VictorJuiz/thesis huggingface dataset:
Structure and Transport Property Characterization of Gas Diffusion Layer Materials using Machine Learning Methods

For the first time, machine learning methods are applied to the gas diffusion layer (GDL) to characterize structural and transport properties. In the first investigation, a benchmark study of seven machine learning methods used to predict the permeability and diffusivity of GDLs in two phase flow conditions was provided. The best performing models could predict single- and two-phase permeability and diffusivity with R2 > 0.95. In the second investigation, numerically generated image data was used to train three CNNs which predicted the porosity of X-ray images from commercial GDL materials (MAE

Keywords: Convolutional Neural Network
Fuel Cell
Gas Diffusion Layer
Machine Learning
Advisor: Bazylak, Aimy
Electron Cryomicroscopy of the Mycobacterial Respiratory Supercomplex

The genus Mycobacterium includes many pathogens. Antibiotics traditionally used to target mycobacteria have given rise to drug resistance, particularly for Mycobacterium tuberculosis, which causes tuberculosis. Oxidative phosphorylation (OxPhos) has recently emerged as a druggable pathway to sterilize mycobacterial infections. OxPhos involves the sequential passage of electrons by a series of membrane protein complexes. In mycobacteria, Complexes III and IV form a CIII2CIV2 supercomplex that is the target of the drug candidate telacebec. CIII2CIV2 contains a flexible superoxide dismutase (SOD) subunit believed to be important for mycobacterial pathogenicity. This thesis presents improved electron cryomicroscopy structures of CIII2CIV2 from Mycobacterium smegmatis. An assay was developed to measure telacebec’s inhibition of CIII2CIV2. Structures of CIII2CIV2 with telacebec bound revealed telacebec’s inhibitory mechanism, which in turn provided insights into the electron transfer mechanism of CIII2CIV2. Finally, new sample preparation and data processing techniques were used to improve understanding of the flexible features of CIII2CIV2.

Keywords: antibiotics
CryoEM
mycobacteria
structural biology
tuberculosis
Advisor: Rubinstein, John L
The Development of a Liposome-Gel Composite Material Intended for the Photothermally-Induced Release of Antibiotics

Near-ubiquitous use of antibiotics has contributed to the rise in antibiotic resistance among common pathogens. In order to slow the development of future resistance, novel antibiotic strategies must be created that minimise the chances of off-target effects. Here, current advances in antimicrobial nanomaterial strategies, an assay for assessing liposome stability, attempts to develop a biocompatible nanobomb, and the creation of a composite hydrogel material for thermally-resolved drug delivery are presented. Lipid formulations with different melting temperatures were made into liposomes and stably embedded in an agarose hydrogel from which liposomal cargo was released in a temperature-dependent fashion with yields recorded over 50%. This was assessed by monitoring the pH-dependent conformational changes of bromothymol blue cargo as it was released from the liposomes. This work establishes a functional system and protocols for future work in photoinduced multidrug delivery.

Keywords: Antimicrobial Resistance
Drug Delivery
Liposomes
Polydopamine Nanoparticles
Advisor: Sullan, Ruby M.A.
Kraatz, ‪Heinz-Bernhard
“She’s just a kid!” How Perceptions of Children’s Mental Capacities Influence Moral Character Judgments

Why are children and adults held to different standards when they commit immoral transgressions? One answer may be how we perceive the minds of children versus adults. Mind perception is essential when evaluating moral status (who is morally responsible and protected from harm). Developmental changes may influence how adults perceive the mental capacities of children across the lifespan, which may affect judgments of moral responsibility and moral character. Experiment 1 assessed lay intuitions as to why children are seen as less morally culpable than adults. We found that lack of moral knowledge and malleability of character were the most common explanations. In Experiment 2, we find that with age perceptions of mental capacities related to moral knowledge, theory of mind, and self-control increase while malleability of character decreases. Additionally, as these capacities change, judgments of moral character become harsher with age whereas judgments of an immoral action remain the same.

