title: Extended-Speed Finite Control Set Model Predictive Torque Control for Switched Reluctance Motor Drives with Adaptive Commutation Angles

subject: Switched reluctance motors

subject: Model predictive control

subject: torque control

subject: electric motors

subject: optimization

subject: power electronics and drives

subject: high speed operation

abstract:
In this thesis, after a comprehensive literature review on different conventional and predictive torque control strategies for switched reluctance motor (SRM) drives, two online methods and one offline multi-objective optimization-based method are proposed to extend the operating speed range of finite control set model predictive torque control (FCS-MPTC) for SRM by adaptively controlling the commutation angles in the entire speed range. Furthermore, a method is proposed to minimize the steady state torque tracking error of FCS-MPTC for SRM drives.
The incapability of the conventional FCS-MPTC in controlling the commutation angles, which is considered as one of the main drawbacks of the conventional FCS-MPTC, limits its application for high-speed torque control of SRM drives. The phase turn-off angle is always selected to be close to the aligned position with the conventional FCS-MPTC regardless of the operating speed. However, commutation angle advancement is required for high-speed torque control of SRM drives to limit the negative phase torque resulting from the current tail after the turn-off angle in the generating region. Excessive negative torque with the conventional FCS-MPTC at higher speeds can result in a degraded performance with high rms current, low average torque, high torque ripple, and reduced efficiency.
The phase turn-off angle can be adaptively controlled as speed changes with the first online commutation angle control strategy proposed in this thesis. This method is based on predicting the free-wheeling phase current in an extended time interval which is much bigger than the prediction horizon of FCS-MPTC. The second online turn-off angle control method is also proposed by improving the optimality condition defined for determining the optimal turn-off angle. The optimality condition is determined by calculating the work done by the conducting phase after the phase is turned off.
The weighting factor of the objective function of FCS-MPTC is kept constant with both proposed online methods. An offline multi-objective optimization-based strategy is proposed to determine the globally optimal turn-off angle and the weighting factor in the entire operating torque and speed ranges. The effectiveness of both proposed online methods and the offline commutation angle control strategy is verified using simulations and experimental results. The results are also compared to the conventional FCS-MPTC and the indirect average torque control with optimized conduction angles which is considered as one of the main conventional torque control strategies for SRM drives.
In order to minimize the torque tracking error as a result of either parameter uncertainties or tracking multiple objectives with a single objective function with weighting factors, a method is proposed which is based on updating the reference torque at each sample time by calculating the average torque tracking error in the previous sample times. The validity of the proposed method is verified using simulations.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Thermal Modelling for Electric Machines Using Thermal Capacitance Calculation Method: External Rotor Switched Reluctance Motor Case Study

contributor:
Emadi, Ali
Mechanical Engineering

subject:
electric motor
SRM
traction
LPTN
transient thermal
thermal capacitance

abstract:
This thesis characterizes the transient thermal response of a 12/16 External Rotor Switched Reluctance Machine (ERSRM) for an E-bike application. A method for calculating coil capacitance based on machine design parameters was introduced and implemented into a standard commercial Lumped Parameter Thermal Network (LPTN). A sizing criterion was proposed for the cuboid number in a physically accurate LPTN coil model design. This sizing criterion considers the change in model size with motor speed or forced convection. The LPTN with a more accurate calculation of capacitance within the coil and a known number of cuboids in the coil was validated with experimental results. An analytical proof was provided that a small number of capacitances is not sufficient to model a typical power-dense coil design.
The validated model was used to study the impact of a more accurate capacitance calculation method on motor temperature. Both overload and rated operation were investigated. During overload conditions, it was found that the standard capacitance calculation from commercial software massively underestimated the heating rate and peak temperature of the coil hot spot, even with the same number of cuboids.
The capacitance of the rest of the motor was able to be varied and investigated for its effects on cooldown dynamics. It was found that for short-time transients the coil could be assumed to act adiabatically in this operating range.  Operating points across the operating envelope for the motor under study were mapped to determine the region where the adiabatic assumption could be made. It was shown that a transition occurred where the adiabatic assumption ceases to be valid.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis deals with the thermal modelling of electric machines for traction applications using lumped parameter thermal modelling. A novel approach is presented for calculating and distributing thermal capacitance in motor coils. A 12/16 External Rotor Switched Reluctance Motor is characterized based on its transient thermal response and the novel methods proposed are validated. The sizing of a coil-based thermal model is discussed and a criterion for physical validity proposed. The validated model is used in a sensitivity analysis of coil and motor capacitances. For severe overload conditions and short periods, a result is obtained showing the coil can be modelled as adiabatic. Finally, a rated load condition is tested, and a transition is suggested between overload conditions and non-overload conditions.


title: Wearable Systems For Health Monitoring Towards Active Aging

contributor:
Deen, M. Jamal
Electrical and Computer Engineering

subject: Smartphone; remote healthcare; mHealth; telehealth; medical device; regulation; smartphone sensorwearable sensors; remote health monitoring; body sensor network; vital sign monitoring; ambulatory monitoring; gait analyzer; gait assessment; discrete wavelet packet analysis; machine learning; healthy aging; inertial sensors; ECG; Atrial fibrilation; Knee joint: Lower-limb joint; Standards; Smart home

abstract:
Global rise in life expectancy has resulted in an increased demand for affordable healthcare and monitoring services. The advent of miniature and low–power sensor technologies coupled with the emergence of the Internet–of–Things has paved the way towards affordable health monitoring tools in wearable platforms. However, ensuring power–efficient operation, data accuracy and user comfort are critical for such wearable systems. This thesis focuses on the development of accurate and computationally efficient algorithms and low–cost, unobtrusive devices with potential predictive capability for monitoring mobility and cardiac health in a wearable platform.
A three–stage complementary filter–based approach is developed to realize a computationally efficient method to estimate sensor orientation in real–time. A gradient descent–based approach is used to estimate the gyroscope integration drift, which is subsequently subtracted from the integrated gyroscope data to get the sensor orientation. This predominantly gyroscope–based orientation estimation approach is least affected by external acceleration and magnetic disturbances.
A two–stage complementary filter–based efficient sensor fusion algorithm is developed for real–time monitoring of lower–limb joints that estimates the IMU inclinations in the first stage and uses a gradient descent–based approach in the second stage to estimate the joint angles. The proposed method estimates joint angles primarily from the gyroscope measurements without incorporating the magnetic field measurement, rendering the estimated angles least affected by any external acceleration and insensitive to magnetic disturbances.
An IMU–based simple, low–cost and computationally efficient gait–analyzer is developed to track the course of an individual's gait health in a continuous fashion. Continuous monitoring of gait patterns can potentially enable detecting musculoskeletal or neurodegenerative diseases at the early onset. The proposed gait analyzer identifies an anomalous gait with moderate to high accuracy by evaluating the gait features with respect to the baseline clusters corresponding to an individual’s healthy peer group. The adoption of a computationally efficient signal analysis technique renders the analyzer suitable for systems with limited processing capabilities.
A flexible dry capacitive electrode and a wireless ECG monitoring system with automatic anomaly detection capability are developed. The flexible capacitive electrode reduces motion artifacts and enables sensing bio–potential over a dielectric material such as cotton cloth. The virtual ground of the electrode allows for obtaining single–lead ECG using two electrodes only. ECG measurements obtained over different types of textile materials and in presence of body movements show comparable performance to other reported ECG monitoring systems. An algorithm is developed separately as a potential extension of the software to realize automatic identification of Atrial Fibrillation from short single–lead ECGs.
The association between human gait and cardiac activities is studied. The gait is measured using wearable IMUs and the cardiac activity is measured with a single–lead handheld ECG monitor. Some key cardiac parameters, such as heart rate and heart rate variability and physical parameters, such as age and BMI show good association with gait asymmetry and gait variation. These associations between gait and heart can be useful in realizing low–cost in–home personal monitoring tool for early detecting CVD–related changes in gait features before the CVD symptoms are manifested.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Wearable health monitoring systems can be a viable solution to meet the increased demand for affordable healthcare and monitoring services. However, such systems need to be energy–efficient, accurate and ergonomic to enable long–term monitoring of health reliably while preserving user comfort.
In this thesis, we develop efficient algorithms to obtain real–time estimates of on–body sensors' orientation, gait parameters such as stride length, and gait velocity and lower–limb joint angles. Furthermore, we develop a simple, low–cost and computationally efficient gait–analyzer using miniature and low–power inertial motion units to track the health of human gait in a continuous fashion.
In addition, we design flexible, dry capacitive electrodes and use them to develop a portable single–lead electrocardiogram (ECG) device. The flexible design ensures better conformity of the electrode to the skin, resulting in better signal quality. The capacitive nature allows for obtaining ECG signals over insulating materials such as cloth, thereby potentially enabling a comfortable means of long–term cardiac health monitoring at home. Besides, we implement an automatic anomaly detection algorithm that detects Atrial Fibrillation with good accuracy from short single–lead ECGs.
Finally, we investigate the association between gait and cardiac activities. We observe that some important cardiac signs, such as heart rate and heart rate variability and physical parameters, such as age and BMI show good association with gait asymmetry and gait variation.


