VictorJuiz/thesis huggingface dataset:
Deep Learning Models for Malicious Web Content Detection: An Enterprise Study

Malicious web content detection remains an important component in enterprise cybersecurity. Exist-ing heuristics-based methods as well as detection models that require feature engineering may not besufficient or scale well. In this work, we gather the HTML strings of approximately 800,000 URLs in a bal-anced malicious:benign classification ratio. Building from existing preprocessing techniques to extractrelevant features into a Bag-of-Tokens style representation, we develop convolutional and sequenced-based deep learning models to perform binary classification and demonstrate that, on balanced datasets,these models perform well, the best model with an average precision of 95%. We also simulate zero-dayattacks by modifying the malicious:benign ratio and training models with alternative loss functions. Inthe context of enterprise cybersecurity as a second step after heuristics-based models, these models aremoderately successful, with average precision scores of 50% and 25% on malicious:benign ratios of 1:10and 1:00 respectively

Advisor: Lawryshyn, Yuri A
The Role and Effects of CD200R Activation in Murine Models of Allergic Airways Inflammation

The CD200/CD200R anti-inflammatory signalling pathway plays an important role in immune homeostasis and has been reported to be dysregulated in asthma, a chronic inflammatory airways disease. We hypothesized that activation of the CD200R will initiate an anti-inflammatory signalling cascade which will reduce features of asthma. We explored the role of the CD200/CD200R signalling pathway in the pathogenesis of an allergic airways inflammation model and evaluated the effects of CD200R activation with the agonist aptamer PEG.CCS13 on the features of asthma. Our results found the CD200/CD200R pathway imbalanced in a chronic model of allergic airways inflammation, suggesting it plays a role in the pathogenesis of the disease. We further found that activation of the receptor with PEG.CCS13 resulted in a reduction in features of asthma including eosinophilic inflammation, airway hyperresponsiveness and goblet cell hyperplasia. We concluded that activation of the CD200R is a promising therapeutic candidate for an asthma treatment.

Keywords: Allergic Airways Inflammation
Aptamer
Asthma
CD200/CD200R
Eosinophilia
PEG.CCS13
Advisor: Chow, Chung-Wai
Fine Position Estimation of the Myocardium using a UWB Radar for Magnetic Resonance Image Guided Cardiac Ablation

Heart surgeries, such as cardiac ablations, require an accurate estimate of the location of the myocardium in millimeters. This thesis develops the use of a UWB radar to track the position of the myocardium in real time. We construct a phantom to simulate the dielectric propagation path from the precordium to the myocardium which includes an obstacle to simulate the chest wall and a motion stage to simulate cardiac motion. We use an off-the-shelf radar operating with 6-10 GHz; however, this large bandwidth is still inadequate. Therefore, we utilize high sampling rates to interpolate, using the Gaussian transmitted signal, to obtain finer resolution. We test our approach by tracking the phantom position with a motion stage simulating sinusoidal and chirp movements. The results show that the radar can provide adequate resolution to track a myocardium phantom. We also successfully performed a preliminary verification on a human subject with ethics approval.

Keywords: Cardiac Ablation
GMM
MRI
Radar
Super Resolution
UWB
Advisor: Adve, Raviraj S.
Mitigation of Classes of Attacks using a Probabilistic Discrete Event System Framework

Cyber-attack models and strategies for their mitigation have been studied recently in a deterministic discrete event system setting. The focus is on whether unsafe behaviour can be prevented using supervisory control. This thesis proposes the use of a probabilistic discrete event system (PDES) framework to incorporate a measure of the likelihood of unsafe behaviour in the attack model. The least unsafe (LU-)supervisor problem is introduced to minimize this unsafe likelihood measure and improve existing attack mitigation techniques. The LU-supervisor problem is reformulated as a Markov decision process (MDP) for analysis. The solution to the LU-supervisor problem is characterized under the assumption of full observability and an algorithm for its computation is developed. For partially observable systems, the LU-supervisor problem is shown to correspond to an infinite horizon partially observable MDP (POMDP) with a suitably chosen cost criterion. Lastly, the implementation of LU-supervisor is discussed and illustrative examples are presented.

