VictorJuiz/thesis huggingface dataset:
Investigating ROI-independent Segmentation and Classification of Glioma in MR Images and of Liver Fibrosis Detection in CT Images

Segmentation and classification of anomalies is a critical problem in medical imaging. Machine learning has demonstrated potential in automating this problem but generally relies on manually annotated segmentations or regions of interest to train the machine learning models. Acquiring the manual annotations demands extensive time and resources from radiologists, and hinders the development and deployment of machine learning solutions for medical imaging problems without fully annotated datasets. This thesis presents a novel approach to brain tumor segmentation in magnetic resonance images that uses generative adversarial networks to remove the need for manual annotations. These segmentations can be successfully applied to downstream clinical tasks such as genetic marker prediction and pathology prediction. This thesis also presents the optimal approach to liver fibrosis detection in computed tomography images using Radiomics and insights into how to develop liver fibrosis detection solutions without the need for manually annotated regions of interest.

Keywords: Classification
Computed tomography
Glioma
Liver fibrosis
Magnetic resonance imaging
Weakly supervised segmentation
Advisor: Khalvati, Farzad
Approximation for Flash Memory to Reduce Energy and Increase Lifetime

Flash memory is commonly used in IoT devices for both data and code storage. Relative to the overall device, flash consumes a significant fraction of energy. This is problematic because IoT devices are energy constrained due to reliance on batteries or energy harvesting. To reduce this energy consumption, we exploit a significant asymmetry; notably, flash operations take unequal amounts of energy depending on if we are flipping a 1→0 versus a 0→1. We propose FlipBit, a hardware-software approximation approach that limits costly 0→1 transitions in flash. Instead of performing an exact write, we write an approximated value that avoids any costly 0→1 bit flips. On machine learning models, we reduce energy by an average of 39% and up to 71% with only a 1% accuracy loss. Additionally, by reducing the number of program-erase cycles, we increase the flash lifetime by 68%.

Keywords: Approximate Computing
Computer Architecture
Flash Memory
IoT
Advisor: Enright Jerger, Natalie
Geometry-Free Prediction of Inertial Lift Forces in Microchannels

Inertial microfluidic devices (IMDs) are a low-cost and high-throughput means of manipulating, separating, and focusing suspended particles on the micrometer scale. The precise nature of the lift force affecting particle motion within IMDs is difficult to determine analytically. As a result, designing these inertial microfluidic devices typically requires either financially costly physical design cycles or computationally costly direct numerical simulation. Existing data-driven attempts at alleviating these costs require the impractical step of generating a new model for every new channel cross-sectional geometry. Herein, we re-formulate traditional expressions for lift force to be completely independent of channel geometry and then use this geometry-free re-formulation to parameterize a fully-connected neural network (FCNN). We train this FCNN on a publicly available lift force dataset for rectangular channels and show that with our parameterization the FCNN is able to generalize to triangular, semicircular, and trapezoidal channel geometries. We suggest possible ways to improve the generalizability of the model --- mostly centered around increasing training data heterogeneity --- with the hope that our model will eventually be integrated into computational fluid dynamics software to drastically reduce the computational burden of simulating IMDs.

Keywords: Cell separator
Lift force
Machine learning
Microfluidics
Neural network
Advisor: Chan, Timothy
Young, Edmond
Privacy-Preserving Network Anomaly Detection via Homomorphic Encryption

Network Anomaly Detection refers to the detection of abnormal network activities due to security breaches or other network issues. Traditional methods of detection often rely on known signatures of anomalies. More recently, the advancement of machine learning has become a more robust mechanism to address this issue. However, the nature of network anomaly detection directly contradicts with the notion of data privacy and confidentiality. Being able to detect anomalies while preserving the privacy of the data has become a hotly researched topic. This thesis proposes a privacy-preserving Random Forest classifier tailored for anomaly detection settings. The system leverages Fully Homomorphic Encryption (FHE) encryption to achieve privacy-preserving classification on encrypted data. This work improves the computation and communications costs compared to previous works. Furthermore, the system is hardware-accelerated by GPUs, resulting in a speedup of up to 160x over a single-threaded CPU. Importantly, the optimization techniques place special emphasis on the scalability of the overall system, so that it can process higher throughput by horizontally scaling the hardware resources. This thesis also proposes a client-server-based protocol for generic random forest predictions, suitable for use cases such as Machine-Learning-as-a-Service (MLaaS). The privacy-preserving Random Forest was evaluated by common classification metrics on a network detection dataset, CIC-DS-2017. Experiments have shown that our system is able to sustain a detection throughput of 15 Kbps with high detection accuracy (F1 $>$ 0.90) on a system with an Nvidia A100 GPU.