title: The examination of OIP5 expression in renal cell carcinoma(RCC) and during RCC progression

contributor:
Tang, Damu
Medical Sciences

abstract: Renal Cell Carcinoma (RCC) is the most lethal kidney cancer and accounts for approximate 2%-3% adult malignant neoplasm. The current risk assessment on which treatment decisions are formulated largely relies on clinical criteria. Improvement in predicting prognosis requires the use of molecular events or biomarkers. OIP5 (Mis18β) is accumulated in telophase-G1 centromere and plays a critical role in centromere formation. Mis18β forms Mis18 heterotetramer with Mis18α and the complex is involved in the deposition of new centromeric protein A (CENP-A) nucleosomes, which is essential for centromere/kinetochore structure and functions. In normal individual, OIP5 is intensively expressed in testis, while recent studies have demonstrated that OIP5 promotes the initiation and progression of several cancers. However, its function in RCC remains unclear. This thesis thus aims to examine the hypothesis that OIP5 plays in RCC pathogenesis. In vitro studies demonstrated that overexpression of OIP5 promoted cell growth, proliferation, and invasion in ACHN pRCC cells. In comparison to ACHN cells stably expressing an empty vector (EV), ACHN OIP5 cells produced xenografts with a significantly enhanced ability with concurrent upregulation of PLK1 and other factors that are likely contribute to cell cycle progression. PLK1 plays important roles in promoting M phase progression, which is in accordance with an important role of OIP5 in centromere formation. Importantly, the PLK1 inhibitor BI2536 led to significantly more cells arrested in M phase compared to OIP5 EV cells, implying a reliance of PLK1 function to drive ACHN OIP5 cells progression through M phase. This property suggests an appealing scenario to treat pRCCs with OIP5 upregulation. Intriguingly, this possibility is supported by our clinical investigation. In our analysis of OIP5 expression in primary RCC (n=57), OIP5 upregulation was found in  both ccRCC and pRCC tumors compared to their adjacent non-tumor tissues. The upregulation is associated with ccRCC and pRCC progression as well as prognosis. Both ccRCC and pRCC tumors with elevated OIP5 expression are correlated with poor overall survival compared to those without the upregulation. Collectively, this thesis reveals a novel and important contribution of OIP5 in RCC, particularly pRCC; targeting PLK1 might be an option in treating pRCCs expressing high levels of OIP5.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Renal Cell Carcinoma (RCC) is the most lethal kidney cancer and accounts for approximate 2%-3% adult malignant neoplasm. The assessment of RCC prognosis and the subsequent treatments are depending on the exclusive clinical criteria, therefore, it is necessary to explore promising biomarkers and therapeutic targets to improve risk assessment and treatment. OIP5 is a relative new protein and its expression was increased in several cancers including clear cell RCC (ccRCC). However, its expression in papillary RCC (pRCC) and its impacts on RCC remain unclear. Therefore, this study is aimed to investigate the role of OIP5 in RCC and during RCC progression. The results suggested that OIP5 enhances the growth, proliferation, and invasion of pRCC cells. Furthermore, by using mouse model of pRCC, OIP5 was found to promote tumorigenesis. In patients, advanced ccRCC and pRCC tumors expressed significantly higher levels of OIP5, and these patients are associated with poor overall survival. From our animal RCC research, we discovered that tumors with increased OIP5 also expressed higher levels of a protein called PLK1; this protein is known to promote cell proliferation. In this context, a PLK1 inhibitor can inhibit the proliferation of pRCC cells expresses high levels of OIP5, suggesting that advanced pRCC with OIP5 expression increased can be treated with PLK1 inhibitor. This possibility should be investigated in future. Should this be confirmed, it will offer the first effective therapy for patients with advanced pRCCs harboring elevated OIP5 expression.


title: Regioselective Hydrolysis of Alkynes Via Organosulfur Intermediates

contributor:
Magolan, Jakob
Chemistry and Chemical Biology

subject:
Chemistry
Organosulfur Chemistry
Alkyne Hydrolysis
Synthetic Method

abstract: Many known synthetic methods enable the hydrolysis of alkynes with Markovnikov regioselectivity. In contrast, the synthetic chemist’s toolbox lacks broadly effective processes for the hydrolysis of alkynes with anti-Markovnikov regioselectivity. This thesis describes the development of new synthetic method that will help address this deficiency. This document begins with a review of the concepts of Markovnikov and anti-Markovnikov regioselectivity and an explanation of the broad extension of this terminology that is applied throughout the remainder of this thesis to encompass all alkyne substrates. Next, a review of the published methods of alkyne hydrolysis is presented, with emphasis on the internal alkyne substrates. The remainder, and bulk, of this thesis details the development of a new synthetic methodology that leverages regioselective radical thiolation chemistry to achieve anti-Markovnikov hydrolysis of alkynes. Internal alkynes are first converted to oxathiolanes or vinyl sulfides with anti-Markovnikov regioselectivity followed by hydrolysis of these moieties to the corresponding anti-Markovnikov ketones. In the case of aryl-alkyl alkyne substrates, complete anti-Markovnikov selectivity is demonstrated with a broad range of examples. Aryl-aryl alkyne substrates offer a mixture of regioisomers favoring anti-Markovnikov products. Finally, the utility of this methodology is demonstrated with its application to the successful first total synthesis of the bioactive natural product isomeranzin.

abstract: Thesis

abstract: Master of Science (MSc)


title: Exploring Synergies at the Interface of the Amyloid and Signaling Fields

contributor:
Melacini, Giuseppe
Chemistry

abstract: The fields of amyloid and signaling have traditionally developed through largely separate routes.  However, several intersections and synergies exist between these two research areas. For example, kinase catalyzed phosphorylation is known to affect self-association in several amyloidogenic proteins. Here, we explore further instances for how methods and concepts originally pioneered in one field may benefit the other. We show how allosteric conformational transitions at the basis of signaling regulation can also serve as a basis to design sensors for binding of ligands to amyloid inhibitory chaperones. Conversely, we also illustrate how signaling benefits from the amyloid field. For example, we show that amyloid formation may serve as a non-classical mechanism for protein kinase A (PKA) activation.  This is in contrast to the classical mechanism for PKA activation, which relies on cAMP-dependent conformational changes of the regulatory subunits. However, the classical cAMP-dependent activation of PKA alone may not suffice to rationalize the phenotype of enhanced PKA activation observed for known disease related mutations in the regulatory subunits of PKA, such as the Carney Complex (CNC), which is a generalized tumor predisposition. Several CNC mutants exhibit reduced affinity for cAMP, which appears incompatible with the overactivation of PKA in the context of a PKA regulation that is dependent on cAMP alone. The activation of PKA by CNC mutation-induced polymerization of inhibitory regulatory subunits and consequent amyloid formation offers a simple but effective solution to solve this apparent paradox and explain CNC phenotypes. Overall, this dissertation highlights several reciprocally beneficial opportunities at the interface between amyloids and signalling.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Making Simulink Models Robust with Respect to Change

contributor:
Wassyng, Alan
Lawford, Mark
Computing and Software

subject:
Simulink
Modularity
Model-Based Development

abstract: PhD Thesis (Software Engineering)

abstract:
Model-Based Development (MBD) is an approach that uses software models to describe the behaviour of embedded software and cyber-physical systems. MBD has become an increasingly prevalent paradigm, with Simulink by MathWorks being the most widely used MBD platform for control software. Unlike textual programming languages, visual languages for MBD such as Simulink use block diagrams as their syntax. Thus, some software engineering principles created for textual languages are not easily adapted to this graphical notation or have not yet been supported. A software engineering principle that is not readily supported in Simulink is the modularization of systems using information hiding. As with all software artifacts, Simulink models must be constantly maintained and are subject to evolution over their lifetime. This principle hides likely changes, thus enabling the design to be robust with respect to future changes.

In this thesis, we perform repository mining on an industry change management system of Simulink models to understand how they are likely to change. Then, we explore the various modelling mechanisms available in the Simulink language to see how they could support modular design with information hiding. Next, we propose a module structure, syntactic interface, and modelling conventions for Simulink designs, which are supported by our open-source Simulink Module Tool. Finally, we apply the proposed techniques on case studies from the aerospace and nuclear domains, in order to demonstrate their practicality and validate their effectiveness. Overall, the approach helped support information hiding by encapsulating secrets and facilitating likely changes. It also had a positive effect on interface complexity, cohesion, and coupling. The larger system also exhibited reductions to cyclomatic complexity, testing effort, and execution time, but the smaller case study benefited less in these areas.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Model Predictive Control of Switched Reluctance Machine Drives

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject: Model predictive control, Switched reluctance machine, predictive current control, predictive torque control

abstract:
Model predictive control (MPC) for switched reluctance machine (SRM) drives is studied in this thesis. The objective is to highlight the benefits of implementing MPC to overcome the main drawbacks of SRMs and position them as an attractive alternative among electrical drives. A comprehensive literature review of MPC for SRM is presented, detailing its current trends as an application still at an early stage. The different features of MPC are highlighted and paired with the most challenging and promising control objectives of SRMs. A vision of future research trends and applications of MPC-driven SRMs is proposed, thus drawing a road-map of future projects, barriers to overcome and potential developments. Several important applications can take advantage of the improved features that SRM can get with MPC, especially from the possibility of defining a unified control technique with the flexibility to adapt to different system requirements. The most important cluster for SRM drives is the high- and ultrahigh-speed operative regions where conventional machines cannot work efficiently. SRMs with MPC can complement then the existing demand for electrical drives with high performance under challenging conditions.