Keywords: attack
control
cyber-security
discrete
mitigation
probability
Advisor: Kwong, Raymond H.
Towards Robotic Cleft Palate Repair: Development and Characterization of a 3 mm Wrist for the da Vinci Surgical System

Surgeons are interested in developing a robotic approach for cleft palate repair to improve outcomes and ergonomics for surgery in the infant oral cavity. However, the current instruments are too large for the workspace. The aim of this thesis was to develop a novel 2-degree-of freedom wrist with cable guide channels as a 3 mm diameter instrument for use with the da Vinci Surgical System. Specifically, a cam mechanism was built to solve the cable slack issue inherent to the novel wrist design. When evaluating motion accuracy, the mean error of moving in the same direction was found to be less than one degree, while the hysteresis resulted in an average error of 14 degrees when switching directions. Finally, proof of concept was demonstrated by using the instrument to suture silicone in a medicine cup, verifying that it is able to perform complex tasks and can apply sufficient forces, despite the hysteresis.

Keywords: cable guide channels
cleft palate
mechanical design
robotic surgery
robotic wrist
surgical instrument
Advisor: Drake, James M
Exploring the Prevalence of Maltreatment amongst Canadian National Team Athletes

The purpose of this study was to assess the prevalence of maltreatment amongst National Team athletes in Canada. In total, 1001 male and female National Team athletes participated in this study, including 764 current athletes and 237 athletes who had retired in the last 10 years. Athletes completed an anonymous 127 item online survey consisting of questions on psychological, physical and sexual abuse, neglect, disclosure and reporting of instances of harm, and mental health outcomes. Athletes reported experiencing psychological harm most frequently, followed by neglect, sexual harm and physical harm. Harmful behaviours were enacted most frequently by coaches, followed by peers, high performance directors and sport administrators. The findings revealed significant and positive relationships between all forms of harm (psychological, physical, sexual and neglect) and the negative health outcomes of engaging in self-harming behaviours, disordered eating behaviours/eating disorders, and having suicidal thoughts. Finally, athletes provided recommendations for advancing safe sport.

Keywords: Athletes
Canadian
Maltreatment
Prevalence
Advisor: Kerr, Gretchen
Polarized Light Microscopy of Human Breast Cancer

It has been shown that the stroma surrounding the tumour can play an important role in cancer behaviour and response to therapy. Polarimetry may be a suitable technique for this application because collagen, a fibrous component of stroma, is anisotropic and interacts strongly with polarized light. Polarimetry is also attractive because it is rapid, widefield, and non-ionizing. We proposed a novel and relatively simple methodology of polarized light microscopy to image thin, unstained histology slides using only crossed linear polarizers. The brightness of birefringent structures under crossed polarizers is dependent on the relative orientation of the structures and the polarizers. By imaging slides at various orientations, we can obtain retardance and fast axis orientation images, important measures of tissue biophysics. From images acquired, morphological features describing the density and alignment of the stroma within the tumour microenvironment are extracted to be used in a future breast cancer prognostication tool.

Keywords: Breast Cancer
Collagen
Polarimetry
Stroma
Tumor Microenvironment
Advisor: Vitkin, Alex
Re-evaluating the Other Accent Effect in Talker Recognition

Talkers are better recognized when they speak a language familiar to listeners than when they speak a language unfamiliar to listeners. This existence of this Language Familiarity Effect in talker recognition is uncontroversial. The Other Accent Effect (OAE), in contrast, is less well-established. Does a listener’s familiarity with a talker’s accent affect how well that talker is recognized? While some studies find an OAE, others do not. To resolve this apparent contradiction, we examined Canadian English listeners’ ability to recognize talkers in four conditions: a familiar language in the listeners’ own accent (Canadian English), a familiar language in another regional accent (Australian English), a familiar language in a non-native accent (Mandarin-accented English), and an unfamiliar language (Mandarin). We predict an OAE for the non-native but not for the regional accent, which is what we observe. We discuss how our findings bring us closer to resolving the OAE debate.