Keywords: Homomorphic Encryption
Advisor: Gulak, Glenn
Inclusive Accessible or Culturally Relevant? Two Perspectives on Accounting for Culture in Community-based Stroke Physical Activity Programs

With the growing prevalence of stroke, recognition of health disparities experienced by ethnically marginalized communities, and growing cultural diversity across Canada, community-based organizations have a distinct opportunity to address the unique barriers and cultural needs of culturally diverse individuals with stroke. This thesis explores how eight program leaders within Canadian community-based organizations account for ethnicity and culture in the development of stroke physical activity programs. Three themes were identified based on interviews with program leaders: (1) multiple definitions of culturally relevant programs, (2) inclusive & accessible and culturally relevant program attributes, and (3) inclusive & accessible mindset versus culturally relevant mindset. The findings of this thesis highlight the variability of program leaders’ perspectives when defining culturally relevant and their approaches to designing and delivering programs for ethnically and culturally diverse people with stroke, including whether or how they integrate cultural needs into programs, which they describe is often a decision made by program leaders rather than a requirement of programs or organizations.

Keywords: Community Services
Culturally Relevant
Physical Activity
Stroke
Advisor: Nelson, Michelle L A
Determining the Effects of Pebiotics through Community-based Metabolic Modeling

The human gut microbiome plays an important role where it performs functions such as promoting immune system development and protecting against enteric pathogens. Amongst many other functions, the microbiome produces metabolites from breakdown of prebiotics that can be beneficial to human health. These metabolites include SCFAs. A recent study found that gut microbiota derived SCFAs can play an important role in repair capacity in response to heart damage. It is hypothesized that this property of the gut microbiome can be utilized to improve the recovery of patients after surgery. The purpose of this study was to simulate the infant gut microbiome in silico and identify prebiotics that could increase the level of SCFAs. In this study, six infant stool samples were taken, and bacterial DNA was extracted and sequenced using 16S and shotgun metagenomics. The shotgun metagenomic sequences were utilized to construct metabolic models of the microbes present in the infant gut. On an average there were 20 metabolic models per sample. The infant gut microbiome was populated with the phylum Actinobacteria, specifically the Bifidobacteriaceae family. Simulations were performed using the metabolic models constructed from the metagenomic data. Upon addition of prebiotics to the simulation, the overall composition did not dramatically change. However, the proportion of SCFAs increased with the addition of prebiotics in the simulation. Metabolic modeling is an invaluable tool to make efficient predictions for the human gut microbiome.

Advisor: Parkinson, John
Environmental Modulations of Microglia in Mouse Brain

Microglia, the resident immune cells of the brain, can adopt pro- or anti- inflammatory states in response to different stimuli. Utilizing advanced techniques such as two-photon serial tomography and deep learning, we examined the effects of Δ9-tetrahydrocannabinol (THC), lipopolysaccharide (LPS), and diet induced obesity (DIO) on microglial density and soma size across both male and female mice. Our findings reveal that THC led to lower levels in microglial density and soma size in females, aligning with its anti-inflammatory properties. Conversely, LPS increased density and soma size in both sexes, indicative of its pro-inflammatory role. DIO showed no significant impact, although a trend suggested potential male-specific pro-inflammatory effects or female-specific protective effects. Our study extends previous research on microglia reactivity and morphological changes, shedding light on potential sex-specific responses and enrich our understanding of microglia response to different environmental stimuli.