Three techniques based on the finite control set model predictive control (FCS-MPC) approach are developed out of the proposed road-map. The first one defines a virtual-flux current tracking technique that improves the existing ones in operating at different speeds and more than one quadrant operation. The method is validated for low- and high- power SRMs in simulations and diverse types of current waveform, making it easy to adapt to existing current shaping techniques. It is also validated experimentally for different operating conditions and robustness against parameter variation. The second technique proposed a predictive torque control that bases its model on static-maps, thus avoiding complex analytical expressions. It improves its estimation through a Kalman filter. The third technique uses a virtual-flux predictive torque control, similar to the first technique for current tracking. The techniques are validated at a wide speed range, thus evidencing superiority in performance without modification on the control structure.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Development of TiAlN PVD Coating Systems for Machining of Compacted Graphite Iron (CGI)

contributor:
Veldhuis, Stephen
Mechanical Engineering

abstract: Compacted graphite iron, with its improved mechanical properties, is the ideal candidate to replace grey cast iron in the automotive industry. Engine blocks made from CGI are lighter, smaller, and show higher fuel efficiency. However, machining compacted graphite iron is extremely challenging compared to grey cast iron, especially in continuous cutting operations. Difficulties in dry turning CGI can be attributed to a lack of a protective tribolayer and its high tendency to stick to the cutting tool, which results in built-up edge formation and adhesion wear. This research attempts to address challenges associated with CGI turning by developing a TiAlN coating with a focus on thickness and low residual stress. The mentioned coating was developed using a new technology called super fine cathode (SFC) which enables better control over residual stress generation and, therefore, enables the deposition of a TiAlN coating with higher thickness compared to its commercial range. The properties and performance of this coating were comprehensively studied using X-Ray diffraction, scanning electron microscopy, micro and nanomechanical indentation, scratch test, optical 3D microscopy, and tool wear studies. The results show that residual stress is the main measured feature limiting coating thickness and affecting wear pattern during the machining of CGI. By using a low substrate bias voltage and a high nitrogen pressure, deposition of a thick TiAlN coating under low compressive residual stress was achieved, which significantly delayed substrate exposure, reduced built-up edge formation, lowered the cutting forces, and improved tool life by 35%. Moreover, to improve the coating quality along the cutting edge, wet blasting was applied before the deposition process, which resulted in better edge quality and consistency.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: With continuous improvement and optimization of the materials used in advanced industrial components, there is an increasing demand for improving machining productivity. This goal can be achieved by prolonging tool life and improving final part quality by tailoring the cutting tool according to the workpiece material. Physical vapor deposition is an effective method to alter superficial tool properties by applying a thin layer of hard coating and, thus, protecting the tool during the machining process. In the present research a TiAlN coating was developed for the machining of compacted graphite iron (CGI) by focusing on thickness, coating properties, and substrate geometry. The developed coating was able to improve tool life by 35% in comparison to commercially available coatings.


title: Electrical Stimulation In Bone Cell Culture Media

contributor:
Wohl, Gregory
Biomedical Engineering

subject:
electrical stimulation
bone cells
Osteocytes
culture media

abstract:
Osteocytes are the most abundant bone cells, however, they are also the least understood. They sense mechanical stress within the bone matrix to control remodelling, but there is debate about the way that this occurs. The bone matrix experiences changes in electrical charge through stress generated potentials in the canaliculi, and piezoelectricity of the collagen-hydroxyapatite junctions. External electrical stimulation (ES) has been shown to increase bone formation, indicating that the cells involved in remodelling are electrically sensitive. However, the effects of ES on osteocytes specifically are under-researched.
Before applying ES in vitro the electrical characteristics of the culture media need to be understood to see if it will negatively impact cells in culture. ES in culture media causes pH changes and gas formation as well as precipitate formation directly on the electrode surface. The resistance of the media increases rapidly upon application of the electrical stimulus and plateaus after 100 - 200 minutes. The pH gradient disperses around the same time frame, with most stimulating currents causing no permanent change to the media pH. Stimulation parameters that cause minimal side effects will be better for the health of cells in culture. This should also make it more clear which outcomes are a result of the electrical stimulation and which come from the electrochemical reactions that are present in the media due to the ES.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Osteocytes are the least understood bone cells and the way that they communicate with the bone matrix and other cells is widely debated. It is assumed that osteocytes sense mechanical stresses within the bone matrix through electrical charges that develop in areas of increased strain. External electrical stimuli have been shown to increase bone formation indicating that the cells are electrically sensitive. The electrical sensitivity of the osteocytes specifically is under-researched causing a gap in knowledge of the behaviour of the cell in the remodelling process. To study the effects of electrical stimulation on osteocytes, an experimental apparatus must be designed to deliver stimulation to the cells in vitro and maintain a stable environment. A culture medium is needed to keep cells alive in vitro To do this, the electrical characteristics of the cell culture medium must be understood in attempts to maintain homeostatic conditions for the cells.


title: Sensitivity Analysis of Convex Relaxations for Nonsmooth Global Optimization

contributor:
Khan, Kamil
Chemical Engineering

subject:
sensitivity analysis
subgradients
directional derivatives
nonsmooth
global optimization
convex relaxation

abstract:
Nonsmoothness appears in various applications in chemical engineering, including multi-stream heat exchangers, nonsmooth flash calculation, process integration. In terms of numerical approaches, convex/concave relaxations of static and dynamic systems may also exhibit nonsmoothness. These relaxations are used in deterministic methods for global optimization. This thesis presents several new theoretical results for nonsmooth sensitivity analysis, with an emphasis on convex relaxations.

    Firstly, the  "compass difference" and established ODE results by Pang and Stewart are used to describe a correct subgradient for a nonsmooth dynamic system with two parameters. This sensitivity information can be computed using standard ODE solvers.

     Next, this thesis also uses the compass difference to obtain a subgradient for the Tsoukalas-Mitsos convex relaxations of composite functions of two variables.

     Lastly, this thesis develops a new general subgradient result for Tsoukalas-Mitsos convex relaxations of composite functions. This result does not limit on the dimensions of input variables. It gives the whole subdifferential of Tsoukalas-Mitsos convex relaxations. Compare to Tsoukalas-Mitsos’ previous subdifferential results, it does not require additionally solving a dual optimization problem as well. The new subgradient results are extended to obtain directional derivatives for Tsoukalas-Mitsos convex relaxations. The new subgradient results and directional derivative results are computationally approachable: subgradients in this article can be calculated both by the vector forward AD mode and reverse AD mode. A proof-of-concept implementation in Matlab is discussed.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Effects of Movement-based Interventions for Children

contributor:
Cairney, John
Health Research Methodology

abstract:
Participation in physical activity (PA) has been linked to positive health and developmental outcomes particularly for children; however, global estimates of physical inactivity range from 67-80% of children. Physical inactivity is also related to increased rates of unhealthy weight, poor school readiness, and mental health concerns among children. Urgent prevention strategies are required to enhance the health and development of children. This thesis explored the use of three study designs to investigate the effects of various movement-based interventions on aspects of health and development in children.
A quasi-experimental study was first conducted to test the effects of a movement- and pre-literacy program among 3- to 4-year-old children. This study found significantly positive improvements in movement skill and pre-literacy skills. Subsequently, a mixed method study was designed to expand the evaluation of the program. A randomized waitlist controlled trial with an embedded qualitative study revealed statistically significant intervention effects, while the qualitative data revealed that the program positively contributed to various aspects of children’s movement and pre-literacy abilities and overall confidence, and enhanced quality of at-home practice. The final study used a randomized controlled trial to test the acute effects of a bout of activity that varied in physical and cognitive demands on executive function. Key findings did not support the hypotheses that a cognitively engaging bout of PA enhances cognitive performance over non-cognitively engaging PA or sedentary activities, and this may have been due to overexertion during the activity and/or depletion of positive affect.
Overall, the thesis findings demonstrated promise of a movement-based intervention for children, elucidated important design considerations of cognitively engaging physical activities, and suggested several new avenues of research. Moreover, the thesis has demonstrated the utility of using multiple designs and highlights the unique methodological considerations of conducting research with young children.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Movement and physical activity (PA) play important roles in children’s development and health.  However, children across the world are engaging in less PA leading to higher rates of physical and mental illness and poor school readiness. There is a need to develop programs designed to enhance the health and development of children over time. This thesis tests the effects of various movement-based interventions on aspects of health and development in children. Results of study 1 provided preliminary evidence in support of a movement- and pre-literacy program called Move 2 Learn (M2L). Study 2 used more rigorous methods to test M2L and found that the program had unexpected positive outcomes for parents. Finally, study 3 findings pointed to the value in ensuring children find joy in PA and are not overly exerting themselves. Overall, this thesis highlights the importance of movement in child development and encourages several new avenues of research.


title: A comparison of different heating and cooling energy delivery systems and the Integrated Community Energy and Harvesting system in heating dominant communities

contributor:
Cotton, James
Lightstone, Marilyn
Mechanical Engineering

subject:
district energy
community energy systems
Modelica
low temperature thermal networks

abstract:
The building sector is one of the largest consumers of energy and producers of greenhouse gas emissions in Ontario, representing 13% of the province’s emissions. Recently, countries have been looking to decrease their emissions in response to climate change. The electrification of space heating and domestic hot water preparation has gained traction in reducing emissions in countries with low emission electricity grids. This thesis proposes a novel energy delivery system called the Integrated Community Energy and Harvesting (ICE-Harvest) system. The ICE-Harvest system is a modified 5th Generation District Heating and Cooling (5GDHC) system. An ICE-Harvest system, much like a 5GDHC system, is a district energy system that incorporates heat pumps to couple the thermal and electrical energy demands of buildings. The ICE-Harvest system uses heat pumps to supply both heating and cooling from a one pipe thermal distribution network. The ICE-Harvest system has unidirectional mass flow in a ring arrangement with branches at each building. Bidirectional energy flow between the network and buildings is permitted, meaning that heat rejection from cooling processes can be recovered in the network to reduce the total system heating load. This concept is referred to as energy sharing.
	The energy needs of the network, and thus the buildings, are serviced through a centralized generation station referred to as the Energy Management Center (EMC). The EMC regulates the supply temperature of the network to the controlled setpoint. Within the EMC, the primary generation source is a Combined Heat and Power (CHP) unit. The purpose of this CHP is to offset the existing centralized natural gas generators on the Ontario electrical grid. These gas generators operate intermittently and inefficiently as a form of dispatchable generation to stabilize the provincial electrical grid. In this research, it is proposed that ICE-Harvest systems with on-site CHPs could replace these gas generators while providing the same support to the electrical grid at a much higher energy utilization ratio. For an accurate comparison, the CHP is constrained to only turn on according to the electricity system operator's gas generator dispatching schedule. An auxiliary boiler is included in the EMC to provide heat when the CHP is not permitted to operate. However, the possibility for Thermal Energy Storage (TES) to replace this boiler is also explored.
	An ICE-Harvest system's ideal design depends on the market conditions, building energy demands, and available waste energy sources. This research presents an ICE-Harvest system in a heating demand dominated community located in Ontario, Canada. The community consists of five buildings. The ICE-Harvest system is compared to conventional and alternative building energy systems using the energy consumption data of these buildings. The systems are compared according to their energy consumption, emissions produced, and impact on the electrical grid at both the distribution and transmission levels. The topic of using thermal energy storage in ICE-Harvest systems is also discussed, and a parameter sweep is performed on the thermal energy storage capacity. The results show that the ICE-Harvest system offers demand management opportunities to electricity system operators, substantially reduces annual emissions, and offers improved energy utilization compared to conventional systems.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Window on the (South)west: The Southwest Iberian Bronze Age from a Long-Term Perspective (ca. 3500 – 800 BCE)

