VictorJuiz/thesis huggingface dataset:
VEPH1 Interaction with ERBB2/HER2 and Inhibition of EGF-induced SHC Activation

VEPH1 is a PH and armadillo domain containing protein that is emerging as a protein scaffold involved in multiple signalling pathways. Work done prior to this thesis identified ERBB2 as a candidate interacting partner of VEPH1, suggestive of an effect on EGF signaling. The adaptor protein SHC links ERBB2 to multiple downstream signalling pathways. This thesis investigated whether VEPH1 interacts with ERBB2 to alter EGF-induced SHC activation and downstream signaling pathways. VEPH1 was found to interact with the kinase domain of ERBB2 through its PH domain and inhibited EGF-induced activation of SHC and downstream effectors (ERK and AKT activation), but in a cell line and serum-dependent manner. Evidence that VEPH1 interacts with SHC was also obtained, with ectopic expression of ERBB2 lessening the VEPH1 inhibition of SHC activation. These studies indicate that VEPH1 likely impacts multiple aspects of the ERBB signalling pathway.

Advisor: Ringuette, Maurice
Brown, Theordore
Replica Exchange MCMC Engine for Combinatorial Optimization Problems

A replica exchange Markov Chain Monte Carlo engine is proposed and implemented with automatic temperature adjustment for solving combinatorial optimization problems. The automatic temperature adjustment ensures that the process is optimized at every stage. This approach is performed by dynamically adjusting temperatures of all replicas, in addition to the capability of automatically inserting new replicas or removing any existing ones to improve the resource efficiency and execution time. The proposed replica exchange algorithm is integrated with parallel evaluation of energy increment and update scheme to increase the time to solution. The replica exchange algorithm alone, is able to achieve a 4-5x speedup in time to solution, over a simulated annealing based optimizer, in addition to eliminating the need for an annealing schedule. The engine is developed in hardware with a capacity of running up to 64 replicas in pipeline, each running a 1024 fully-connected network in parallel.

Keywords: Combinatorial Optimization
Field-Programmable Gate Array
Graphics Processing Unit
Ising Model
Markov Chain Monte Carlo
Replica Exchange
Advisor: Sheikholeslami, Ali
The Role of Allosteric Networks in Facilitating Enzymatic Catalysis of the Homodimer, Fluoroacetate Dehalogenase

Many oligomeric enzymes act through half-of-the-sites reactivity, in which the substrate engages with only one protomer at a time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, vacancy of one protomer is required for catalytic function. Substrate binding to one protomer induces disorder in the empty protomer, entropically driving the reaction forward. The enzyme utilizes a regulatory cap domain above the substrate access channel which prohibits substrate access to the empty protomer. At high substrate concentrations, a second substrate binds to a site along the binding channel of the occupied protomer, inhibiting catalysis. A key mutation of this site, K152I, effectively halts second site binding, resulting in abrogation of substrate inhibition and an order of magnitude drop in catalytic rate. At low substrate concentrations, the allosteric pocket acts as a conduit to desolvate the substrate. These results illustrate the role of dynamics along allosteric networks in facilitating chemical function.

Keywords: Allostery
Dynamics
Enzyme
Kinetics
Advisor: Prosser, Robert S
A Hamiltonian Engine for Radiotherapy Optimization

We apply a new hardware and software platform called Hamiltonian Engine for Radiotherapy Optimization (HERO) to the problem of beamlet intensity optimization in Intensity-modulated radiation therapy (IMRT). HERO solves large general-form binary optimization problems by decomposing them into sub-problems and approximating them by a quadratic pseudo-boolean function. Optimizing the resulting function becomes a quadratic unconstrained binary optimization (QUBO) problem which is widely studied and has numerous applications in different fields. In addition, we propose a new method to compute the IMRT objective function using a binary search approach. We exploit a GPU to perform the evaluations and also present a novel update scheme to perform groups of related evaluations together with better computational efficiency. We evaluate HERO on 10 prostate IMRT cases with clinical objectives, each involving approximately 700 beamlets. HERO solves most of the cases in about 2 minutes, with significantly lower objective function scores than the simulated annealing.