Keywords: children
mental capacities
moral character
moral status
moral transgressions
morality
Advisor: Starmans, Christina
Policy Mixes for Accelerating Zero-emission Vehicle Transition: Experiences in Quebec, British Columbia and Ontario

Many jurisdictions have adopted different policies to accelerate Zero-Emission Vehicle (ZEV) transition. This study identifies, categorizes, and analyzes, through document analysis and expert interviews, various policies influencing the light-duty ZEV transition in the three-leading provinces in Canada, i.e., Quebec, British Columbia, and Ontario. To this end, two analytical frameworks are employed. The first one is used to categorize identified policies into four main categories, namely demand-side, infrastructure, supply-side, and institutional. The second analytical framework is applied to emphasize the ZEV transition from the creative destruction approach to discussing how provincial policies might influence socio-technical elements around the incumbent regime and the emergent niche. Findings show that the three provinces have collectively employed similar policy mixes. However, closer inspection of their specific policy instruments, policy strength, policy continuity, ambitions to phase out internal combustion engine vehicles, and transition to electric mobility along with their socio-political conditions show differences across the provinces.

Keywords: Creative Destruction
Diffusion
Electric Mobility Transition
Electric Vehicles
Policy Mix
Zero-Emission Vehicles
Advisor: El-Diraby, Tamer T
Robinson, John J
Performance Stability of Electromagnetic Acoustic Transducers

The signal amplitude stability of non-destructive testing systems based on electromagnetic acoustic transducers (EMATs) and guided ultrasonic waves is investigated. The study is focused on three factors: sensor lift-off, specimen thickness, and dynamic permeability. The objectives are to determine a minimum lift-off to achieve adequate stability and signal-to-noise ratio, and evaluate the effect of variable specimen thickness on the propagation of the ultrasonic dispersive SH1 mode. The analysis is performed through finite element simulations, which are validated experimentally. It was found that a magnetostriction-based transmitter is less sensitive to lift-off than a Lorentz force transmitter. Specimen thickness variations in a direction perpendicular to ultrasonic wave propagation can focus or divert SH1 wave energy such that the resulting signal fluctuations are large enough to interfere with defect detection. Both magnetostriction-based and Lorentz-based EMAT inspection systems were found to be unaffected by random variations of dynamic permeability.

Keywords: Electromagnetics
NDT
Stability
Ultrasonic
Advisor: Filleter, Tobin
Sinclair, Anthony
Density Functional Theory (DFT) Study on Selective Reductive Amination of Sodium Triacetoxyborohydride (STAB) with Respect to Imines over Aldehydes and Ketones

Reductive amination is one of the most important methods to synthesize amines, having a wide application in the pharmaceutical, agricultural, and materials industry. In general, the reaction begins with a dehydration between a carbonyl and amine compound, forming an imine, which is then reduced to an alkylated amine product. Sodium triacetoxyborohydride (STAB) is a popular choice for reducing agent, as it shows selectivity for imines over aldehydes and ketones, which is particularly important in direct reductive amination. Herein, a density functional theory (DFT) investigation of STAB selectivity with respect to imines over aldehydes and ketones is reported. It was found the reduction of imines over their respective carbonyl compound reactants was both thermodynamically and kinetically favoured, with Brønsted–Lowry and Lewis acids playing pivotal roles in these reactions. Overall, the imine formation and subsequent reduction were both favoured over the carbonyl compound reduction, confirming literature reports of STAB imine selectivity.

Keywords: density functional theory
imine
reductive amination
sodium triacetoxyborohydride
Advisor: Morris, Robert H
Taylor, Mark S
Pancreatic Stem Cells: Their Origin during Development

Adult pancreatic precursors display partial multipotentiality and limited self-renewal ability (in mice) in vitro, bringing into question their stemmness and role in development. Here, I show that pancreatic stem cells (PSCs) can be isolated from the pancreatic progenitor stage of mice, and as early as the pancreatic endoderm stage of human embryonic stem cell differentiation. Further, PSCs were isolated from embryonic day 16 of mice and demonstrated self-renewal capabilities, unlike those derived from adult mice. In addition, it was shown that dexamethasone promotes retinal stem cell self-renewal and retinal stem and progenitor proliferation. In contrast, I show that dexamethasone decreases pancreatic stem/progenitor proliferation/survival. Together, I provide evidence that pancreatic stem cells emerge early in pancreatic development, and their further characterization may clarify what role they play during development. Isolating highly proliferating self-renewing pancreatic stem cells during development may introduce novel ways of isolating new sources of therapeutic beta cells.

