VictorJuiz/thesis huggingface dataset:
Optimization of Hydrodynamics in Full-scale Multi-cassette Flat Sheet Membrane Bioreactors using Computational Fluid Dynamics Modeling

The porous medium approach has been used to study hydrodynamics in hollow-fiber (HF) membrane bioreactors (MBR), and often a single MBR component was considered. This study aims to expand the application of the porous medium approach to a flat-sheet (FS) configuration and explore the use of computational fluid dynamics (CFD) on optimizing the global hydrodynamics in full-scale multi-cassette FS MBR tanks. The present work first developed a numerical calibration method of the porous parameters for FS membranes. The results suggested that the two-phase flow should be used, and the viscous loss term should not be omitted. Next, three-dimensional CFD models of full-scale FS MBR tanks were developed. The results showed that modifying the tank geometry could be a more efficient option to optimize the flow distribution across the whole tank. In addition, for the first time, the capability and limitation of the porous medium approach were discussed.

Keywords: computational fluid dynamics
flat-sheet
full-scale MBR
hydrodynamics
membrane bioreactor
porous medium
Advisor: Lawryshyn, Yuri
The Functional Properties of Inhibitory Neurons in the Brainstem Circuit Mediating the Optokinetic Reflex

Reflexes are ideal systems to study how sensory information mediates behavior. For instance, the optokinetic reflex (OKR) is an oculomotor behaviour critical for stable vision. The OKR is driven by the brainstem accessory optic system (AOS), containing neurons encoding the information about the visual field. The AOS neurons are genetically and functionally diverse. However, it remains unknown whether genetically defined AOS populations, such as inhibitory neurons, encode different information in the AOS. By paring in vivo electrophysiology with optogenetic tagging, I studied the spatial frequency and direction selectivity of AOS inhibitory neurons. I found that inhibitory AOS neurons encode lower spatial frequencies and are less direction selective, shedding light on the roles of inhibitory neurons in the OKR.

Keywords: inhibition
neuron
not-dtn
optogenetics
optokinetic reflex
visual
Advisor: Liu, Baohua
Investigating the Role of GLI3 Repressor in Human Kidney Organoid Formation

Individuals with Pallister-Hall syndrome (PHS) present with variably penetrant renal malformations that are associated with a spectrum of truncating GLI3 mutations. Previous mouse models suggest that constitutive expression of GLI3 repressor (GLI3R) impairs renal development, however, the mechanisms underlying GLI3 mutations in humans remain unclear. Here, I have generated an in vitro model of PHS using iPSC-derived human kidney organoids. Truncating GLI3 mutations were introduced into control iPSC lines and analyzed for relative expression levels of GLI3 activator and repressor. My results suggest that organoids with increased levels of GLI3R exhibit impaired nephron induction during early organoid formation (D4), followed by a reduction in nephron-like structures formed (D18). Wholemount imaging and microarray analyses also demonstrate an increase in stromal cells and increased expression of medullary stromal genes. Together, these findings suggest that the presence of a functional and constitutive GLI3R impairs nephron and stromal differentiation in human kidney organoids.

Advisor: Rosenblum, Norman D
Implementation of a Kinase-Phosphatase Redox Cycling Pathway to Improve D-Xylose Fermentation in Engineered Saccharomyces cerevisiae

Unbalanced redox cofactor levels are responsible for low xylose metabolism in Saccharomyces cerevisiae. The NADPH-preferring xylose reductase (XR) and NAD-dependent xylitol dehydrogenase (XDH) enzymes usually expressed in S. cerevisiae have conflicting cofactor requirements. Accordingly, S. cerevisiae produces more xylitol than ethanol, the desired product. This is especially true anaerobically. In our work, we aimed to rebalance the cofactors using a kinase-phosphatase cycling (KPC) pathway featuring NADH kinase (NADHK) and NADP phosphatase (NADPase). In silico, KPC maximized ethanol output at any XR cofactor ratio and under most oxygen conditions. In vivo, NADPase accentuated the redox issues and inhibited growth. Synergistic activity of NADPase and ScUTR1 NADHK helped restore growth and increase xylose utilization, while POS5Δ17 NADHK offered an additional negative contribution. NADPase and ScUTR1 did not lead to growth improvement with respect to the background. We concluded that benefit from KPC activity relies on the optimization of the NADPase/NADHK flux ratio.