Keywords: Microglia
Neuroinflammation
Two Photon
Advisor: Pausova, Zdenka
Opportunities, Challenges, and Curricular Insights Identified by Graduate Orthodontic Educators During the 2020/21/22 Academic Years at the University of Toronto

This study investigated the opportunities and challenges associated with pandemic-related changes to didactic and clinical teaching. Seven instructors that deliver didactic, and/or clinical components of the graduate orthodontics program at the University of Toronto were interviewed virtually on their teaching experiences during the 2020/2021/22 (Fall term) academic years. The data were analyzed using the thematic analysis technique described by Braun and Clarke (2006). The key curricular insights, and the opportunities and challenges of the modified didactic and clinical teaching were identified. Educators’ preferred mode of didactic teaching varied, and preferences were course-specific. Educators preferred to return to the pre-pandemic clinical curriculum. There was enthusiasm towards adopting a hybrid model and implementing online and digital tools in both didactic and clinical curricula. Educators indicated the need for institutional support (technological/ infrastructural/human resources, incentives, and training) to promote adoption of online didactic teaching, and better preparedness for the future.

Keywords: Clinical Curriculum
COVID-19
Didactic Curriculum
Educator Insights
Online Education
Orthodontics
Advisor: Dempster, Laura
Mendes, Vanessa
Cardiovascular Physiology During Orthostasis in Healthy Older Women

The ability to sustain an upright posture is a common daily stressor for humans and requires integrated cardiovascular and autonomic adjustments to adequately compensate for the increased gravitational load that accompanies standing. This thesis examined the normal circulatory response to a 10-minute active stand in a group of self-reported healthy older women. Concurrent right heart catheterization and arterial line monitoring were used to describe changes in hemodynamic variables between supine and standing positions. Standing was associated with an increase in heart rate (8±5 to 14±6 bpm) which was maintained above supine levels over the duration of the 10-minute stand. Blood pressure did not change significantly with standing. Cardiac filling pressures tended to fall, while stroke volume (-31±6%) and mixed venous oxygen saturation (-10±4%) decreased persistently in all participants. In summary, the physiologic response to a 10-minute active stand test in healthy older women involves a complex cardiovascular and circulatory response.

Keywords: cardiology
orthostasis
Advisor: Mak, Susanna
Sex-specific Differences in Heart Rate Variability in Bipolar Disorder

Women diagnosed with bipolar disorder (BD) were reported to have elevated cardiac risk relative to men, yet the etiology underlying this has not been determined. Heart rate variability (HRV) is a predictor of cardiac health that can evaluate the state of the autonomic nervous system. We assessed 24-hour HRV parameters (i.e., Root Mean Square of Successive Differences (RMSSD), Standard Deviation of Normal-to-Normal (NN) intervals Index (SDNNI), Standard Deviation of Average NN intervals (SDANN), and HRV Triangular Index (RTI)) from 35 participants using wearable technology to investigate differences in HRV between men and women with BD. When controlling for family history of psychiatric disorders, we observed lower SDANN in women, but no significant differences for the other parameters. Autonomic dysfunction may be a mechanism underlying the observed difference, but our conclusions are limited by the sample size. Future studies with larger samples are encouraged to minimize Type I/II errors.

Keywords: Autonomic Dysfunction
Bipolar Disorder
Cardiovascular Disease
Heart rate variability
Vascular-bipolar link
Wearable Technology
Advisor: Ortiz, Abigail AO
Hybrid Electromagnetic Acoustic Transducer (EMAT) Systems for the Non-Destructive Detection of Corrosion-Induced Defects in Steel

Four combinations of Electromagnetic Acoustic Transducers operated at two frequencies are tested on an industrially representative 1018 Low Carbon steel plate and pipe section with an artificial pitting defect. The combination involving a Periodic Permanent Magnet EMAT as the transmitter and a Magnetostrictive Meander Line Coil EMAT as the receiver was found to be the most favourable due to its strong signal strength in non-defect regions and signal reduction in areas with defects. It was also generally found that operating at the lower of a pair of operating frequencies and using the Magnetostrictive EMAT as the receiver led to better overall defect sensitivity. Two of the four combinations were hybrid versions, which demonstrated heightened signal strength over their homogeneous counterparts. Finite element simulations and additional experiments were conducted to theoretically supplement and verify the above results and trends.

