VictorJuiz/thesis huggingface dataset:
Electron Cryomicroscopy of the Mycobacterial Respiratory Supercomplex
Keywords: antibiotics
CryoEM
mycobacteria
structural biology
tuberculosis

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.
The Development of a Liposome-Gel Composite Material Intended for the Photothermally-Induced Release of Antibiotics
Keywords: Antimicrobial Resistance
Drug Delivery
Liposomes
Polydopamine Nanoparticles

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.
“She’s just a kid!” How Perceptions of Children’s Mental Capacities Influence Moral Character Judgments
Keywords: children
mental capacities
moral character
moral status
moral transgressions
morality

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.
Policy Mixes for Accelerating Zero-emission Vehicle Transition: Experiences in Quebec, British Columbia and Ontario
Keywords: Creative Destruction
Diffusion
Electric Mobility Transition
Electric Vehicles
Policy Mix
Zero-Emission Vehicles

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.
Performance Stability of Electromagnetic Acoustic Transducers
Keywords: Electromagnetics
NDT
Stability
Ultrasonic

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.
Density Functional Theory (DFT) Study on Selective Reductive Amination of Sodium Triacetoxyborohydride (STAB) with Respect to Imines over Aldehydes and Ketones
Keywords: density functional theory
imine
reductive amination
sodium triacetoxyborohydride

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.
Pancreatic Stem Cells: Their Origin during Development
Keywords: beta cells
cells
embryogenesis
lineage
pancreas
stem

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.
Photophysical and Electronic Properties of Axially Bridged Boron Subphthalocyanines
Keywords: BsubPc
capacitor
chromophore
organic electronics
subphthalocyanine

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).
The Anti-Saccade Eye Movement Task to Screen for Cognitive Dysfunction in Patients with Amyotrophic Lateral Sclerosis
Keywords: amyotrophic lateral sclerosis
anti-saccade
cognition
cognitive dysfunction
eye movement
eye paradigm

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.
Control of the Current Shaping MMC to Enable High Step-down AC/DC Power Conversion
Keywords: AC/DC power conversion
high step-down
modular multilevel converter

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.
Quantifying the Effect of Metal-substrate Interaction on Catalytic Properties by Combining Machine Learning and First-principles Calculations
Keywords: Adsorption energy
Heterogeneous catalysis
High entropy alloy
Machine learning
Neural network
Single atom catalyst

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.
Evaluating the Effectiveness of Rhythmic Vibrotactile and Auditory Stimulation for a Biofeedback Gait Training System for Individuals with Lower Limb Amputation
Keywords: amputation
biofeedback
entrainment
gait
rehabilitation
rhythmic stimulation

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.
Investigating the Potential of Isolating and Expanding Lymphocytes from Adult Sarcoma
Keywords: Adoptive Cell Therapy
Adult Sarcoma
Immunotherapy
Osteosarcoma
Soft Tissue Sarcoma
Tumour Infiltrating Lymphocytes

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.
Developing a Method of Identifying Distractions in Surgery with Eye-tracking Technology
Keywords: Distractions
Eye Tracking
Laparoscopy
Operating Room
Surgery
Visual Attention

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.
Design and Optimization of Buoyant Photocatalysts for Passive Degradation of Trace Organic Pollutants in Drinking and Industrial Process-affected Water
Keywords: 1
4-dioxane
Detoxification
OSPW
Remediation
TiO2

The 1.6•10^12 L of oil sands process-affected water (OSPW) in sedimentation ponds in northern Alberta contains 20-120 mg L-1 of naphthenic acids (NAs), a class of molecules acutely toxic to aquatic life [1]. Photocatalytic degradation of NAs in OSPW has been demonstrated by TiO2 containing buoyant photocatalysts [2], [3]. Composed of a buoyant hollow glass microsphere, TiO2, and a silica binder, the buoyant photocatalyst degrades the NAs in a passive advanced oxidation process. However, nucleophilic attack on the silica binder by hydroxide ions of the alkaline OSPW reduce the durability of the buoyant photocatalyst. Formulation changes to the buoyant photocatalyst resulted in the adoption of alumina hydrosol as a more durable binder over the previously used silica. In a second study, the improved buoyant photocatalyst was then used to detoxify water containing trace amounts of 1,4-dioxane, an emerging and recalcitrant pollutant found in drinking water.
Measuring Gradients in Gaseous Elemental Mercury Using a Passive Air Sampler
Keywords: Mercury
Passive air sampler
Sampling rate
Spatial gradients