Keywords: Cofactor engineering
Metabolic engineering
NADH kinase
NADP phosphatase
Saccharomyces cerevisiae
Xylose utilization
Advisor: Mahadevan, Radhakrishnan
Development and Application of Sampling and Extraction Methods for Microplastics in Drinking Water

To-date, no standardized methods have been proposed for analyzing microplastics in drinking waters. This study assessed known methods to collect and extract microplastics from treated drinking waters and identified two common limitations: use of insufficient water, and lack of method recovery assessment. In response, this study developed an in-line filtration method, which improved accuracy when compared to in-laboratory filtration methods. In-line filtration was shown to have higher recoveries for the reference microplastics examined (+37% for PVC fragments, +23% for PET fragments, +22% for nylon fibers and +7% for PET fibers) and a greater potential to reduce microplastic contamination. The filtration capacity of in-line filtration method was observed to exceed 350 L of treated water. Application of in-line filtration was validated using ultrafiltration (UF) influent and effluent from two full-scale drinking water treatment facilities. UF represents an effective technology which is capable of removing ~95% of microplastics from drinking water.

Keywords: Drinking Water
Methods
Microplastic
QA/QC
Advisor: Andrews, Robert RCA
Characterizing Murine Compensatory Renal Growth following Unilateral Nephrectomy

Following the surgical removal of a single kidney, the remaining kidney shows a striking ability to compensate for this loss by rapidly initiating an acute growth program, coupled with increased function. The organ size change halts once normal function is restored, but the signals regulating this change in kidney size remain unknown. This work describes murine compensatory renal growth on the level of organ size, function, and cellular changes up to 28 days post-surgery. The data suggests that the extent of remnant kidney growth may be related to the ratio of kidney weight-to-body weight prior to surgery, potentially hinting at a predictive factor of postoperative renal mass recovery and implicating a size sensing mechanism in this process. We also developed an image processing pipeline to analyze kidney cross-sections, and identified trends in nuclear size and density changes, suggesting the contribution of both hypertrophy and hyperplasia to compensatory renal growth.

Advisor: Kafri, Ran
A Weakly Supervised Framework For the Generation of Instance Segmentation Labels of Contextual Information

This thesis presents a novel Weakly Supervised Mask Data Distillation technique, WeSuperMaDD, to generate Pseudo Segmentation Labels (PSLs) to automate the process of creating image segmentation labels typically created by human annotators. WeSuperMaDD uniquely generates PSLs using learned image features extracted by Convolutional Neural Networks (CNNs) not trained for image segmentation for datasets that are not diverse. WeSuperMaDD introduces a mask refinement system that automatically searches for the PSL with the fewest foreground pixels that satisfies cost constraints. WeSuperMaDD was validated using scene text detection datasets. WeSuperMaDD was found to produce PSLs with higher segmentation accuracy than existing weakly supervised approaches, and comparable accuracy to the state-of-the-art semi-supervised text PSL generation method without requiring fully labeled data. When PSLs generated by WeSuperMaDD were used to train a CNN for context segmentation, improvements in segmentation accuracy in comparison to a CNN trained using Naive PSLs were found.

Keywords: Environment Context Identification
Robot Navigation and Exploration
Segmentation and Labeling
Weakly Supervised Learning for Robots
Advisor: Nejat, Goldie
Teaching Educators About Acquired Brain Injury: A Usability Study Evaluating the Teach-ABI Module

Acquired brain injury (ABI) is a leading cause of death and disability in children, yet it is a “silent voice” in the Ontario education system and Ontario educators do not receive any related training. This study examined Ontario educators’ satisfaction with the Teach-ABI module, an innovative, e-Learning module that provides information about ABI, its outcomes, and classroom strategies to support students with ABI. Eight educators engaged in one-on-one usability sessions over Zoom, involving a concurrent think-aloud protocol, task completion and participant observation, completion of the System Usability Scale, and an exit interview. Educators identified no significant usability issues with the module and were very satisfied with its content, design, and navigation. Results also revealed that educators were very engaged with the content and felt that it increased their knowledge of ABI. The implications of this study on the development of the Teach-ABI module and future research are discussed.

