by FPGAs. However, in the context of data centers, there could be hundreds or thousands of FPGAs deployed to accelerate one large-scale application, and the scalability of FPGAs is not well-researched in the academic field. In this thesis, we focus on extending the scalability of the Galapagos framework and propose a multi-cluster Galapagos project. We develop a tool, called Cluster Builder, for partitioning large-scale applications into multiple Galapagos clusters. To further increase the efficiency of the communication portion of the workloads, we propose to add one extra layer on top of the current Galapagos Stack, called the Galapagos Messaging Interface (GMI), which provides the necessary collective communication capabilities to the multi-cluster Galapagos framework. We also design an efficient multi-FPGA transformer model and use the Cluster Builder to deploy it on the multi-cluster Galapagos framework. Lastly, we propose a modified Galapagos framework that supports the AMD Versal Adaptive Compute Acceleration Platforms (ACAPs) [1] architecture. Based on the modified Galapagos framework, we estimate the performance of the transformer.

Advisor: Chow, Paul
NMDA Receptor Hypofunction in the Mouse Anterior Cingulate Cortex Associated with a De Novo GRIN1 Mutation at the M2 Reentrant Loop

The dysfunction of N-methyl-D-aspartate receptors (NMDARs) is consistently observed in a wide range of neurodevelopmental disorders and neurodegenerative diseases. Mutations of the GluN1 subunit of NMDARs have been shown to impair receptor trafficking and function which is thought to contribute to deficits in cognitive function observed in GRIN1-related neurodevelopmental disorders. Other clinical characteristics of GRIN1 variants such as altered pain sensitivity highlight a possible role of the anterior cingulate cortex (ACC), although the effects of GRIN1 variants at excitatory ACC synapses have not yet been studied. Whole-cell electrophysiology was used to examine NMDAR-mediated synaptic transmission and the intrinsic membrane properties of ACC layer II/III pyramidal neurons. The presence of the GRIN1_G620R missense mutation was associated with significant reductions in evoked NMDAR-mediated synaptic transmission, as well as changes to membrane input resistance and capacitance suggesting altered neuronal morphology. Our findings indicate that the ACC, a major region implicated in the processing of pain and emotion, is severely affected by the GRIN1_G620R missense variant in regard to the impairment of excitatory synaptic transmission.

Keywords: Anterior cingulate cortex
Electrophysiology
G620R missense mutation
GRIN1 disorder
NMDAR
Advisor: Collingridge, Graham L
Zhuo, Min
Towards the Design of Small, Inexpensive, Cable-Driven Dynamic Quadrupedal Robots

There has been a trend towards ever smaller and more capable quadruped robots. Continuing this trend, however, will require the use of smaller, higher-speed electric motors, which in turn will require the use of higher reduction ratio transmissions. Existing transmission designs are unable to achieve these ratios due to excessive friction, inertia, and size, but a cable-driven capstan could solve all of these problems. This project aims to demonstrate the suitability of this design for small quadruped robots by designing, simulating, and testing a physical prototype. Appropriate control methods will be developed and adapted. The resulting quadruped will be significantly lighter and cheaper than the state of the art.

Keywords: Capstan
Quadrupedal
Advisor: Schoellig, Angela P
Redesigning the Surgical Pathway: Optimizing PReOperative assessMent in Anesthesia Clinic for Adult Surgical Patients (PROMoTE)

Postoperative delirium (POD) is an acute, reversible disturbance in brain function affecting 20-40% of older adults undergoing major surgery. POD is associated with an increased risk of dementia, morbidity, and mortality. While current pharmacological treatments are limited and ineffective, simple multicomponent non-pharmacological approaches can prevent 30-50% of delirium cases. Although it can be reversible, POD still remains a pervasive issue with many cases unrecognized and undertreated. This thesis aims to address some knowledge gaps present in the existing literature. In this thesis, we conducted a prospective observational cohort study of data gathered from 92 participants with cognitive impairment in Phase I of the PROMoTE study. We will examine the effect of pre-operative cognitive impairment (pre-CI) severity on the incidence and severity of post-operative delirium (POD). In addition, we will compare delirium detection rates through in-hospital and remote delirium assessments as well as seasonal variation (spring-summer vs autumn-winter).