Keywords: accented speech
language familiarity effect
phonology
speech perception
speech processing
talker recognition
Advisor: Johnson, Elizabeth K
Using Layered Division Multiplexing for Mixed Unicast-broadcast Service Delivery in 5G-MBMS

Point-to-multipoint (PTM) transmission is a key enabler for emerging 5G New Radio (NR) applications. For more efficient use of spectrum, 3GPP is working on a 5G multimedia broadcast multicast service (5G-MBMS) subsystem to provide effective mixed services on a unified platform. This thesis shows in many cases, capacity of the current multi-cell unicast service is limited by co-channel interference. Using a reduced transmission power will not impact the system performance. Meanwhile, for broadcast services using single frequency network (SFN), there is no co-channel interference. Slightly reducing the broadcast service emission power will not impact the system quality of service (QoS). This provides a good opportunity to apply layered division multiplexing (LDM) to combine broadcast and unicast services in one RF channel by power sharing. This work demonstrates that, in a 5G-MBMS with two-layer P-NOM/LDM, broadcast and unicast services can be efficiently and effectively delivered using the same spectrum resource.

Keywords: 5G
Injection Levels
layered Division Multiplexing
MBMS
Mixed Service Delivery
Non-Orthogonal Multiplexing
Advisor: Sousa, Elvino S
Understanding Math Anxiety in School-aged Children

This study investigated the effectiveness of measuring math-anxiety in elementary school students using real-time facial expression software (emotient) and self-reported Math anxiety using the Achievement Emotions Questionnaire- Elementary Students (AEQ-ES). Students aged 11-14 were asked to complete the AEQ-ES. Students were then given 5 standardized math questions taken from the Education Quality and Accountability Office (EQAO) and asked to rate how difficult they found each question (1-4). It was hypothesized that math anxiety would be related to difficulty ratings of math questions and performance on the math task, while parent ratings of their child’s math abilities was expected to affect the development of child’s math anxiety and math performance. This study will inform research on development of math anxiety and possible areas for intervention.

Keywords: Developmental psychology
Education
Educational tests measurement
Elementary education
Mathematics education
Psychology
Advisor: Woodruff, Earl
Chemical Characterization of Automotive Coverstock and Biomass Burning Emissions

Indoor and outdoor sources emit organic compounds which can have substantial impacts on human health and climate change. In this study, volatile organic compounds (VOCs) from automotive interior materials and from laboratory biomass burning were analyzed to identify specific sources that lead to their emissions. VOC emission profiles from finished and raw materials used in automotive coverstock were compared. Four compounds originating from raw liquid materials were identified as sources of odor in the finished products. Organic particles emitted from biomass burning play an important role in the Earth's radiative balance and are related to climate change. A laboratory tube furnace system was constructed to generate and collect organic aerosols from biomass thermal decomposition in a consistent manner. Methoxyphenol compounds were the most abundant compound group identified. Temperature and combustion environment were found to be two important variables that determine product abundance and distributions.

Advisor: Chan, Arthur W.H.
Logit-based Accessibility Measures: A Destination-mode Choice Model for Morning-peak Commuting in the GTHA

Accessibility has been a popular indicator for measuring system performance and policy effects in the transportation planning field; however, the measurement of the accessibility itself remains controversial. This study proposes utility-based accessibility measures to evaluate morning-peak access to workplaces in the GTHA by building a nested destination-mode choice model. Eight sets of parameters are estimated for full-time and part-time employees with an occupation type of General Office, Manufacturing, Professional, or Sales/Services. The workplace accessibility results indicate a significant difference between the employees with different occupation types as well as between full-time and part-time employees. Spatial variation is further examined, and distinctive patterns of workplace accessibility are observed for the employees in different occupation groups and employment statuses. The contribution of this study is the proposal of occupation-specific workplace accessibility measures, which allows evaluation of equity and identify gaps within each group as well as across the groups.