Keywords: beta cells
cells
embryogenesis
lineage
pancreas
stem
Advisor: van der Kooy, Derek VDK
Photophysical and Electronic Properties of Axially Bridged Boron Subphthalocyanines

Boron Subphthalocyanines (BsubPcs) are a family of conjugated, bowl-shaped small molecules that have shown promise as organic semiconductors in organic light emitting diodes and organic photovoltaics. Dodeca-fluorinated BsubPcs (F12BsubPc) are highly photo-stable and exhibit highly reversible reductions making them a promising candidate as both an electron acceptor and redox capacitor. Dimeric F12BsubPc bound through the axial position were found to undergo quenching in their photoluminescence spectra while maintaining the reversible reductions characteristic of monomeric F12BsubPcs in solution. Composite electrodes utilizing the redox activity of F12BsubPc were prepared by coupling the axial Br- derivative Br-F12BsubPc to Multi-Walled Carbon Nanotubes functionalized with nucleophilic groups (COOH, OH).

Keywords: BsubPc
capacitor
chromophore
organic electronics
subphthalocyanine
Advisor: Bender, Tim
Monocular 3D Object Detection and 3D Multi-object Tracking for Autonomous Vehicles

In this thesis, we first tackle the monocular 3D object detection task. The main challenge in monocular 3D detection lies in predicting depth, which must be inferred due to the lack of range measurement. We propose CaDDN, which predicts a categorical depth distribution for each pixel to project feature information in 3D space. We then use the bird's-eye-view projection and single-stage detector to produce the final output detections. Next, we tackle the 3D multi-object tracking task, where associating tracks to detections remains challenging. Our proposed solution, InterTrack, introduces the Interaction Transformer to generate discriminative object representations for data association. We extract track and detection features, and aggregate global information via attention. We then use each track/detection feature pair to estimate affinities, and use a two-stage data association and track management approach to produce the final tracks. We perform validation on autonomous vehicle datasets and achieve state-of-the-art performance.

Advisor: Waslander, Steven L
The Anti-Saccade Eye Movement Task to Screen for Cognitive Dysfunction in Patients with Amyotrophic Lateral Sclerosis

Up to 50% of patients with amyotrophic lateral sclerosis (ALS) have frontotemporal cognitive deficits. These deficits are diagnosed by a lengthy neuropsychological assessment. However, these assessment tools have limited reliability in patients with declining motor control. As the ocular motor neurons are spared, the interleaved pro- and anti-saccade task (IPAST), which probes executive and working memory functions of the frontal lobes, can be used to assess cognitive function in ALS. This study compared the IPAST performance of patients with ALS with varying cognitive function, healthy controls, and patients with behavioural-variant frontotemporal dementia, and determined the neuropsychological and clinical variables linked to the performance. The results showed that patients with ALS and differing cognitive levels have different IPAST performances. The IPAST performances were mainly attributed to the level of executive dysfunction and attention-working memory. The results supported IPAST as a promising cognitive screening tool in ALS.

Keywords: amyotrophic lateral sclerosis
anti-saccade
cognition
cognitive dysfunction
eye movement
eye paradigm
Advisor: Zinman, Lorne
Control of the Current Shaping MMC to Enable High Step-down AC/DC Power Conversion

This thesis introduces a new control strategy for the Current Shaping Modular Multilevel Converter (CS-MMC), a recently proposed DC/DC converter intended for medium voltage applications. This new control formulation allows the same CS-MMC to accommodate a vastly wider range of input voltages while also reducing the output current ripple. Experimental results are presented using a 1 kW laboratory scale prototype. It is then shown that this introduced control strategy enables the CS-MMC to also accommodate AC input voltages. To achieve this, the topology must be slightly modified, with the new topology termed the AC/DC CS-MMC. While the CS-MMC is intended for the future DC grid, the AC/DC CS-MMC can be powered from existing AC distribution feeders. Simulation results for a 10 kW system are presented. The input current distortion is shown to be in compliance with the IEEE 519-2014 standard.