Keywords: cognitive testing
multicomponent intervention
perioperative cognition
postoperative delirium
surgery
Advisor: Choi, Stephen
The Impact of COVID-19 on the Curriculum of Graduate Orthodontic Programs in Canada: A Survey of Program Directors, Recent Graduates and Current Residents

Purpose: This study evaluated the impact of the COVID-19 pandemic on graduate orthodontic programs in Canada from the perspective of program directors, recent graduates and current residents.Methods: Two electronic surveys tailored to program directors (N=6) and recent graduates/current residents (N=144) were distributed via REDCap. Results: The response from program directors and residents/recent graduates was 100.0% and 43.1%, respectively. All programs utilized hybrid learning and most reported an increase in transfer cases and a decrease in new cases assigned to residents during the pandemic. Most programs incorporated virtual patient care. Residents from our cohort had a reduced case load and case exposure but similar reported satisfaction levels when compared to Noble et. al., 2009. Conclusion: With the exception of hybrid learning, programs plan to return to their pre-pandemic clinical and didactic curriculum. Overall, the COVID-19 pandemic did not appear to have a negative impact on graduate orthodontic programs in Canada.

Keywords: Canada
COVID-19
graduate orthodontic programs
orthodontics
program directors
residency
Advisor: Daskalogiannakis, John
Examining Links Between General Fatigue in Myasthenia Gravis with Objectively Measured Sleep

Examining Links Between General Fatigue in Myasthenia Gravis with Objectively Measured SleepJinyuru Yang Master of Science Institute of Medical Science University of Toronto 2023 Abstract Myasthenia gravis (MG) is an autoimmune disease that affects the neuromuscular system. Previous research has demonstrated a high prevalence of general fatigue in MG, which negatively impacts quality of life. Limited research has examined the association between sleep disorders and general fatigue in MG. This study investigated whether obstructive sleep apnea (OSA) severity in MG was correlated with the presence of general fatigue. We secondarily assessed the association of general fatigue in MG with other sleep disorders. Participants completed a home sleep apnea test (HSAT) and questionnaires assessing for general fatigue, sleep disorders, psychomotor vigilance, and depression. Our results showed that OSA did not have a significant association with general fatigue in MG. However, we found a significant association between poor sleep quality and reduced psychomotor vigilance with general fatigue in MG. Therefore, sleep quality and psychomotor vigilance may be contributing factors to general fatigue in MG and should be investigated in future studies.

Keywords: General Fatigue
Home Sleep Apnea Test
Myasthenia Gravis
Sleep Apnea
Sleep Disorder
Advisor: Boulos, Mark I
Groundwater Flow and Transport Model of Chloroanilines, Chlorobenzenes, and Dichloronitrobenzenes at an Industrial Site in Brazil.

Groundwater contamination is a widespread problem across many industrial areas. The application of modelling tools that can improve the understanding of how contaminations behave can offer great help for remediation activities. The project constructed a tri-dimensional finite difference groundwater model to simulate groundwater flow and contaminant transport using MODFLOW and RT3D250, respectively. Groundwater flow was modelled to understand the general flow direction and potential water transfer between layers. Multiple aquifer scenarios were simulated to assess how concentrations of Chlorobenzenes, Chloroanilines and Dichloronitrobenzenes would behave. Contaminant migration was found to be significantly affected by increasing the aquifer’s distribution coefficient and the contaminant’s decay rates. Source decay plays an important role in how plume concentrations evolve. Multiple limitations were observed during the model development and were mainly caused by the lack of data available for key parameters, such as boundaries, groundwater elevations and contaminant concentrations. The conclusion is that it was possible to develop an applicable groundwater flow and transport model. However, relevant data gaps must be addressed to enhance the model’s capabilities.

Keywords: Groundwater
Modeling
MODFLOW
Advisor: Sleep, Brent E
Exploring the 15-minute City: Access Sufficiency, Travel Behaviour, and Perceptions of Accessibility in the City of Toronto

The populations of cities have been increasing, so ensuring that cities provide a high quality of life for their residents has become an increasingly important goal in urban planning. Compact cities are considered the most sustainable urban form which has led to the recent popularity of the 15-minute City concept. Using the City of Toronto as a case study, this thesis explores different aspects of the 15-minute City to determine the relationship between 15-minute accessibility and travel behaviour in a North American context. The results suggest that residents of Toronto tend to use slower more sustainable modes of transport if they provide complete sufficient 15-minute access to destinations. Additionally, perceptions of accessibility improve as 15-minute access becomes more complete. However, several issues, notably Toronto’s current urban form, prevent the 15-minute City from being realized in all parts of the city.