Keywords: Accessibility
Accessibility measures
Destination-mode choice
Logit model
Advisor: Miller, Eric J.
Comparison of Methods for Longitudinal Analysis of Quantitative Traits in Genome-wide Association Studies

Longitudinal genome-wide association studies provide us more information on the relationship between repeated-measured traits and genetic variants (SNPs) than cross-sectional ones. The Linear Mixed Model (LMM) has been a popular tool for such analysis but is deficient in computational speed. Inspired by fast methods proposed by Sikorska et al. which work as an approximation of LMM, we extended previous simulation scenarios and made comparison on cross-sectional, longitudinal SNP effects and joint test inference between fast methods and LMM. We also applied fast methods on real data for each of two renal outcomes. Results showed that using fast methods, we detected several SNPs with longitudinal effects on the two outcomes. These fast methods are effective and much faster than LMM, however they differ in computational efficiency and speed. We also discuss limitations existing in our simulation study and application to real data, along with discussion of future directions.

Keywords: DCCT/EDIC
fast methods
GWAS
LMM
longitudinal
quantitative
Advisor: Paterson, Andrew D
A Novel Methodology for Assessing Children's Heart Rate and Stress

Childhood stress is pervasive, which can result in serious physical and mental health problems. The conventional assessment such as self-report, cortisol samples and electrocardiogram (ECG) are challenging to use with children. The present study used a novel method called Transdermal Optical Imaging (TOI) technology which uses the conventional video camera in a smartphone to create an image facial blood flows. Using this method, I measured 99 Chinese children's heart rate and basal stress level and compared them with data from ECG and children self-report. The results showed that TOI measured children's heart rate that strongly corresponded to that with the ECG monitor, and the TOI stress indexes correlated significantly with children's self-reported academic stress. These findings taken together suggest that TOI can be used to monitor children's heart rate and stress in a convenient, contactless and remote way and therefore a potential technology to help manage academic stress.

Keywords: Chinese children
heart rate
heart rate variability
stress
stress assessments
transdermal optical imaging
Advisor: Woodruff, Earl
Lee, Kang
Quantifying Interhemispheric Connectivity between Motor Cortices during Finger Movement with MEG

For hemispherically lateralized tasks, stroke patients frequently exhibit increased activation of the contralesional hemisphere (cH), which may be either beneficial or detrimental to functional recovery. It is theorized that the cH exerts an inhibitory influence on the lesioned hemisphere, impairing recovery, but little empirical evidence of interhemispheric inhibition (IHI) is available. With the goal of quantifying IHI from magnetoencephalography data, we examined connectivity signals between motor cortices during single finger movements. Evidence of directed connectivity from moving to non-moving M1 in the beta band appearing 500 ms after movement onset was detected through several complementary connectivity measures. We hypothesize that beta band connectivity can index IHI from an activated region to its homologous counterpart, and propose further experiments to confirm this. Ultimately, the establishment of electrophysiological markers of IHI can guide post-stroke interventions for both motor and cognitive impairments.

Keywords: Finger tapping
Functional connectivity
Interhemispheric inhibition
MEG
Motor cortex
Advisor: Meltzer, Jed A.
Nanoscale Non-destructive Testing with the Atomic Force Microscope

Through implementing ultrasound detection with the AFM, a new branch of subsurface non-destructive testing has emerged which allows for nanoscale defect characterization. A systematic study was carried out with AFAM to determine its subsurface detection limitations on a stiff material. AFAM was able to reliably detect 2.5 μm diameter holes through a maximum graphite thickness of 570 nm and sub 100 nm holes through 140 nm of graphite. Various operating parameters such as contact force and cantilever eigenmode were found to increase contrast of the subsurface holes, however the smallest detectable defect remained the same. In an attempt to push the detection sensitivity, a humidity study was performed with AFAM where the presence of water showed negligible effects on subsurface contrast. HFM was implemented and showed comparable sensitivity to AFAM on detecting nanosized defects through graphite. Lastly, AFAM showed proficiency in detecting delamination at the interface of a graphite-polymer nanocomposite.