Keywords: Graphics Processing Unit
Intensity-modulated radiation therapy
Ising model
Markov Chain Monte Carlo
Optimization
parallel computing
Advisor: Sheikholeslami, Ali
Characterization of Unmanned Aerial Vehicle’s Single and Co-axial Propellers Performance Considering Geometrical and Environmental Factors

Many studies have investigated the behavior of coaxial propellers for drones considering different design configurations and various external geometrical and environmental factors. However, to date, most studies have been focused on a limited number of influential factors, and no comprehensive study into the complex interactions between design configuration, operating condition, and overall propeller performance has been carried out. In this study, a parameterized CFD model is developed to characterize the performance of single and coaxial propellers based on the individual and compound effects of geometrical and environmental factors such as propeller diameter, number of blades, and inflow velocity magnitude and direction. Through this study, it was found that in a coaxial configuration, corotating propellers generate 60% more thrust than contrarotating propellers in close stacking distance between two propellers. However, by an increase of distance, contrarotating propellers show a higher thrust and efficiency compared with corotating propellers by 6% on average.

Keywords: Coaxial Propellers
Computational Fluid Dynamics
Drone
Single Propeller
Advisor: Behdinan, Kamran B.K.
Canadian Election Integrity Initiatives and Domestic Disinformation: Investigating the 2019 Canadian Federal Election Across Sectors

This thesis examines several efforts to address the threat of online disinformation to the 2019 Canadian federal election, and considers the degree to which election integrity initiatives by government, industry, and civil society stakeholders accounted for the role of domestic actors within the disinformation ecosystem. While much contemporary discourse on disinformation and election integrity focuses on foreign influence, the phenomenon also implicates domestic actors like political parties, third party groups, mainstream and partisan media, and average social media users. Through qualitative analysis of key legislative, policy, and public awareness initiatives, this thesis draws out common themes, strategies, and perspectives in Canada’s approach to disinformation across sectors, alongside a supplementary analysis of Canadian mainstream media coverage related to the election. It concludes with a critical policy analysis that considers whether Canadian election integrity initiatives sufficiently account for domestically-driven disinformation, particularly given increased political polarization and far-right influence in Canada.

Keywords: Disinformation
Election integrity
Elections Modernization Act
Media literacy
Political advertising
Social media
Advisor: Regan Shade, Leslie
Resting-state fMRI and DTI Analysis of Prolonged Recovery following Mild Traumatic Brain Injury

Currently there is an incomplete picture of the changes in brain physiology associated with prolonged recovery following mild traumatic brain injury (mTBI), with the majority of previous studies focusing on the short-term changes or a single aspect of pathophysiology. This study combined resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) to examine both functional and structural alterations in brain physiology, including their association with clinical measures. Compared to healthy controls, mTBI patients with persistent symptoms showed significant alterations in cortical connectivity and white matter integrity, that were associated with symptom severity and performance on neurocognitive tests. The present study suggests that hyperconnectivity is an adaptive compensation to enhance neural function, whereas glial scarring is associated with unresolved symptoms.

Keywords: DTI
fMRI
functional connectivity
hyperconnectivity
mild traumatic brain injury
persistent symptoms
Advisor: Schweizer, Tom
Research Gaps in the Study of Microplastics: Method Development for Raman Automation, and Examining Relationships between Ecological Traits and Anthropogenic Particle Ingestion in a Deep-sea Food Web

Microplastics and other anthropogenic microparticles are an emerging class of contaminants in marine ecosystems. I explore two research gaps within the field of microparticle pollution: one related to improving efficiency and accuracy of microparticle quantification, and another related to the fate of microparticles in food webs. First, I validated the use of a non-polymeric adhesive to improve automated spectroscopy methods, as well as tested subsampling strategies to improve quantification efficiency. Second, I characterized the amount and diversity of microparticles ingested by species from a deep-sea food web of Monterey Bay, California. I assessed differences in particle ingestion in the context of ecological traits including habitat, diet, feeding strategy, and body size. I determined that species who occupied the lower-mesopelagic and bathypelagic zones were associated with a less diverse assemblage of particle morphologies compared to epipelagic and upper-mesopelagic species suggesting that where an animal lives in the water column influences exposure.