contributor:
Carter, Tristan
Anthropology

subject:
Archaeology
Iberia
Prehistory
Bronze Age
Neolithic
Chalcolithic
Rural Archaeology
Alentejo
Settlement Studies
Aggregation
Place-making
Portugal
Iberian Archaeology
Iberian Prehistory

abstract:
This study combines long-term settlement data with short-term excavation data to explore the conditions that led late prehistoric communities in Iberia’s southwest to aggregate during the Late Bronze Age [LBA]. This long-term approach involves the application of geographic information systems [GIS] to identify settlement patterns in the Central Alentejo from the Late Neolithic [LN]/Chalcolithic to the Late Bronze Age (ca. 3500 – 800 BCE). In the Serra d’Ossa microregion of the southwest there are 176 sites that date to the Neolithic/Chalcolithic, only two that date to the EBA/MBA, and 27 that date to the LBA. This shift is directly related to the Chalcolithic “collapse” that occurred in the mid/late third millennium BCE, influenced by both sociocultural and environmental factors.
The LBA of the southwest has long been defined by the emergence of a new culture associated with a concern for defensiveness and warriorship, represented on stone stelae by warrior iconography, and by the emergence of large-fortified upland sites that appear during this period. A distinct lack of small-scale settlement data has previously led to insufficient interpretations and characterizations of the period. In turn, this thesis incorporates short-term data from excavation at the large-fortified upland site of Castelo Velho da Serra d’Ossa, the one excavated example of such a site in the Serra d’Ossa microregion and one of the few excavated LBA sites in the wider southwest. The short-term excavation data are discussed in the context of the long-term settlement patterns to better characterize the LBA of the Iberian southwest, a period previously underrepresented in the region. The central focus of study is to investigate the emergence of these settlements (up to 15 ha in size) and the communities that inhabited them; considering the processes underpinning place-making and aggregation both locally and within its broader prehistoric context.

abstract: Thesis

abstract: Master of Arts (MA)


title: Intimate Partner Violence in the South Asian Diaspora

contributor:
Anand, Sonia
Health Research Methodology

subject:
South Asian
Intimate Partner Violence

abstract:
Background: Little is known about the perspectives of South Asian mothers with regards to the
experience of intimate partner violence (IPV), including risk and protective factors, impacts of
exposure, and help-seeking. This thesis is comprised of two sub-studies. In the first study, a
scoping review was conducted to identify and map the literature on IPV amongst South Asian
women residing outside of South Asia. The second study consists of a qualitative project to explore
how IPV is perceived among South Asian mothers living in Ontario, Canada.
Methods: The first study was a scoping review conducted using the 5-stage framework outlined
by Arksey and O’Malley, and later advanced by Levac et al. Four health and social science
databases, including Embase, CINAHL, Medline, and PsychINFO were systematically searched
from inception to June 2020 using the themes “intimate partner violence” and “South Asian.”
Studies were screened for inclusion based on pre-determined eligibility criteria, and relevant data
with regards to study location, journal type, and sample characteristics were abstracted by two
independent reviewers. Studies were organized and synthesized into thematic categories. Then a
qualitative descriptive study was conducted with a purposeful sample of 6 South Asian mothers
from the Greater Toronto and Hamilton Area, recruited from a sub-sample of the SouTh Asian
biRth CohorT Study (START). Semi-structured interviews were conducted to explore their
perceptions and experiences of IPV in their community. The interview data were analysed using
reflective thematic analysis.
Findings: The scoping review revealed that most studies qualitatively explored the experiences
and perceptions of IPV amongst women of the South Asian diaspora; however, there was a paucity
of quantitative literature to ascertain the impacts of exposure to IPV. Similarly, there was a dearth
of literature on the prevention of IPV in this population. Other research gaps included the lack of
clinical samples, the underrepresentation of some South Asian ethnicities over others, and the
overrepresentation of studies conducted in the USA. The qualitative descriptive study revealed
that among this sample of South Asian mothers, they expressed that in-laws play a significant role
in contributing to violence from in-laws, which can lead to IPV, and in increasing a woman’s risk
of experiencing IPV by adhering to traditional gender roles. Participants identified that the IPV
can manifest as unequal sharing of responsibilities between partners and women’s education can
be protective against IPV. Participants believed that their concern for their children’s well-being
along with cultural expectations of South Asian females, played a key role in the decision to seek
help for IPV. Participants identified that physicians could play an important role in helping women
who have experienced IPV by asking about IPV and offering resources.
Discussion: This scoping review, which identified and mapped IPV literature, and qualitative
study, which investigated the perceptions of IPV amongst South Asian mothers, contribute to the
body of IPV literature amongst women in the South Asian diaspora. The findings can help inform
future research directions, and can contribute to the general understanding of stakeholders, such
as service providers for IPV, about how IPV is understood, experienced, and addressed among
South Asian mothers.

abstract: Thesis

abstract: Master of Science (MSc)


title: Confidence Distillation for Efficient Action Recognition

contributor:
Chiang, Fei
Zheng, Rong
Computing and Software

subject:
Deep Learning
Computer Vision
Artificial Intelligence
Efficient Inference
Regularization
Loss Function
Machine Learning
Distillation

abstract:
Modern neural networks are powerful predictive models. However, when it comes
to recognizing that they may be wrong about their predictions and measuring the
certainty of beliefs, they perform poorly. For one of the most common activation
functions, the ReLU and its variants, even a well-calibrated model can produce incorrect
but high confidence predictions. In the related task of action recognition, most
current classification methods are based on clip-level classifiers that densely sample a
given video for non-overlapping, same sized clips and aggregate the results using an
aggregation function - typically averaging - to achieve video level predictions. While
this approach has shown to be effective, it is sub-optimal in recognition accuracy
and has a high computational overhead. To mitigate both these issues, we propose
the confidence distillation framework to  firstly teach a representation of uncertainty
of the teacher to the student and secondly divide the task of full video prediction
between the student and the teacher models. We conduct extensive experiments
on three action recognition datasets and demonstrate that our framework achieves
state-of-the-art results in action recognition accuracy and computational efficiency.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: We devise a distillation loss function to train an efficient sampler/classifier for video-based action recognition tasks.


title: Psychometric validation of the CLEFT-Q patient reported outcome measure: A prospective study to examine construct validity and responsiveness following four cleft-specific operations

contributor:
Klassen, Anne
Health Research Methodology

subject:
Patient reported outcome measure
Psychometric validation
Construct validity
Responsiveness
Minimally important difference

abstract:
CHAPTER 1: Introduction: The most common craniofacial congenital anomaly is the cleft lip and/or palate (CLP). The CLEFT-Q is the first condition-specific comprehensive patient reported outcome instrument (PROM) for patients with CLP. Other measures used in assessment of patients with CLP are Child Oral Health Impact Profile (COHIP) and Cleft Hearing, Appearance and Speech Questionnaire (CHASQ). The development and validation of the CLEFT-Q have been completed in three phases. In phase I, 138 patients with CLP from six countries were interviewed, and data were used to form 13 scales measuring appearance, facial function and health-related quality of life (HR-QOL). In phase II, scales were field-tested internationally with 2434 patients to examine reliability and validity as well as develop a common scoring algorithm for international use. Phase III, the focus of this thesis, aimed to examine further construct validity and responsiveness of the CLEFT-Q scales.
CHAPTER 2: Methods: Patients were recruited at six cleft centres in Canada, USA and UK between January 2018 and October 2019. The sample included patients aged 8-29 seeking rhinoplasty, orthognathic, cleft lip scar revision and alveolar bone graft (ABG) operations. Before and six months after surgery, participants were asked to complete the CLEFT-Q scales relevant to their operation and two other PROMs frequently used in cleft research, i.e., COHIP and CHASQ. Cross-sectional construct validity was examined by testing prespecified hypotheses about expected relationships between CLEFT-Q, CHASQ and COHIP instruments. Internal responsiveness was examined using the distribution-based method. Data were analysed using paired sample t-tests and calculation of effect sizes (ESs) and minimally important differences (MIDs).
CHAPTER 3: Results: Examination of cross-sectional construct validity of the CLEFT-Q scales using the COHIP and CHASQ subscale resulted in 39/53 (74%) hypotheses having been supported by the results. The required sample size to examine responsiveness using the anchor-based approach was not reached. Assessment of internal responsiveness using the distribution-based approach demonstrated that the appearance scales were highly responsive to change following cleft-specific surgeries, with statistically significant results and ESs ranging from 0.4 (small) to 1.8 (large). Change on the CLEFT-Q HR-QOL scales was not statistically significant. As predicted, the ESs on scales measuring facial aspects most affected by rhinoplasty and orthognathic surgeries were larger than the ESs on scales measuring facial aspects least affected by these surgeries. MIDs for each scale in each operation were determined.
CHAPTER 4: Discussion: Assessment of cross-sectional construct validity demonstrated that CLEFT-Q performs as it was intended when compared with other similar measures (i.e., CHASQ and COHIP). The CLEFT-Q appearance scales were responsive to change following rhinoplasty, orthognathic and cleft lip scar revision operations. As predicted, the CLEFT-Q appearance scales did not detect change following the ABG operation as this operation does not result in visible difference. As hypothesized, the CLEFT-Q HR-QOL scales were less responsive to change than appearance scales as HR-QOL is a more distal construct than appearance in relation to the cleft-related surgeries performed. The preliminary MIDs estimated by the distribution-based approach should be confirmed in studies with diverse CLP populations and larger sample sizes using the anchor-based approach. The findings of this phase III study build on the results of another CLEFT-Q validation study, which demonstrated the ability of the CLEFT-Q scales to detect differences between groups with varying surgical status, i.e., need surgery, have had surgery and never needed surgery.
CHAPTER 5: Conclusion: Cross-sectional construct validity of the CLEFT-Q scales was supported by most prespecified hypotheses. The CLEFT-Q scales were found to be responsive to change. MIDs were determined. The results of this phase III study should be confirmed in a larger and more culturally diverse patient population. Future studies to examine reproducibility and measurement error as well as external responsiveness of the CLEFT-Q scales may be beneficial to add to the psychometric evaluation process.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating Autoantibodies in the Pathophysiology of Platelet Underproduction in Immune Thrombocytopenia