Keywords: acquired brain injury
online module
pediatric
school-based rehabilitation
teacher training
usability study
Advisor: Scratch, Shannon E.
Martinussen, Rhonda
Metals in Particulate Matter and Deciduous Teeth

Numerous studies have linked airborne metal exposure to adverse health outcomes. Inter-related characteristics of metals were investigated to gain a better understanding of metal exposure in Toronto including the metal composition of size-resolved road dust particles, potentially bioavailable fractions of metals (water-soluble metals) in PM2.5, spatial variability of PM2.5-bound metal concentrations, and the use of deciduous teeth as a novel biospecimen to reconstruct metal exposure timing. High crustal element content and low intrinsic toxicity were found for road dust particles. Local emissions and possible atmospheric processing were found to affect levels of water-soluble Fe, Cu and Mn in PM2.5. Land-Use Regression modelling of Fe, Cu, Ba, Mn, Zn and Pb in PM2.5 revealed different spatial patterns across Toronto. Microstructure identification and micro-spatial trace metal concentration measurement of primary teeth were performed to support Toronto children metal exposure studies.

Keywords: Deciduous teeth
Metal exposure
Metals
PM2.5
Advisor: Evans, Greg J.
Brook, Jeffrey R.
A Systematized Review of Youth Mental Health Courts: An Evaluation of the Courts' Operations and Outcomes

In this study I reviewed the Canadian and international published literature examining youth mental health courts to provide an overview of their processes, mechanisms of change, and outcomes. A systematized literature review was conducted using the PRISMA-ScR checklist as a guideline following a search of PsychINFO, ERIC, ASSIA, MEDLINE, Sociological Abstracts, Social Services Abstracts, Criminal Justice Abstracts with Full Text, and Child and Adolescent Studies databases. Inclusion criteria stipulated that studies be original research, and examine at least one aspect of the courts’ operations or outcomes. Twenty articles satisfied inclusion criteria. Results showed considerable similarities among intake, referral and case monitoring procedures across courts, and recidivism outcomes. Youth reported courts to be collaborative and supportive, with stakeholders reporting reduced case processing times, improved access to treatment services and reduced recidivism. I highlight findings on operations and outcomes of youth mental health courts that have important implications for policy and practice.

Keywords: Court
Mental Health
Program Operations
Program Outcomes
Recidivism
Youth
Advisor: Peterson-Badali, Michele
Skilling, Tracey
Evaluation of Enzyme Activity for Monitoring Biofiltration Performance in Drinking Water Treatment

Recent studies have proposed that enzyme activity may be used as an indicator of biofilter function, as supposed to adenosine triphosphate (ATP), as it provides a means to quantify biodegradation which may allow for a more accurate measure of biofilter performance. This study, 1) developed a methodology for enzyme extraction from filtration media, and 2) evaluated the use of enzyme activity for monitoring biological processes by examining full- and pilot-scale filters to assess impacts associated with pre-treatments, sources waters, and operating conditions. An optimized biomass extraction method for filter media is proposed. Results confirmed that ATP was not a reliable monitoring tool for organics reduction in biofilters whereas strong relationships between esterase and chitinase activity and organics reduction were observed. This study showed that enzyme activity may be appropriate for monitoring biological processes within drinking water filters and may act as a surrogate for the removal of organic compounds.

Advisor: Andrews, Robert C
Anomaly Detection for Cybersecurity Attacks on NetFlow Data

Cybersecurity has become an increasingly important topic in recent years, as concepts such as cloud computing are becoming more and more popular. In this thesis, we will investigate various techniques for detecting cybersecurity attacks using data from NetFlow routers. We will investigate popular techniques such as neural networks and autoencoders and more recent techniques including graph neural networks and variational autoencoders. Our particular experiment shows that binary classfiers such as feed forward neural networks (FNN) work better than one-class classifers such as autoencoders and variational autoencoders. We also found that for port scanning attacks, graph neural networks can further improve detection performance.