Keywords: AC/DC power conversion
high step-down
modular multilevel converter
Advisor: Lehn, Peter
Quantifying the Effect of Metal-substrate Interaction on Catalytic Properties by Combining Machine Learning and First-principles Calculations

Heterogeneous catalysis is the central pillar of chemical industry, but they are mostly developed via “trial-and-error” approach, which is labour consuming. The central challenge lies in the difficulty of quantifying the catalyst’s metal-substrate interaction and its effect on catalytic properties. This thesis leverages machine learning to capture the structure-property relationship of these catalysts, thereby accurately screening candidate catalysts order-of-magnitude faster than experimental approach. We examine three types of metal alloys: high-entropy alloys, single-atom alloys and 2D material-supported single-atom catalysts, whose development is hindered by the vast chemical design space. This thesis successfully developed models which are trained on relevant density functional theory calculations and demonstrate chemical accuracy for predicting the adsorption energy of key intermediates. This work has high practical impact as it offers a platform from which optimal catalyst material combinations can be rapidly pinpointed and subsequently synthesized via currently available methods, such as incipient wetness impregnation and dealloying.

Keywords: Adsorption energy
Heterogeneous catalysis
High entropy alloy
Machine learning
Neural network
Single atom catalyst
Advisor: Singh, Chandra Veer
Evaluating the Effectiveness of Rhythmic Vibrotactile and Auditory Stimulation for a Biofeedback Gait Training System for Individuals with Lower Limb Amputation

Individuals with lower limb amputation (LLA) often exhibit asymmetrical gait patterns, which can be a result of insufficient gait training. This often leads to secondary musculoskeletal problems, including joint degeneration and osteoarthritis. A wearable biofeedback system using rhythmic stimulation can enhance motor learning through the synchronization of gait and an external rhythm. This can encourage symmetrical walking patterns and provide supplemental physiotherapy to this population. Here, able-bodied adults with an induced ankle-weight asymmetry are provided rhythmic vibrotactile stimulation (RVS) and rhythmic auditory stimulation (RAS) to improve stance time symmetry ratio (STSR). RVS and RAS improved STSR, without worsening cadence, velocity, and stride length. RVS showed statistically significant changes in improving STSR. Evaluating if rhythmic stimulation is effective in improving gait symmetry is an integral step in developing an innovative and widely accessible biofeedback system that can enhance the mobility and quality of life of individuals with LLA.

Keywords: amputation
biofeedback
entrainment
gait
rehabilitation
rhythmic stimulation
Advisor: Andrysek, Jan
Investigating the Potential of Isolating and Expanding Lymphocytes from Adult Sarcoma

Sarcomas are a heterogeneous group of mesenchymal neoplasms, which many are associated with a high risk of metastasis and poor prognosis. Conventional chemotherapy and targeted therapies have varying effects across individuals and tumour subtypes. They frequently provide limited clinical benefit; hence, more effective treatments are urgently needed. Recent advances in immunotherapy – such as checkpoint inhibition or adoptive cell therapy (ACT) – show potential in increasing efficacy by providing a more personalized treatment. Through optimizing an expansion protocol for tumor infiltrating lymphocytes (TILs) from primary sarcoma samples, TILs were isolated and cultured from 55 of 92 patients. The isolated TILs varied in CD4+ and CD8+ Tcell compositions and retain their ability to release IFNγ upon stimulation. Overall, I have identified TILs in a subset of sarcomas; furthermore, by expanding and characterizing these TIL populations I have developed a means by which this can potentially be applied towards ACT in he future.