title: ANTIPLATELET ANTIBODY INHIBITION OF PLATELET PRODUCTION

contributor:
Nazi, Ishac
Arnold, Donald
Kelton, John
Biochemistry and Biomedical Sciences

subject: ITP, Platelets, Megakaryocytes, Autoantibodies

abstract: Immune thrombocytopenia (ITP) is a heterogeneous immune-mediated blood disorder with multiple pathologies that cause thrombocytopenia. The primary source of this thrombocytopenia is platelet destruction by antiplatelet autoantibodies. Although several treatment options are available for ITP, they are often transient, and responses can be difficult to predict. Different studies show ITP plasma and autoantibodies can also inhibit platelet production, but the mechanism and its impact in causing thrombocytopenia remains unknown. By identifying the different mechanisms causing ITP thrombocytopenia, it may be possible to identify more effective and patient specific treatment options, as well as identify patients who could be at an increased risk of bleeding. To study the antibody mediated inhibition of platelet production, I developed a peripheral blood based megakaryopoiesis assay that used the patient’s own hematopoietic stem and progenitor cells (HSPC) as a starting cell source to grow megakaryocytes. I demonstrate this assay can use a small amount of peripheral blood to grow mature megakaryocytes that are capable of thrombopoiesis. Using this assay, I investigated the effect patient plasma had on platelet production. As such, this study is the first autologous investigation of the effect ITP plasma has on platelet production. I found no inhibition of megakaryopoiesis, but did find an effect on thrombopoiesis, indicating that the plasma is affecting the end stages of platelet production. Secondary observations also show that some ITP HSPC have an enhanced megakaryopoiesis potential, generating more mature megakaryocytes than what was observed with healthy donors. While screening monoclonal antiplatelet antibodies, I discovered an anti-GPIb antibody that inhibited megakaryocyte maturation and found this affect was also present with the Fab antibody fragment. From my research I have developed several tools that can be used to investigate impaired platelet production in ITP and further our understanding of this pathology.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Immune thrombocytopenia (ITP) is an immune mediated blood disorder where autoantibodies target and destroy platelets, cells that are crucial for preventing blood loss. Evidence from different studies show that ITP autoantibodies are also affecting the cells producing platelets (megakaryocytes), but the mechanism of this effect remains unknown. To study antibody mediated inhibition of megakaryopoiesis, I developed a peripheral blood based megakaryopoiesis assay that used the patient’s own cells as a starting source to grow megakaryocytes. With this assay, I investigated the effect patient plasma had on platelet production. I found no inhibition of megakaryocyte growth but did find an effect on their ability to produce platelets. I also found a model antibody that affected the maturity of the megakaryocytes during their development. These tools can now be used to further investigate impaired platelet production in ITP patients and determine the impact this inhibition has on ITP pathology.


title: Distortion of Temporal Fine Structure cues in Speech and Analysis of resulting Speech Intelligibility

contributor:
Bruce, Ian
Electrical and Computer Engineering

subject:
Phase Distortion
Speech Intelligibility

abstract:
Auditory nerve fiber models provide further insight into the inner workings of the
ear and brain. These models have helped us to develop physiologically based speech
intelligibility metrics, to assess the difficulty of understanding speech objectively.
Several metrics have been developed, but they have been developed using a range
of auditory nerve (AN) fiber models. A full comparison of different metrics on even
footing should be performed to evaluate the accuracy of their predictions.
Speech intelligibility is understood to be dependant on both temporal fine structure
and envelope cues in the acoustic speech signal, which are however linked in a way
where they are very difficult to split. This makes the evaluation of speech intelligibility
metrics tricky, as metrics often aim to analyze mean rate and fine timing information
in the auditory nerve representation of the acoustic cues.
In this study, a method of phase distortion was developed, with the goal of degrading
the fine timing information of a speech signal to the point where only the mean rate
representation in the AN is contributing to the speech intelligibility. Also, the neural
cross correlation coefficients developed in Heinz & Swaminathan (2009) were adapted
from the Zilany & Bruce (2007) auditory nerve model to the Bruce, Erfani & Zilany
(2018) AN model.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Placing Immigration, Settlement and Integration in a Canadian City

contributor:
Newbold, Bruce
Geography

subject:
economic immigration
newcomer youth mental health
refugee resettlement
cultural brokering
voluntary sector
structuration theory
international students
place-based policy

abstract: International migration flows and patterns shaped by the determinants, processes and outcomes of social, political, and economic conditions have led to important transformation of society and human geographies. As Canada continues to effectively manage its immigration system and uphold its commitment to international refugee protection and resettlement, it is critical for Canada to do so with an understanding of the changing context of immigration, which are reinforced by shifting policies and their impact, in our contemporary society. In this thesis, the migration trajectory of three groups of newcomers to Canada; international students, Syrian refugees, and refugee youth, are explored by examining policies and conditions that can create group risks and vulnerabilities in immigration, settlement, and integration as groups transition to life in Canada after arrival. As suggested by Castle (2010) migration researchers can advance the field by embedding their work in broader theories of social change to facilitate understanding of the complexity, interconnectedness, variability, contextuality, and multi-mediation of migratory process in the context of rapid change. This thesis employs a geographical lens of place to deepen understanding of processes and outcomes in our contemporary society, while responding to these evolving contexts in one mid-size, post-industrial Canadian city. In three separate research, this thesis examines: 1) economic immigration flow under Express Entry in 2015 and 2016; 2) the role of the voluntary sector during the Syrian Refugee Resettlement Initiative in Hamilton, Ontario in 2016; and 3) the place of school-based settlement in bridging and brokering school-based mental health for newcomer youth.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: As Canada continues to effectively manage its immigration system and uphold its commitment to international refugee protection and resettlement, it is critical for Canada to do so with an understanding of the changing context of immigration in our contemporary society. In this thesis, I examine the migration trajectory of three groups of newcomers to Canada; international students, Syrian refugees, and refugee youth, by asking two overarching research questions that explores policies and conditions that can create group risks and vulnerabilities in immigration, settlement, and integration. This thesis seeks to understand how policies could be addressed to improve successful outcome for newcomers. This thesis employs a geographical lens of place to deepen understanding of processes and outcomes in our contemporary society, while responding to these evolving contexts in one mid-size, post-industrial Canadian city.


title: An Interpretive Description of the Experience of Receiving Telephone-Based Diabetes Health Coaching Among Community-Based Adults with Type 2 Diabetes Mellitus

contributor:
Sherifali, Diana
Health Sciences

subject:
diabetes coaching
type 2 diabetes mellitus
community
adults
self-management support
nurse-led coaching

abstract:
Background:  Over the last decade, diabetes health coaching, also referred to as diabetes coaching, has emerged as a patient-centered intervention to assist individuals with type 2 diabetes mellitus (T2DM) in acquiring independence with self-management. The structure and delivery of such interventions have varied greatly while showing improvements in glycemic control. However, literature continues to show a gap around the patient experience of receiving diabetes coaching support.
Objective: To explore the perceived experience of receiving telephone-based diabetes health coaching among community-based adults with T2DM within the Canadian context.
Methods: A qualitative exploration with an interpretive descriptive design was carried out. Participants from the intervention group of a larger randomized controlled trial who had received a telephone-based diabetes coaching intervention over one year were invited to participate in a telephone interview with open-ended questioning.
Findings: A total of 12 participants were interviewed and four major themes were identified. (1) Adapting to life with T2DM reflects how coaching helped individuals to integrate diabetes into their lives by addressing misconceptions, providing knowledge, encouraging awareness, and easing transition onto insulin. (2) Heightened mindfulness of diabetes-related wellness captured the greater attention participants’ gave to their overall well-being and self-management behaviours. (3) Behaviour change guided by the participant highlights the differences in participants’ motivation, readiness to make changes, external factors that influenced their ability to make self-management behaviour changes. (4) Lastly, valuing a supportive relationship illustrates that participants felt the unique coach-client relationship was reliable, holistic, non-judgmental, and encouraging.
Conclusion: Overall, participants found diabetes coaching to be positive and highlighted the various ways it was able to support their ability to more effectively self-manage their diabetes.