Keywords: bioaccumulation
food web ecology
microplastics
Monterey Bay
raman spectroscopy
trophic transfer
Advisor: Rochman, Chelsea M
Thermal Control of a Novel Microsatellite Bus with Deployable Components

With the emerging need for ever more capable microsatellites, the development of a novel microsatellite bus with deployable components was undertaken by Space Flight Laboratory. This platform, called DEFIANT, will provide a strong foundation for the next generation of microsatellites that will enable satellite constellations. As this is a new novel platform, there is a need for the development of a thermal control subsystem for the DEFIANT platform. This work presents an overview of heat transfer principles and orbital mechanics as is relevant for developing thermal control subsystems. The primary methods of thermal control for small spacecraft are introduced. A lumped mass network model is constructed and the impact of deployable structures predicted using a transient orbital analysis. A finite element model for the DEFIANT microsatellite platform is developed, the development philosophy is discussed, and the thermal control design is analyzed under simulation.

Keywords: Deployable
Microsatellite
Spacecraft
Thermal Control
Advisor: Zee, Robert
Effects of Mix Design and Curing on Resistance of Mortar and Concrete to Physical Sulfate Attack

Physical sulfate attack (PSA) is a serious mechanism of concrete deterioration spurred by temperature and humidity changes. Current standard tests assessing sulfate attack measure length change whereas PSA manifests in mass loss. A preliminary test using mass loss as an indicator was developed previously and used to evaluate the influence of mix design on mortar resistance against PSA. This study extended this research by: further assessing the viability of this test method, evaluating different wet curing durations, and extending the research to concretes. Prisms were stored in 30% by volume (24.5% by mass) sodium sulfate solution and cycled for 100 thermal cycles between 5 and 30 °C. Lowering the water-to-cementitious materials ratio and adding slag cement were found to increase resistance against PSA for mortars and concretes. The effect of wet curing is less conclusive due to interference from differential sulfate exposure occurring during initial cycling using this test method.

Keywords: Concrete
Curing
Durability
Physical Sulfate Attack
Sodium Sulfate
Sulfate Attack
Advisor: Hooton, Douglas R.
Quantized Analog Signal Processing Techniques for Wireless Receiver Front-ends

Quantized analog signal processing was originally proposed in "Quantized Inverter Amplifier," Electronics Letters [1]. It decomposes the input signal into N paths and allows the output signal amplitude larger than the supply voltage. This leads to a large improvement in the maximum achievable signal-to-noise ratio. Base on quantized analog signal processing, this thesis proposes a digital noise canceling technique, which is designed to partially remove the thermal noise generated in the system. As a result, the noise removal can largely improve the signal-to-noise ratio in the system. Moreover, a quantized analog wireless receiver front-end circuit prototype will be presented in this thesis. This receiver achieves an input 1dB compression point (P1dB) of 6.5dBm and an input-referred third-order intermodulation product (IIP3) of 21dBm.

Advisor: Liscidini, Antonio
Energy Injection for Mechanical Systems through the Method of Virtual Nonholonomic Constraints

This thesis develops a theoretical foundation for the framework of virtual nonholonomicconstraints, which are relations between the generalized coordinates and generalized momenta of a mechanical system that can be enforced via feedback control. The theory is applied towards energy injection for two standard underactuated systems: the variablelength pendulum and the acrobot. Virtual nonholonomic constraints are designed for each system by examining human motion, and energy injection properties of these constraints are proven rigorously. The acrobot constraint is tested on a real-world acrobot, demonstrating highly effective energy-injection properties and robustness to a variety of external disturbances.