Keywords: AFM
Atomic Force Microscopy
Non-Destructive Testing
Subsurface Imaging
Ultrasonic Atomic Force Microscopy
Advisor: Filleter, Tobin
A Physiology-based Mathematical Model for the Selection of Appropriate Ventilator Controls for Lung and Diaphragm Protection

Mechanical ventilation is used to sustain respiratory function in patients with acute respiratory failure. To aid clinicians in consistently selecting lung- and diaphragm-protective ventilation settings, a physiology-based decision support system is needed. To form the foundation of such a system, the Lung- and Diaphragm-Protective Ventilation (LDPV) model has been developed. It centers around respiratory drive and uses patient-specific parameters as inputs and outputs predictions of a patient's transpulmonary and esophageal driving pressures as well as their blood pH. Ventilation and sedation parameters were demonstrated to modulate the model outputs in accordance with what is currently known in literature. The model was also proven to be able to provide robust predictions of model outputs for patient parameters with realistic variability. The usability of the model was improved by applying machine learning methods to the system inputs, allowing several patient-specific input parameters to be inferred.

Keywords: decision support
machine learning
mathematical modelling
mechanical ventilation
respiration
Advisor: Chan, Timothy C.Y.
Flow Separation Control using Piezoelectric Micro-blowers

A compact piezoelectric micro-blower was characterized as a potential synthetic jet using PIV to measure the velocity field near the jet exit for both continuous and burst modes. The jet produced relatively high exit velocities but had varying characteristics between micro-blowers. Regions of counter-rotating vortex pairs were generated in burst mode and the maximum velocity decreased with increasing excitation frequency. Wind tunnel experiments were conducted to investigate the effect of actuation on flow separation via a span-wise row of micro-blowers installed in a NACA 0012 airfoil at an angle-of-attack of 22 and chord-based Reynolds number of 150 000. Low and high frequency excitation were used to target flow instabilities and effects of actuation were determined through the pressure distribution, lift coefficient, and flow visualization. Both low and high frequency excitation showed small improvements in the lift coefficient, but smoke-wire results suggest that high frequency excitation is more effective.

Keywords: Flow control
Synthetic jets
Advisor: Sullivan, Pierre E
Experimental Study of Laterally Offset RHS X-connections in Branch Axial Compression

To investigate the effect of laterally offset branch members on the strength of welded Rectangular Hollow Section (RHS) connections, a series of 14 full-scale connection tests, consisting of 10 laterally offset and four non-offset configurations, was conducted on cold-formed RHS-to-RHS X-connections with the branch loaded in quasi-static axial compression. Comparison has been made between the structural behaviour of laterally offset connections and their standard counterparts, where appropriate. Recommendations are made for handling such laterally offset connections based on current design standards, and an analytical model is proposed and evaluated to give a good prediction of the static strength. The relevant limit states for local compression loading on RHS sidewalls, per AISC 360-16, are reviewed based on the data from the full-width, non-offset specimens herein, supplemented by experimental results from a further 76 X-connection tests from the literature. Design recommendations are proposed for handling transverse compression loading on RHS sidewalls in AISC 360.

Keywords: branch offset
hollow structural sections
rectangular hollow sections
steel structures
truss connections
welded joints
Advisor: Packer, Jeffrey A
Characterizing a New Tissue-selective Agonist for the Farnesoid X Receptor with Potential to Treat Liver Disease

Nuclear receptors (NRs) are near ideal drug targets, which makes them excellent potential therapeutic targets for multiple diseases. Of the 48 human NRs, most of them are ‘orphan’ nuclear receptors as their ligands are unknown. Recently, a new farnesoid X receptor (FXR) agonist, 8215 ethyl was identified in a drug screen carried out in our transgenic zebrafish system referred to as the ‘ligand trap (LT)’ system. FXR is mainly involved in bile acid and cholesterol homeostasis, fatty acid oxidation, and triglyceride clearance. Its emerging role in lipid metabolism makes FXR a probable therapeutic target for treating lipid-related diseases such as Non-Alcoholic Fatty Liver Disease (NAFLD). A known FXR agonist, obeticholic acid (OCA) was successful in treating patients with NAFLD, but its side effects have limited its use. Therefore, today, we need a safer and more potent drug to treat NAFLD. Herein, I report findings that suggest 8215 ethyl may have therapeutic potential.

Advisor: Krause, Henry