abstract: Thesis

abstract: Master of Science in Nursing (MSN)


title: Characterizing a Single Plane Illumination Microscope for Imaging Fluorescence Correlation Spectroscopy

contributor:
Fradin, Cecile
Physics and Astronomy

subject:
SPIM-FCS
Light sheet
FCS
Diffusion
Concentration
Optics

abstract:
In many systems, in vitro or in vivo, it has become important to experimentally obtain
dynamical information at many different positions simultaneously. This is a challenge
as conventionally, dynamic information in biological systems is probed with a confocal
microscope to perform either fluorescence correlation spectroscopy (FCS) or fluorescence
recovery after photobleaching (FRAP), which can be damaging due to phototoxicity, and
yields information at a single position. Advances in camera sensors have allowed their
use in place of single point detectors and the implement of imaging FCS by way of single
plane illumination microscopy (SPIM). In this modality, a light sheet with a thickness of
only a few microns illuminates the sample and the fluorescence is projected orthogonally
onto the camera chip. By imaging small regions of interest at a very high frame rate, we
can determine dynamic parameters such as diffusion coefficients and local concentrations
in a 2D array of pixels. In this thesis, I discuss the theoretical background, hardware
setup, design and characterization of a SPIM which I have built in order to perform
imaging FCS.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterizing the role and regulation of growth arrest specific FABP4 in chicken embryo fibroblasts

contributor:
Bédard, André
Biology

subject:
quiescence
reversible growth arrest
fatty acid binding protein 4 (FABP4)
AP2
P20K
Lipocalin
chicken embryo fibroblast (CEF)
Growth arrest specific gene (GAS)
C/EBP-beta
oxidative stress
hypoxia
lipid peroxidation
membrane stress response
lipid damage response
reactive oxygen species
contact inhibition

abstract: Conditions which promote reversible growth arrest, such as hypoxia and high cell density, lead to activation of a diverse network of proteins known as growth arrest specific (GAS) genes. Fatty acid binding protein 4 (FABP4), a lipid chaperone involved in the regulation of metabolic and inflammatory responses, has been shown to be part of the GAS program. While the induction of FABP4 in oxygen-deprived environments is well characterized, its functionality and regulation in such conditions remains unclear. In this study, we describe how mis-expression of FABP4 affects cell viability and survival within low oxygen conditions. Loss of FABP4 using shRNA was shown to be associated with a significant increase in oxidative stress and lipid peroxidation, a reduction in lipid droplet formation and a greater incidence of apoptosis. Hypoxia-mediated expression of FABP4 was also found to be positively correlated with cellular levels of C/EBP-beta, an essential activator of p20K in quiescence. FABP4 and p20K are both lipocalins that have been shown to share similar induction patterns and ability to assist in the maintenance of lipid trafficking in cellular stress circumstances. Unexpectedly, the depletion of FABP4 or p20K results in loss of the other in limited oxygen concentrations. This occurs independently of disruption to the broad GAS gene program, suggesting the two proteins may be co-regulated in a shared hypoxic-signalling pathway. C/EBP-beta appears to be the transcriptional activator shared by FABP4 and p20K in quiescence, and the three may be part of an intricate system to sense and respond to reactive oxygen species and lipid radicals. However, the forced expression of either FABP4 or p20K when the other is repressed only moderately restores cell survival through alleviating oxidative stress, indicating the two are both necessary for optimal response to hypoxia. In all, these studies suggest that analogous to the p20K lipocalin, FABP4 plays a critical role in lipid homeostasis and cell survival in conditions of limited oxygen concentrations, and its stimulation is dependent on C/EBP-beta activity.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: A study investigating the role of FABP4 and p20K in conditions of reversible growth arrest with an emphasis on cell survival, lipid homeostasis and mitigating the effects of oxidative stress, and regulation of the two lipocalins by C/EBP-beta.


title: Predicting Monthly Precipitation in Ontario using a Multi-Model Ensemble and the XGBoost Algorithm

contributor:
McNicholas, Dr. Paul D.
Li, Dr. Zoe
Statistics

subject:
climate modeling
machine learning
precipitation
variable selection
statistical downscaling

abstract: There is a strong interest in the climate community to improve the ability to accurately predict future trends of climate variables. Recently, machine learning methods have proven their ability to contribute to more accurate predictions of historical data on a variety of climate variables. There is also a strong interest in using statistical downscaling to predict local station data from the output of multi-model ensembles. This project looks at using the machine learning algorithm XGBoost and evaluating its ability to accurately predict historical monthly precipitation, with a focus of applying this method to simulate future precipitation trends.

abstract: Thesis

abstract: Master of Science (MSc)


title: Micropaleontological (Foraminifera, Testate Amoeba) and µXRF Analysis of the Upper Cretaceous (Turonian) Notom Delta, Ferron Sandstone Member, Mancos Shale Formation, Central Utah, USA

contributor:
Reinhardt, Eduard
Earth and Environmental Sciences

subject:
Ferron Sandstone
Upper Cretaceous
Morphogroup analysis
Foraminifera
Testate amoebae
marginal marine settings
paleoenvironments
Itrax-µXRF core scanner

abstract:
In this thesis, the results of microfossil, biofacies, and geochemical analyses (µXRF) of the Upper Cretaceous (Turonian) Ferron – Notom delta, Utah, USA are reported and discussed. The Notom delta is the oldest of three clastic deltas in the Ferron Sandstone Member, Mancos Shale Formation. Foraminifera and testate amoebae were recovered from ninety-eight mudstone samples among five well-exposed outcrops (Caineville North, Steamboat, Blue Hills, Neilson Wash, and Coalmine Wash). Detailed observations showed foraminifera, and testate amoebae tests have undergone post-burial compression (flattening), dissolution, and transport/reworking; therefore, identification of these assemblages to their species level is difficult.

The micropaleontological analysis of the Ferron-Notom delta consists of three studies. Morphogroup analysis was applied on foraminifera and testate amoebae, where a relationship between the test morphology and habitat was established. Morphogroup analysis resulted in four main morphogroups and eleven morphotypes and were assigned to life mode, environment, and feeding strategies. Three foraminifera morphogroups and one testate amoebae morphogroup were established indicate a range of environments, from shallow shelf to shallow shelf to lagoon/estuary environments. Biofacies analysis using the morphotypes was applied on three outcrops (Caineville North, Steamboat, and Blue Hills). We use the morphotypes to define the four main biofacies using cluster analysis, and biodiversity indices. Four biofacies showed marine and fluvial (freshwater) influences. Salinity and OM indices were derived from the relationship of foraminifera morphotypes (BiS, TrS, TS) and testate amoebae morphotypes (Ta-F, Ta-D, Ta-S) that follows lithofacies trends.  Because of the under-representation of calcareous foraminifera (due to taphonomic and/or diagenetic factors), the biodiversity indices are treated herein as relative measures. Despite this taphonomic bias, the agglutinated foraminifera and testate amoebae morphogroups show trends with salinity both among the outcrops and stratigraphically within the outcrops. The Blue Hills outcrop represents the most landward and lowest salinity environment (tidally-influenced backwater), Steamboat is more coast proximal with a higher salinity of the delta front and fluvial estuarine environments, and the Caineville North outcrop represents the most coast proximal (fluvial/estuarine to deltaic/prodeltaic) with salinities ranging from low to medium. It appears that the landward transport and coastward of tests was a significant source of taphonomic bias. Nonetheless, the assemblages provide useful depositional information that correlates with previously documented lithofacies data. A salinity index based on a ratio of trochospiral taxa versus testate amoebae was found to provide a useful measure of coastal proximity that matches lithofacies trends.

The µXRF analysis was conducted on twenty-nine mudstone samples from the Caineville North outcrop to examine elemental proxies for paleo-salinity (Sr/Ba), organic matter (K/S), redox (V/Ni), and sediment sources (Zr/Rb, Ti/Fe, Ti/Ca). Twenty-nine surface mudstone samples collected from four lithofacies representing prodelta, delta front, fluvial valley fill and shelf environments. Fourteen elements (Ti, Fe, Ca, Sr, Ba, Ni, Rb, Zr, S, V, Cu, Mn, Si, and K) were used to calculate proxy ratios to detect variations in terrigenous sediments, carbonate production, salinity, grain size, and fluvial inputs in the Caineville North outcrop. Elemental data showed good correspondence between the elemental data and the lithofacies and microfossil indices. Sr/Ba and Ca/Fe showed relationships with carbonate content and proximity to the shoreline. The paleo-salinity proxy (Sr/Ba) did not respond to salinity, but was more responsive to lithological change of carbonate content. The microfossil salinity index seems to be a more accurate paleo-salinity indicator. The proxy for fluvial input of sediment (Zr/Rb and Ti/Fe) agree well with the lithofacies trends, and Zr/Rb and Ti/Fe showed highest values within the fluvial valley fill facies, with higher variability of Ti/Fe compared to the other lithofacies (prodelta, delta front, and shelf), corresponding to response to the proximity of the depositional sites to a fluvial sediment source. The redox proxy V/Ni matched the previously derived microfossil OM index ("bolivind-type" taxa) showing a strong relationship between eutrophication and redox trends. The study aims to establish important baseline geochemical compositions of sediment sources to establish patterns and trends with sediment succession in the deeper basin (offshore; i.e. Mancos Shale). Potentially, these nearshore to fluvial trends will provide important geochemical data to assess changes in paleoclimate, and sea-level in offshore sediment successions.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Effects of cyclotraxin-b treatment on endometriotic lesion survival in an immunocompromised mouse model

contributor:
Foster, Warren
Delaney, Kathleen
Scattolon, Sarah
Health Sciences

subject:
endometriosis
cyclotraxin-b
treatment
animal model

abstract: Endometriosis is a steroid-dependent common gynecological condition characterized by the growth of endometrial epithelial and stromal cells outside of its cavity. Estrogen dependence, progesterone resistance, in situ estrogen production, increased inflammation, resistance to apoptosis, active cell growth and proliferation, and overall disease’s heterogeneity makes it challenging to treat patients without compromising fertility. BDNF and its high affinity receptor TrkB has been shown to be dysregulated in women with endometriosis suggesting their role in disease progression. Immunocompromised mice (Rag2γc) (n=25) underwent an implantation surgery during which a cell suspension consisting of human endometrioma cells was injected into the animals’ peritoneal cavity. Upon lesion stablishment all animals were divided into five groups and treated with either high (7.5mg/kg/day), medium (5mg/kg/day) or low (2.5mg/kg/day) dose of TrkB inhibitor cyclotraxin-b, negative control (saline) or 0.04mg/kg/day letrozole. After four weeks of treatment all animals were sacrificed, all major organs were collected and assessed with routine histology for potential adverse effects of the treatment, all endometriotic implants were analyzed with routine histology and IHC for a panel of markers: BDNF, TrkB, anti-human mitochondrial protein, CD31, VEGFa, VEGFR1, VEGFR2. Treatment did not cause any significant side effects. There was a dose-dependent trend in reduction of endometriotic implants’ volume and number. IHC confirmed expression of the angiogenic markers within endometriotic implants. A larger study may be required to replicate results and advance the search for novel non-hormonal endometriosis treatment.