Keywords: energy injection
virtual nonholonomic constraints
Advisor: Maggiore, Manfredi
High Dispersion Planar Antennas for Frequency Beam Scanning

Leaky-wave antennas scan their main beam through space as frequency is modulated and are useful for many applications. Planar, loaded transmission-line antennas are a type of leaky-wave antenna that can be easily fabricated with commercial PCB facilities. In this work the scanning sensitivity, or relation between scan angle and frequency, is investigated for planar loaded transmission line leaky-wave antennas. Methods are developed to realize unit cells with a desired scan dispersion, which can be used to design antennas that scan through large areas of space within a small bandwidth. Examples are designed and fabricated in the Ka-band and tested to validate the methods used. One design has a measured scan sensitivity of 10.5 degrees-per-percent-bandwidth, the highest of any known work of this type. Another design exhibits a smaller beamwidth and larger gain, illustrating some trade-offs inherent to antennas with enhanced scan sensitivity.

Keywords: antenna
frequency-scanning
leaky-wave
Advisor: Eleftheriades, George V
Functional Characterization of Actin-interacting Protein 1 in the Drosophila Follicular Epithelium

Actin filaments (F-actin) are essential for many cellular functions. Their dynamic remodeling allows various processes, including cell division, cell adhesion, cell polarization, and formation of stress fibres and cellular protrusions. One factor contributing to actin remodeling is Actin-interacting protein 1 (AIP1), a cofactor for cofilin in F-actin depolymerization. I used the Drosophila follicular epithelium to investigate the function of AIP1 in regulating the actin cytoskeleton and associated structures. AIP1 depletion caused an increase in F-actin amounts in the apical cytocortex and ectopic globular F-actin aggregates. Additionally, it resulted in microvilli of altered length, extended basal stress fibres, and defects in the distribution of adherens junction components and the spectrin cytoskeleton. Moreover, AIP1 reduction led to nuclear enlargement and multi-nucleation in follicle cells, suggesting defects during cytokinesis. These findings suggest that AIP1-mediated actin turnover is critical for normal actin organization, which is important for cellular protrusions, cell adhesion, and cell division.

Keywords: Actin
Actin-interacting protein 1
AIP1
Drosophila
Epithelium
F-actin
Advisor: Godt, Dorothea
Investigating a Question Prompt List to Support Patient-Centred Care for Women with Hypertensive Disorders of Pregnancy at Risk for Cardiovascular Disease

Introduction: Hypertensive disorders of pregnancy (HDP) lead to increased cardiovascular disease (CVD) risk. Clinicians, and consequently women, are unaware of this link. Question prompt lists (QPL) may improve patient-centred care (PCC) by supporting discussions about HDP and CVD risk.Methods: This thesis included a scoping review to identify the characteristics of effective QPLs; and qualitative interviews to understand how a QPL might support PCC for women with HDP. Results: The scoping review included 53 studies. QPLs were most commonly 1 page long and had 38 questions. Interviews included 22 women with HDP. All women said a QPL would improve PCC, by raising awareness about HDP and CVD risk, helping them avoid clinician dismissal, and helping them prepare for consultations. Conclusions: This thesis contributes to a greater understanding of QPLs, and PCC for women with HDP, which may ultimately lead to improved PCC and equality in the healthcare system.