Keywords: Corrosion
Defects
Electromangetic Acoustic Transducer
Finite Element Modelling
Non-Destructive Testing
Pipelines
Advisor: Filleter, Tobin
Sinclair, Anthony
Infant Nasal Microbiome and Respiratory Health Outcomes in Early Childhood in the CHILD Cohort

The microbes that reside on the surface of our nose and sinuses make up the nasal microbiome. Using the data from the CHILD Cohort Study, a large Canadian prospective longitudinal cohort, we sampled the nasal microbiome and examined which environmental factors were associated with nasal microbiome alpha diversity and differential abundance, the effects ofviral presence on the nasal microbiome and if the nasal microbiome was associated with early life respiratory disease (asthma, wheeze, and allergic rhinitis). The infant nasal microbiome was associated with many environmental factors including prenatal smoke exposure and older siblings.Infants with viral presence had decreased alpha diversity and increased Moraxella sp.8 and Haemophilus sp.41. Additionally, the change in alpha diversity and individual operationaltaxanomic units (OTUs) between 3 and 12 months was associated with when infants had viral presence. Finally, infants with high asthma risk, wheeze and allergic rhinitis had multiple differentially abundant OTUs in infancy.

Advisor: Subbarao, Padmaja
Detection of Vaulting Gait with Multi-Modal Non-Linear State Estimation

A methodology for automatically detecting distinct gait modes is presented in this thesis. Two distinct gait models are parameterized based on collected data from the literature, representing a normal gait pattern and a vaulting gait pattern. Structural observability analysis is performed on the dynamic models, taking into account available output measurements from a simple, low cost sensor package. A state estimation system, comprised of Unscented Kalman Filter variants and an Interacting Multiple Model estimator, is applied to simulated and live data to automatically detect the gait mode.

Keywords: Bipedal locomotion
Control theory
Non-linear systems
State estimation
Vaulting
Advisor: Taylor, Josh A
Regulation of Neuropeptide Y by MicroRNAs in Hypothalamic Neuronal Cell Models

Orexigenic neuropeptide Y (NPY) neurons within the hypothalamus stimulate feeding behaviour and suppress energy expenditure, and dysregulation to these neurons may contribute to overeating and obesity. Hypothalamic microRNAs (miRNAs), a class of small non-coding RNAs, are essential for energy balance. Several miRNAs have been identified as indirect regulators of Npy and whether miRNAs can directly modulate Npy remains unclear. Five putative Npy-targeting miRNAs were present in hypothalamic cell lines. We examined the effects of putative Npy-targeting miRNAs using miRNA mimics, and we found that miR-143-3p, miR-140-5p, miR-29b-1-5p and let-7b-3p altered Npy expression in two hypothalamic cell lines, mHypoE-41 and mHypoE-46. Importantly, miR-143-3p targeted the mouse Npy 3’ untranslated region (UTR). Bisphenol A, an endocrine disruptor with obesogenic properties, also dysregulated the expression of hypothalamic miRNAs. Overall, this study discovered a hypothalamic miRNA that targets the 3’ UTR of mouse Npy, emphasizing the direct involvement of miRNAs in the NPY system.

Advisor: Belsham, Denise
Prescient Migration for Data-Dependent Distributed Transactions

Deterministic databases reduce the need for expensive commit protocols, which enables scaling transaction processing in distributed environments. However, workloads with intra-transaction cross-node dependencies still impose significant overheads. Our aim is to efficiently support distributed transactions with intra-transaction dependencies, which we call data-dependent distributed transactions. We propose using a combination of 1) transaction scheduling and transaction migration policies to reduce the overhead of data dependencies, and 2) data migration policies to reduce the number of distributed transactions. We implement these policies in the Caracal deterministic database. We evaluate these policies and identify the types of workloads that benefit from these policies.