Keywords: Adoptive Cell Therapy
Adult Sarcoma
Immunotherapy
Osteosarcoma
Soft Tissue Sarcoma
Tumour Infiltrating Lymphocytes
Advisor: Andrulis, Irene L
Wunder, Jay S
GPUPool: A Holistic Approach to Fine-Grained GPU Sharing in the Cloud

As GPUs evolved into popular computing platforms in the cloud, GPU virtualization has become a highly desirable feature to lower datacenter operating costs. In this work, we explore fine-grained GPU sharing, which has a larger potential in improving hardware utilization compared to coarse-grained sharing adopted in Nvidia’s virtualization solutions. However, fine-grained sharing causes performance unpredictability due to workload-dependent interference, which makes it extremely challenging to provide quality-of-service (QoS) guarantees in the cloud. We present GPUPool, a GPU sharing system that unlocks the performance potential of fine-grained sharing at both systems and hardware levels. GPUPool predicts co-execution performance of arbitrary job combinations, and assigns compatible GPU jobs onto the same hardware to maximize hardware sharing. Our experimental results show GPUPool reduces the number of GPUs required to meet job- specific QoS requirements by 32% and 21.3%, compared to a system with no sharing and one with coarse-grained sharing respectively.

Advisor: Pekhimenko, Gennady
Investigating New Directions for Boron Subphthalocyanines: Formation of Intentional Organic Alloys and π-extension to Boron Subanthracocyanines

Boron subphthalocyanines (BsubPcs) have become materials of interest in organic photovoltaics (OPVs) due to their strong absorption in the visible spectrum and their ease of synthetic tuning. Synthetic modification at the axial boron-linked group and peripheral isoindoline sites have been well studied. Two under-explored methods of modification include alloy formation through careful mixing of compatible BsubPcs and π-expansion of the BsubPc framework to form the fused triple-benzene ring variant, the boron subanthracocyanine (BsubAc). While there is some literature on boron subnaphthalocyanine (BsubNc) alloys and BsubPc mixtures, the work in this thesis expands on the understanding of BsubPc alloying. Peripherally- and axially-varied mixtures of BsubPcs were shown to be co-crystallizable into a singular lattice. The axially-varied mixtures were tested in OPV devices where the mixture layer behaved as an alloyed material of unique properties. One potential pathway to BsubAc synthesis was identified and tested, exhausting all available reaction parameters.

Advisor: Bender, Timothy P.
Biomimetic Mineralized Collagen Fibrils and Their Effect on Osteogenic Differentiation

Autograft alternatives have not met the performance of autografted, native bone. It is unknown whether the ultrastructural organization of mineral and collagen in bone is significant for osteogenic differentiation and improved bone healing. Here I explore the literature and mechanisms regarding biomimetic mineralized collagen fibrils (BMCFs) and their effect on osteogenic differentiation. I also investigated the effect of various ultrastructural features on the osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (hBM-MSCs). These conditions were: aligned, intrafibrillar mineral; aligned, intrafibrillar mineral with misaligned surface mineral; and unaligned extrafibrillar mineral. With n=1 donor, I report the preliminary result that BMCFs with aligned, intrafibrillar mineral promote the expression of mature osteoblast markers even without osteogenic medium. Additionally, morphological differences resulted upon exposure to differences in surface mineral. These results, along with those pending from other hBM-MSC donors, could inform the development of autograft alternatives, with close attention paid to ultrastructural aspects.

Advisor: Sone, Eli D
Viswanathan, Sowmya
Developing a Method of Identifying Distractions in Surgery with Eye-tracking Technology

Distractions are a suspected major contributing factor to the preventable surgical errors that occur. Current methods used in observational studies face limitations that warrant improvement. Limitations include subjective, team-based methods to identify distractions that can miss distracting events. This thesis aims to develop a method of identifying distractions that begins addressing these reported methodological limitations. This aim was achieved through three objectives that led to the development of a method that uses the OR Black Box® platform to prevent missing distracting events and a remote eye-tracker that provides an objective measure of the main operating surgeons’ visual attention deviation. Eleven surgeries were assessed, and results identified 8 of 50 potential distractions as distractions based on a drop of surgical related percentage gaze time during the potential distractions analyzed. This novel method can provide data to improve the understanding of the relationship between distractions and preventable surgical errors.

Keywords: Distractions
Eye Tracking
Laparoscopy
Operating Room
Surgery
Visual Attention
Advisor: Grantcharov, Teodor