Keywords: 15-minute City
GIS
Travel Behaviour
Urban Form
Urban Planning
Urban Transportation
Advisor: Higgins, Christopher
Deep brain stimulation for potentiation of underactive basal ganglia pathways in Parkinson’s disease

Bradykinesia is a hallmark of Parkinson's disease (PD). In PD, inhibitory inputs to the globus pallidus internus (GPi; via striatum) and subthalamic nucleus (STN; via globus pallidus externus; GPe) are hypoactive. We hypothesized that long-term potentiation (LTP) of inhibitory synaptic connections using deep brain stimulation (DBS) would improve parkinsonian bradykinesia. We collected data from patients with PD undergoing awake DBS surgery of the GPi (n = 7) or STN (n = 10). We measured hand movements and inhibitory synaptic efficacy before and after delivery of a high-frequency stimulation protocol. LTP-like effects of striato-pallidal projections were observed in GPi (p = 7.08e-17), which coincided with increased hand pronation/supination amplitude (p = 0.040) and frequency (p = 0.009). GPe-STN plasticity and hand movement results were non-significant in STN (p > 0.05). This study is among the first to investigate clinical implications of subcortical LTP induction, paving the way for new therapeutic strategies.

Keywords: Deep-brain stimulation
long-term potentiation
Parkinson's
synaptic plasticity
Advisor: Milosevic, Luka
An Intelligent Social Robot for Assisting with Multiple Daily Activities

As the population ages, there is an increasing demand for support with activities of daily living (ADLs) in the homes of older adults and in long term care. Socially assistive robots (SARs) have shown success in increasing ADL independence by providing adaptive assistance for a variety of tasks including eating and dressing. The objective of this thesis is to develop new technologies for improving the design of SARs for ADL assistance. Namely, this thesis develops: 1) a novel social robot and wearable sensor system for assisting with the ADL of dressing, and 2) a new deep learning ADL recognition architecture for autonomously recognizing and monitoring known and unknown ADLs. Experiments evaluate performance using classification accuracy and real-time functionality using metrics such as usefulness and reliability. Results for classification performance show the developed methods outperform existing work while interaction experiments validate the systems for use with a variety of diverse users.

Keywords: Activity Assistance
Activity Recognition
Deep Learning
Human Robot Interaction
Robot Learning
Social Robot
Advisor: Nejat, Goldie
Examining the Sexual Violence Prevention Approaches of Toronto Universities: Focus on Varsity Athletic Programs and Sports

Sexual violence is an ongoing issue that plagues Canadian Universities. This research explores the relationship between university athletics and how this impacts a culture of sexual violence. Student athletes disproportionately represent sexual violence offenders on university campuses; despite this, athletes continue to play an active and public role within university communities (Beaver, 2019). This research explores the sexual violence policies of three predominant universities within the city of Toronto Ontario, Canada. Uncovering through archival analysis and policy review, the lack of preventative intervention available to students. This highlights the ongoing issue of reactive policy that does little to protect students and proactively address the pattern of violence against women as pertains to athletics and sports. Addressing an overrepresented group of perpetrators allows insights into the interconnection between sports and the student athlete within the context of sexual violence which can lead to positive prevention initiatives.

Keywords: Athletics
Education
Gender Stereotypes
Rape Prevention
Sexual Violence
Sports Media
Advisor: Todorova, Miglena S
Relationship Between Admission Body Mass Index (BMI), Nutritional-Inflammatory Biomarkers, and In-Hospital Outcomes among Hospitalized COVID-19 Patients

Background: COVID-19 continues to present challenges, as certain patients require hospitalization due to pre-existing risk factors or the severity of the illness, possibly leading to adverse clinical outcomes. This thesis aims to investigate the association between BMI categories, biomarkers and in-hospital outcomes.Methods: This retrospective study analyzed data from 241 hospitalized COVID-19 patients from March 2020 to May 2022 to examine the association of patient characteristics, including BMI categories and patient outcomes. Results: Obesity was independently associated with decreased in-hospital mortality after adjusting for potential confounders. Obese patients were predominantly female, younger in age, with elevated admission levels of albumin. Moreover, a higher decrease in albumin level in COVID-19 patients was linked to prolonged hospital stays. Also, deceased patients showed significantly elevated Neutrophil-to-Lymphocyte Ratio. Conclusion: BMI, along with albumin at admission and Neutrophil-to-Lymphocyte Ratio, might serve as indicative factors for assessing the prognosis and morbidity of hospitalized COVID-19 patients.

Keywords: Biomarkers
BMI
Body mass index
COVID-19
In-Hospital Outcomes
SARS-CoV-2
Advisor: Shafiee, Mohammad MS