Keywords: Data Dependencies
Databases
Distributed Systems
Migration
Advisor: Goel, Ashvin
An Investigation and Exploration into the Use of Repetitive Transcranial Magnetic Stimulation as an Intervention for Promoting Positive Self-Regulatory Behavior in Children with Autism Spectrum Disorder

Background: Children with autism spectrum disorder (ASD) often present with impairments in social, educational, and occupational settings. Impairments in these settings may be caused by deficits in self-regulation and can lead to unwanted behaviors. Thus, interventions targeted toward self-regulation are needed.Objectives: (1) To identify how repetitive transcranial magnetic stimulation (rTMS) may improve symptoms of ASD; and (2) to assess the feasibility of rTMS as an intervention technique for children with ASD. Methods: (1) Systematic review methodology was used to synthesize literature on rTMS in pediatric ASD. (2) A double-blind, randomized controlled trial was conducted to explore the feasibility and tolerability of rTMS. Results: (1) Further investigation is needed to determine the most efficacious rTMS metrics. (2) rTMS shows therapeutic potential for ASD, but barriers to feasibility must be addressed. Conclusion: This dissertation will inform future clinical trials exploring the feasibility of therapeutic interventions for pediatric ASD.

Keywords: Autism spectrum disorder
Emotional regulation
Problem behavior
Repetitive transcranial magnetic stimulation
Advisor: Beal, Deryk S
Development of 197Hg-Labelled Panitumumab for Auger Electron Radioimmunotherapy of Triple-Negative Breast Cancer

Objective: The cytotoxicity of anti-EGFR monoclonal antibody panitumumab directly radiolabelled with 197Hg or conjugated to S-2-(4-isothiocyanatobenzyl)-1,4,7,10-tetraaza-1,4,7,10-tetra(2-carbamoylmethyl)cyclododecane (p-SCN-Bn-TCMC) and radiolabelled with 197Hg was evaluated in EGFR-overexpressing human MDA-MB-468 triple-negative breast cancer (TNBC) cells. Methods: 197Hg-TCMC-panitumumab and 197Hg-panitumumab were constructed and characterized in vitro using analytical techniques that measured their homogeneity, EGFR binding affinity, radiochemical purity, and binding specificity to MDA-MB-468 cells. In addition, the cytotoxicity of the radioimmunoconjugates was studied in a clonogenic survival assay. Results: 197Hg-TCMC-panitumumab was homogeneous with approximately 2 TCMC molecules bound per panitumumab molecule and had high EGFR binding affinity (1.16 x 10-13 M). 197Hg-TCMC-panitumumab and 197Hg-panitumumab had high radiochemical purity (90% measured using instant thin layer silica gel chromatography) and demonstrated EGFR-specific binding to MDA-MB-468 cells. Clonogenic survival of MDA-MB-468 cells showed that 197Hg-TCMC-panitumumab and 197Hg-panitumumab were significantly more cytotoxic than panitumumab, which did not affect the survival of MDA-MB-468 cells. These radioimmunoconjugates are promising therapeutic agents for TNBC and warrant further in vitro and in vivo preclinical evaluations (e.g. serum stability study, γ-H2AX assay, cell fractionation assay, biodistribution study, tumour imaging study).

Keywords: Auger electron radioimmunotherapy
Mercury-197
Panitumumab (mAb of EGFR)
Triple-negative breast cancer
Advisor: Reilly, Raymond M
International Graduate Students' Experience with University Career Services: A Case Study at a Southern Ontarian University

This study explores international graduate students’ experiences using university career services for their career development at a southern Ontario university. The research draws on findings from the previous literature regarding services provided by the university career centres and international graduate students’ experience in using them. Employing a qualitative single-case study approach, I analyzed two career centres’ websites and interviewed two career centre staff and seven international graduate students at the institution. The inductive, problem-oriented study aimed to discuss how its findings spoke to the existing literature about international graduate students’ challenges in using university career services. The findings revealed that career centres provided diverse career services, but those services were not sufficient and customized for international graduate students’ specific needs. The study enriches the existing knowledge and suggests the need for more tailored and accessible career services for international graduate students’ career development.

Keywords: career development
career services
case study
international students
Advisor: Manion, Caroline