abstract: Thesis

abstract: Master of Science in Medical Sciences (MSMS)

abstract: Endometriosis is a chronic pain condition affecting more than 176 million women worldwide. Despite its commonality and severity its gold standard diagnosis is performed through invasive laparoscopy and there is no cure resulting in low quality of both physical and mental health of the affected individuals. Levels of a neurotrophic factor - BDNF and its high affinity receptor TrkB have been found increased in women with endometriosis and thus, BDNF-TrkB signaling cascade appears to be a promising therapeutic target. This study investigated an effect of TrkB inhibitor – cyclotraxin-b on reduction of endometriotic lesion number and volume within an immunocompromised model. Replication of results and increase of sample size may provide more details about cyclotraxin-b clinical relevance for treatment of endometriosis.


title: Tetralogy of Fallot Surgical Repair and Associated Right Ventricular Remodeling

contributor:
Whitlock, Richard
Health Research Methodology

subject:
tetralogy of fallot
congenital heart disease
outcomes
observational studies

abstract:
Tetralogy of Fallot (TOF) is the most common cyanotic congenital cardiac defect with a global annual incidence of 40,000 cases. Advances in surgery and perioperative care led to improvements in perioperative mortality and, thus, a growing number of survivors. TOF survivors often suffer from complications related to a failing right ventricle. Follow-up studies evaluating TOF repair strategies suggest an association between the type of surgical repair strategy and late right ventricular health. However, surgical practices remain unchanged and led by institution-level biases. The body of evidence addressing outcomes based on TOF surgical repair strategy is weak and controversies persists on the management of these patients.
This thesis comprises 6 chapters that form the foundation of a multi-centre research program on outcomes after TOF surgical repair. The program uses various methodologies to generate evidence with a vision to change surgical practices.
Chapter 1 is an introduction providing background on TOF and contemporary areas of controversy.
Chapter 2 presents the results of a retrospective analysis evaluating the use of early echocardiogram parameters in predicting late cardiac magnetic resonance imaging evaluation of the right ventricle.
Chapter 3 presents the results of a retrospective cohort exploring the association between TOF repair strategy and development of right bundle branch block.
Chapter 4 presents the results of a multinational survey aiming to explore contemporary biases in TOF surgical repair strategy selection.
Chapter 5 presents the background, rationale, design and baseline cohort characteristics of the Tetralogy of Fallot for Life (TOF LIFE) study. The study is a multi-centre inception cohort study with a follow-up period of 2 years.
Finally, Chapter 6 discusses the conclusion, limitations, and future implications of this research program.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: Velocity Influences the Relative Contributions of Visual and Vestibular Cues to Self-Acceleration Perception

title: Velocity and Self-Acceleration Perception

contributor:
Shedden, Judith
von Mohrenschildt, Martin
Psychology

subject:
Acceleration
Motion simulator
Multisensory integration
Vestibular system
Self-motion
Optic flow

abstract: Self-motion perception is based on the integration of visual (optic flow) and vestibular (inertial) sensory information. Previous research has shown that the relative contribution of visual and vestibular cues can change in real time based on the reliability of that information. The present study assessed whether initial velocity and acceleration magnitude influence the relative contribution of these cues to the detection of self-acceleration. Participants performed a simple response time task with visual and vestibular self-acceleration cues as targets. Visual optic flow was presented at three possible initial velocities of 3, 9, or 15 m/s, and accelerated to result in three possible final velocities of 21, 27, or 33 m/s. Corresponding vestibular cues were presented at magnitudes between 0.01 and 0.04 g. The self-acceleration cues were presented at three possible stimulus onset asynchronies (SOAs): visual-first (by 100 ms), in-sync, and vestibular-first (by 100 ms). We found that presenting the cues in-sync resulted in the fastest responses across all velocities and acceleration magnitudes. Interestingly, presenting the visual cue first resulted in a relative advantage over vestibular-first at the slowest initial velocity of 3 m/s, and vice versa for the fastest initial velocity of 15 m/s. The fastest overall responses for visual-first and in-sync were observed at 9 m/s. The present results support the hypothesis that velocity of optic flow can alter the relative contribution of visual and vestibular cues to the detection of self-acceleration.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
This thesis contributes valuable insight into the emerging literature on how visual and
vestibular cues are integrated to result in reliable self-motion perception. Specifically, this thesis
provides evidence that velocity of optic flow plays an important role in mediating the relative
weighting of visual and vestibular cues during acceleration perception.


title: Strategies for Promoting Physical Activity Maintenance Among Individuals with Stroke

contributor:
Richardson, Julie
Rehabilitation Science

subject:
Stroke
Physical Activity
Maintenance
Exercise
Rehabilitation
Behavior
Behaviour Change Technique

abstract: Physical activity can have beneficial effects on post-stroke recovery, but only if it is maintained. Current evidence shows that physical activity levels of individuals with stroke do not meet recommended guidelines. This thesis investigated current programs and proposed a novel trial design to aid stroke survivors with maintaining their activity levels in free-living environments. The first study was a systematic review of the effects of current interventions in post-stroke recovery. The review reported no differences between intervention and control groups for steps walked/day at 3-month (standardized mean difference (SMD) 0.19; 95% CI -0.30 to 0.69; I2 = 47%; GRADE rating: Very Low), time spent in moderate-vigorous physical activity at 3-month (SMD -0.03; 95% CI -0.73 to 0.68; I2 = 52%; GRADE rating: Very Low), or self-reported physical activity at the 6-month follow-up (SMD 0.40; 95% CI -0.02 to 0.82; I2 = 0%; GRADE rating: Very Low). However, the pooled estimate of the self-reported physical activity at the 3-month follow-up was above the line of no-effect (SMD 0.22; 95% confidence intervals, 0.01 to 0.42; I2 = 0%; GRADE rating: Very Low). Intervention characteristics associated with physical activity maintenance could not be explored due to the low number of trials. Insights from this review were used to design an Adaptive Treatment Strategy where high-intensity interventions are sequentially tailored to participants following the identification of increased needs. A protocol of a proof-of-concept pilot Sequential Multiple Assignment Randomized Trial was outlined to assess trial feasibility, participants’ acceptability with changes in interventions, participants’ and staffs’ satisfaction with the treatment strategy, and to provide preliminary estimates of effect of physical activity and self-efficacy for physical activity. Together, these two studies provide direction about intervention design, physical activity maintenance assessment, and proposes the design of a novel pilot SMART trial.

abstract: Thesis

abstract: Master of Science Rehabilitation Science (MSc)

abstract: Physical activity can help with recovery after stroke if it is maintained. This thesis examined ways to support stroke survivors with remaining active in their daily lives. The first study was a review of existing programs to investigate their effects on the physical activity levels of individuals with stroke. Findings from this study showed that current programs produced a small improvement in physical activity that was short-lived, and no program component was better than others at promoting activity maintenance. Insights from this review were used to design a new study that provides increased support to stroke survivors in steps to cater to individual needs. This study will investigate whether this program is practical, acceptable by stroke survivors and people delivering it, and helps to improve and maintain physical activity. Together, these studies provide directions for designing future programs, assessing activity maintenance, and propose the design for a novel study.


title: New Strategies for Kinetic Energy Density Functionals

contributor:
Ayers, Paul W.
Chemistry and Chemical Biology

subject: kinetic energy, density functional, resummation, hyperasymptotics

abstract:
Orbital-free density functional theory requires accurate approximations for the
noninteracting kinetic energy as a functional of the ground-state electron den-
sity. For explicit functionals in real space, it has proved difficult to supersede
the quality of the gradient expansion, truncated at second order. This is partly
because the gradient expansion diverges for atomic and molecular densities.
In an effort to include information about higher-order terms in the gradient
expansion but avoid divergences, we consider resummations for the series using
Padé approximants and Meijer-G functions. To regularize terms that appear
in the denominator, we consider various damping functions, which introduces
parameter(s) that can be fit to atomic data. These results improve upon the
second-order truncation, but do not achieve the exquisite accuracy that would
be required for practical orbital-free density-functional theory calculations.

abstract: Thesis

abstract: Master of Science (MSc)


title: Developmental Dynamics of the Human Brain Transcriptome

contributor:
Kathryn, Murphy
Neuroscience

subject:
Human
Neurodevelopment
Transcriptomics
Bipolar Disorder
Ageing
Brain

abstract: Large-scale transcriptomic studies are among of the most comprehensive accounts we have of the biological processes underlying human brain development and ageing. However, many analyses and descriptive models applied to gene expression data implicitly assume that developmental change is continuous and uninterrupted. Perhaps this bias is often overlooked because the emphasis is on what is changing during development rather than how development itself is changing. Indeed, despite the richness of transcriptomic data and its capacity to recapitulate higher-order functions, few have used it to understand the dynamics of brain development. Gene expression is determined by complex, high-dimensional interactions of the gene regulatory network. Dynamic systems theory states that the interactions of components in any complex systems will converge on certain stable patterns, also known as attractor states. To approximate these stable states, the current study leveraged robust and sparse k-means clustering to identify tissue samples with similar patterns of gene expression across the transcriptome. Sample ages were then used to visualize when in developmental time these stable patterns are present. The resulting model describes the developmental dynamics of the brain transcriptome as a series of non-linear, overlapping states that progress across the lifespan.