Keywords: Cardiovascular Disease
Hypertensive Disorders of Pregnancy
Implementation Science
Patient-Centred Care
Question Prompt Tool
Women's Health
Advisor: Gagliardi, Anna R.
Exploring the Impacts of Motion-based Technology on Balance, Movement Confidence, and Cognitive Function Among People with Dementia and Mild Cognitive Impairment

Motion-based technologies can encourage exercise, but the impacts of motion-based technologies for people with dementia and Mild Cognitive Impairment (MCI) are underexplored. This study examined the impacts of a motion-based technology intervention on balance, movement confidence, and cognition among people with dementia and MCI. Twenty-eight participants took part in a group motion-based technology intervention twice weekly for 10 weeks. Participants completed the Mini Balance Evaluation Systems Test and the Montreal Cognitive Assessment at pre- and post-intervention. Intervention video recordings were captured during weeks one, five, and 10 to examine movement confidence. Data were analyzed using related-samples Wilcoxon signed rank tests. While participants experienced substantial cognitive, balance, and mobility impairments, their movement confidence was relatively high at baseline. Among participants who completed the study, there were no significant changes in balance, movement confidence, or cognition. The study highlights a need for physical rehabilitation for this population, alongside interventions for their cognition.

Keywords: Balance
Cognition
Dementia
Exercise
Motion-based technology
Movement
Advisor: Astell, Arlene J
Discipline Punishment: The Impact of Policies on Children

Institutional discipline of child behaviour sanctioned through the education system as well as the legal system displays a disparity in the application of discipline, where racialized children and youth are overrepresented in those penalized. It is through this thesis that the disparities in discipline across the Toronto District School Board will be analyzed and understood as a product of institutional inequalities that are ingrained in the structure of the education system, pedagogy, and practice. It will be argued that these three components that collectively create the institution of education, are responsible for the results we see in disproportionate discipline. It is through this inward glance at the institution, that it becomes clear that an institution built upon the pretense of inequality, perpetuates inequalities. Policy will be analyzed, for its ability and limitations to solving an institutional issue, as well as the future potential of policy’s role in achieving equitable education.

Advisor: Dei, George J. S.
Bascia, Nina
Multifunctional Bio-based Chitin Materials: Fabrication, Characterization and Applications

Chitin is the second most abundant biopolymers in the world owning outstanding mechanical strength, biocompatibility, and potential of functionalization. The development of various functional chitin materials aims for the high performance as well as the sustainability in different applications. This thesis reviews the current progress of chitin processing and multifunctional chitin materials, addressing two concerns in terms of the dispersion of chitin nanowhiskers in epoxy nanocomposites and development of a non-toxic chemical crosslinker for chitin aerogels. The first study developed an ionic liquid-chitin-epoxy composite with high chitin nanowhisker loading by incorporating ionic liquids. The samples have been characterized for structure-property relationship, demonstrating the reinforcing effect of chitin nanowhisker and dispersing role of ionic liquids. The second study developed a double crosslinked chitin aerogel via etherification with high porosity, low density, and improved mechanical properties. EGDE has been demonstrated an effective crosslinker and excessive of which causes emulsion and macroporous structure.

Keywords: aerogel
chitin
ionic liquids
nanowhiskers
thermosets
Advisor: Naguib, Hani E.
A Big Data Approach to Accounting Fraud Detection Using Data Envelopment Analysis and One Class Support Vector Machine

This thesis investigates a method to use Data Envelopment Analysis (DEA) in the context of big data to improve data analysis for the volume and velocity aspects of big data. First, DEA is used to identify fraud indicators in a large dataset. One class support vector machine (OC-SVM) is then used to identify outliers in the same dataset to evaluate the performance of the proposed DEA model. A second DEA model is proposed as a variable selection tool to enhance the performance of an OC-SVM model. The results show that although the proposed DEA model on its own is not as effective in detecting anomalies as OC-SVM, there is potential to use DEA as a variable selection tool to enhance the training and prediction process for anomaly detection using OC-SVM. The parameters and methods examined in this thesis are not exhaustive, but it does provide a baseline for future work.

Keywords: Anomaly Detection
Data Envelopment Analysis
One Class Support Vector Machine
Advisor: Paradi, Joseph C