Mercury (Hg) monitoring is necessary to constrain the global Hg cycle and to develop policies for reducing Hg emissions. Passive air samplers (PAS) are an accessible method for monitoring gaseous elemental mercury (GEM). I tested the suitability of PAS for recording GEM gradients at widely varying scales. Vertical gradients on the scale of centimeters to tens of meters measured over soil and within a forest allowed for the observation of GEM uptake in growing vegetation, the determination of the air-surface exchange direction, and the estimation of evaporative fluxes from contaminated soil. When PAS were deployed above a field with known soil contamination, slightly different spatial contamination patterns suggest horizontal GEM advection. on a continental scale, the PAS were also used to map annually averaged GEM levels across South and Central America. Accounting for the effect of wind speed on the PAS sampling rate is necessary to distinguish small concentration differences.
Clearing Up The Smoke: Clinical and Radiographic Characterization of a North American Cohort of Childhood Moyamoya
Keywords: children
moyamoya
neuroimaging
stroke

Moyamoya (MMA) is a progressive cerebral steno-occlusive angiopathy which can lead to strokes. Its natural history derives from adult East Asian cohorts with idiopathic disease. Clinical differences in pediatric, non-Asian and syndromic patients are reported but understudied. This study aimed to: 1) characterize clinical and radiographic features of a North American cohort of childhood moyamoya; 2) identify risk factors of ischemic event recurrence (IEC) and poor outcome; and 3) design an IEC predictive model. Idiopathic MMA presents with transient ischemic attacks (TIA) and bilateral disease and have a higher risk of IEC while the neurofibromatosis type 1-related syndromic form tends to be unilateral and indolent. A young age, infarcts, bilateral and advanced disease predict poor outcome. Significant angiographic posterior deep collaterals and lack of leptomeningeal collaterals predict poor outcome, but good revascularization response. Asian ancestry, TIA, ophthalmo-ethmoidal, leptomeningeal, and middle meningeal collaterals and steal phenomenon on functional MRI predict IEC.
A Deep Generative Model for Missing Data Imputation
Keywords: Computer Networks
Deep Learning
GANs
Generative Models
Machine Learning
Missing Data

Machine learning relies on data. However, real-world datasets are far from perfect. One of the biggest challenges in working with these datasets is missing data. In this work, we present a novel deep generative model for missing data imputation. What makes our method unique is the focus it puts on classification accuracy while it imputes missing data. This makes our model particularly useful for classification problems. We formulate our proposal as a sequential game and show that it learns the true data distribution. Furthermore, we propose a new algorithm for optimizing our objective. Our proposal is able to learn the feature importance and impute critical features more accurately. Experimental results show our method outperforms existing methods in terms of classification accuracy.
Probabilistic Methods for Crowd-sourced Indoor Localization
Keywords: Indoor Localization
Machine Learning
Noise Sensitive Regression

Despite its shortcomings, fingerprinting \textit{Received Signal Strength} (RSS) localization is still one of the most widely used methodologies for indoor localization. One of its shortcomings is due to its limited accuracy (around 3 meters). Based on empirical data, it is known that its limited accuracy is because of the data quality. This empirical data is however not justified by the currenct model of the RSS data. In this thesis a model is proposed for RSS signals which is in a better agreement with observations from the real data. By means of this model a lower bound is provided for localization error which explains the fact that this localization method can not attain sub-meter accuracies in practise. Aside from its limited localization accuracy, fingerprinting RSS localization has some practical challenges as well. A main challenge of RSS localization is its dependence on a high quality radio map. This makes RSS localization a labour intensive task as it requires technicians to collect RSS data on a regular basis to update the fingerprint database. In this thesis algorithms are proposed to reduce the sensitivity of localization algorithms to noisy data in radio map, making the use of crowd provided RSS, which are usually of less quality, feasible.
Showing Off: Relocating Performance, Reclaiming Shame
Keywords: Acting
Autoethnography
Memoir
Performance Studies
Queer Theory
Theatre

By tracking my year of struggle and discovery as a theatre practitioner in the world of theatre scholars, this autoethnographic thesis investigates how my own theory of performance has come to be, and how early childhood trauma has fueled my practice. As a 58-year-old theatre practitioner, I have taken intellectual refuge in the Academy, which has emotional doors - the first and most significant being into a space of shame. Scholarship initiated this journey, beginning with Fred Moten and Stefano Harney's The Undercommons (2013), then finding its way into performance theology with Claire Maria Chambers Performance Apophatics (2017), and then finally queer theory with Maggie Nelson’s The Argonauts (2015) and the work of Eve Kosofsky Sedgwick. The thesis itself is a kind of performance that weaves through knowing into feeling by investigating my own work, my queerness, my journey through faith, and finally, my shame: its roots and its affect.