abstract: Thesis

abstract: Master of Science (MSc)


title: Developing a Multi-Dimensional Patient Assessment System for Community Paramedicine Home Visit Programs in Ontario, Canada

contributor: Clinical Health Sciences (Health Research Methodology)

subject:
Community Paramedicine
Patient Assessment

abstract: A practical result of the research conducted through completion of thesis was the interRAI Community Paramedicine Home Visit Assessment instrument.

abstract: This thesis presents a systematic framework for developing and evaluating a multi-dimensional patient assessment system for community paramedicine home visit programs.  Underlying all of this work was a hypothesis that multi-dimensional patient assessment systems hold clinical utility to inform care planning activities, which in turn can direct appropriate patient care.  I outline considerations for using assessment instruments to assist in the assessment process including strengths and weaknesses of using single-dimension or multi-dimensional assessment instruments when attempting to complete a consistently organized, multi-domain, and comprehensive assessment.  The thesis includes a framework that outlines the major stages in developing and evaluating a new multi-dimensional patient assessment system.  The framework uses community paramedicine home visit programs as an example of its application and subsequent chapters present and discuss key research questions related to each stage of the development and evaluation process; establishing a comprehensive set of clinical observations to be assessed and the related application of assessment findings to care planning activities.  Two chapters explore existing assessment practices in community paramedicine home visit programs with findings that informed creation of a prototype assessment system that was pilot-tested.  The fifth chapter describes results of the pilot-test and the sixth chapter investigates the clinical utility of the prototype assessment system to care planning of community paramedics.  The development approach is informed by next-generation assessment practices and my work evaluating community paramedicine home visit programs provides a basis for appraisal of evidence in an emerging practice setting that does not have broadly established clinical practice guidelines.  The accumulation of the evidence established in my thesis has led to the creation of a multi-dimensional patient assessment system for community paramedicine home visit programs.  My research methods and findings can assist clinicians, decision makers or other researchers where a multi-dimensional assessment system is being developed or implemented.

abstract: Thesis

abstract: Candidate in Philosophy


title: LANE TRACKING USING DEPENDENT EXTENDED TARGET MODELS

contributor:
Kirubarajan, Thia
Electrical and Computer Engineering

subject: Lane detection

subject: lane tracking

subject: Multi target tracking

subject: Probability data association

subject: Joint probability data association coupled filter

subject: Multi output Gaussian process

subject: Dependent multiple target tracking

subject: Kernel based JPDACF

abstract:
Detection of multiple-lane markings (lane-line) on road surfaces is an essential aspect
of autonomous vehicles. Although several approaches have been proposed to detect
lanes, detecting multiple lane-lines consistently, particularly across a stream of frames
and under varying lighting conditions is still a challenging problem. Since the road's
markings are designed to be smooth and parallel, lane-line sampled features tend
to be spatially and temporally correlated inside and between frames. In this thesis,
we develop novel methods to model these spatial and temporal dependencies in the
form of the target tracking problem. In fact, instead of resorting to the conventional
method of processing each frame to detect lanes only in the space domain, we treat
the overall problem as a Multiple Extended Target Tracking (METT) problem.
In the first step, we modelled lane-lines as multiple "independent" extended targets
and developed a spline mathematical model for the shape of the targets. We showed
that expanding the estimations across the time domain could improve the result of
estimation. We identify a set of control points for each spline, which will track over
time. To overcome the clutter problem, we developed an integrated probabilistic data
association fi lter (IPDAF) as our basis, and formulated a METT algorithm to track
multiple splines corresponding to each lane-line.In the second part of our work, we investigated the coupling between multiple extended targets. We considered the non-parametric case and modeled target dependency
using the Multi-Output Gaussian Process. We showed that considering
dependency between extended targets could improve shape estimation results. We
exploit the dependency between extended targets by proposing a novel recursive approach
called the Multi-Output Spatio-Temporal Gaussian Process Kalman Filter
(MO-STGP-KF). We used MO-STGP-KF to estimate and track multiple dependent
lane markings that are possibly degraded or obscured by traffic. Our method tested
for tracking multiple lane-lines but can be employed to track multiple dependent
rigid-shape targets by using the measurement model in the radial space
In the third section, we developed a Spatio-Temporal Joint Probabilistic Data
Association Filter (ST-JPDAF). In multiple extended target tracking problems with
clutter, sometimes extended targets share measurements: for example, in lane-line
detection, when two-lane markings pass or merge together. In single-point target
tracking, this problem can be solved using the famous Joint Probabilistic Data Association
(JPDA)  filter. In the single-point case, even when measurements are dependent,
we can stack them in the coupled form of JPDA. In this last chapter, we expanded
JPDA for tracking multiple dependent extended targets using an approach called
ST-JPDAF. We managed dependency of measurements in space (inside a frame) and
time (between frames) using different kernel functions, which can be learned using
the trained data. This extension can be used to track the shape and dynamic of
dependent extended targets within clutter when targets share measurements.
The performance of the proposed methods in all three chapters are quanti ed on
real data scenarios and their results are compared against well-known model-based,
semi-supervised, and fully-supervised methods. The proposed methods offer very promising results.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: An Intelligent Energy Management Strategy Framework for Hybrid Electric Vehicles

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject:
energy management strategy
electrified vehicles
optimization methods
intelligent control

abstract: This thesis proposes a novel framework for solving the energy management problem of Hybrid Electric Vehicles (HEVs). We aim to establish a practical and effective approach targeting an optimal Energy Management Strategy (EMS).  A situation-specific Equivalent Consumption Minimization Strategy (ECMS) is developed to minimize fuel consumption and improve battery charge sustainability while maintaining an acceptable drive quality.  The investigated methodology will be broadly applicable to all HEV applications; however, it will be well-suited for hybrid electric delivery applications.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Bivariate Functional Normalization of Methylation Array Data

contributor:
Canty, Angelo
Mathematics and Statistics

subject:
methylation
methylation data
partial least squares
bivariate
bivariate quantile
applied statistics
preprocessing
normalization
machine learning

abstract:
DNA methylation plays a key role in disease analysis, especially for studies that compare
known large scale differences in CpG sites, such as cancer/normal studies or between-tissues
studies. However, before any analysis can be done, data normalization and preprocessing of
methylation data are required. A useful data preprocessing pipeline for large scale comparisons
is Functional Normalization (FunNorm), (Fortin et al., 2014) implemented in the minfi
package in R. In FunNorm, the univariate quantiles of the methylated and unmethylated
signal values in the raw data are used to preprocess the data. However, although FunNorm
has been shown to outperform other preprocessing and data normalization processes for
these types of studies, it does not account for the correlation between the methylated and
unmethylated signals into account; the focus of this paper is to improve upon FunNorm by
taking this correlation into account. The concept of a bivariate quantile is used in this study
as an attempt to take the correlation between the methylated and unmethylated signals
into consideration. From the bivariate quantiles found, the partial least squares method is
then used on these quantiles in this preprocessing. The raw datasets used for this research
were collected from the European Molecular Biology Laboratory - European Bioinformatics
Institute (EMBL-EBI) website. The results from this preprocessing algorithm were then
compared and contrasted to the results from FunNorm. Drawbacks, limitations and future
research are then discussed.

abstract: Thesis

abstract: Master of Science (MSc)


title: Realistic Galaxy Simulations: Feedback, Magnetic Fields and the ISM

contributor:
Wadsley, James
Physics and Astronomy

subject:
galaxies
hydrodynamics
supernova
magnetic fields
magnetohydrodynamics
galaxy evolution
high performance computing

abstract: The evolution of galaxies rely on a wide variety of physics, and numerical simulations are one of the main tools used to study them. In this thesis we develop a framework for what models can be used to realistically simulate galaxies and study their evolution. We begin with setting specific requirements on the numerical resolution of galaxies, and then test the effects of different stellar feedback models on isolated disk galaxies. We then investigate the addition of magnetic fields into the simulations, and what role they play in determining the contents, behaviour, and star formation, within the interstellar medium of galaxies.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: We develop a framework used to realistically simulate the evolution of galaxies. Specifically we investigate the addition of supernova and magnetic field models, and provide solutions to eliminate the dependence of those models on numerical resolution.


title: Moral Integrity and Interrogational Torture in the War on Terror

contributor:
Igneski, Violetta
Philosophy

abstract: In this thesis I will argue that interrogational torture, understood as the infliction of severe pain and suffering in order to acquire information from someone, is morally impermissible. I will begin by considering two arguments in support of interrogational torture: the consequentialist argument and the rights-based argument. I will argue that both of these arguments are flawed and fail to establish the conclusion that interrogational torture is morally permissible. I will then provide a philosophical analysis of the concept of moral integrity, and show how this idea of moral integrity applies to state institutions and government officials who represent those state institutions. I will argue that any government official who engages in an act of torture degrades their own moral integrity as a representative of state institutions, along with the moral integrity of state institutions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: In response to the terrorist attacks of September 11, 2011, the United States government engaged in acts of torture to acquire information from terrorists. In this thesis, I will argue against the use of torture by focusing on the concept of moral integrity. I will argue that common arguments used to justify the use of torture are flawed for a variety of different reasons. I will then argue against the use of torture by arguing that torture violates the moral integrity of state institutions and government officials. Government institutions and the state officials who represent those institutions ought to embody the moral principles that help form the moral foundation of the state, and I will argue that committing acts of torture go against these moral principles and, hence, degrade the moral integrity of state institutions and government officials.