Keywords: anomaly detection
cybersecurity
machine learning
NetFlow
Advisor: Leon-Garcia, Alberto
The Protein Interaction Landscapes of the Apicomplexan Parasites Toxoplasma gondii and Plasmodium falciparum

Apicomplexan parasites, Toxoplasma gondii and Plasmodium falciparum, represent a significant burden to human health. With growing resistance to frontline drugs, new therapeutics are needed to combat these parasites. Their lifecycles are driven by the proteome of its unique cellular architecture: much of which is not fully resolved or characterized. Here we seek to gain insight into the global organization of proteins and identify novel protein complexes by generating high confidence maps of protein interactions in both organisms. This thesis evaluates the quality of these networks by rigorous benchmarking with available biological datasets. Predicted protein complexes successfully recapitulate experimentally characterized complexes from literature and predict novel complexes, including novel mitochondrial and apicomplexan-specific organelle localized complexes. These analyses identify novel components to parasitic pathways, such as host invasion and host interactions. In addition, these networks provide a scaffolding platform for the apicomplexan research community to integrate genomic-scale datasets and generate testable hypotheses.

Keywords: Plasmodium falciparum
Protein protein interaction
Toxoplasma gondii
Advisor: Parkinson, John
Characterizing the Role of Host Lipid Metabolism on Microsporidia Infection in Caenorhabditis elegans

Microsporidia are fungal obligate intracellular pathogens that primarily manifest in immunocompromised individuals. Microsporidia have reduced metabolic capabilities and so they have strong host-dependence for many metabolic processes. However, despite their growing medical importance, microsporidia are poorly understood. I investigated the impact of host lipid metabolism on microsporidia infection using the nematode Caenorhabditis elegans and its natural microsporidian pathogen Nematocida parisii. A previous metabolomics screen performed on N. parisii infected C. elegans identified upregulation of lipid metabolites in three lipid biosynthesis pathways: phosphatidylcholines, acylcarnitines and ceramides. I also identified an increase in the level of lipid droplet associated lipase, ATGL-1, upon infection. In addition, by screening 25 lipid mutant strains, animals defective in producing sphingosine showed resistance to infection whereas supplementing sphingosine increased susceptibility, suggesting sphingosine may be involved in promoting microsporidian growth. Together, my research of lipid regulation by microsporidia can help to determine new therapeutic targets for microsporidian infection.

Advisor: Reinke, Aaron
Dual Photoredox/HAT Chemistry in Carbohydrate Functionalization

Chemical synthesis of carbohydrate derivatives has attracted much attention due to their prevalence in natural products. The methods for the derivatization of carbohydrate monomers are, however, still mainly focused on the functionalization of hydroxyl groups rather than the carbon-backbone. This thesis describes the exploration of a method for the regioselective C-H alkylation of the anomeric position of 1,2-unprotected carbohydrate diols using hydrogen-atom transfer (HAT)/photoredox chemistry and borinic acid catalysis. Initial experiments yielded mixtures of alkylated products, culminating in the investigation of reaction kinetics and stability of radical intermediates by computational analysis. A second research direction aimed at the transformation of 2-O-acylated pyranosides to 3-keto-2-deoxypyranosides using another HAT/photoredox system is also described. These products are suggested to arise by hydrogenatom abstraction at the C3-position of the pyranoside, followed by C2-O bond cleavage via spincenter shift. Compatibility with variously configured mono-acylated substrates suggest wide applicability for the preparation of rare, deoxygenated carbohydrates.

Keywords: Anomeric
C-H Functionalization
Carbohydrate
HAT
Photoredox
Spin-center shift
Advisor: Taylor, Mark
Comparing the Oxidative Potential of Fine Ambient Particulate Matter Across Airsheds in Canada

Oxidative potential (OP) and oxidative burden (OB) are being explored as more health-relevant metrics for assessing the risk of particulate matter. Correlations with different metals have been reported, although the findings are often conflicting, and thus not readily generalizable across locations or airsheds. Approximately 1000 PM2.5 samples, collected from June 2016 until December 2018 in forty cities across Canada, were analyzed using three standardized acellular assays: ascorbate (AA), glutathione (GSH) and dithiothreitol (DTT). Linear and multilinear correlations analyses revealed that different metals were influencing OP and OB to different degrees across the airsheds. In particular, OB values for all three assays were associated with Cu and Fe, and in addition, OBAA with S and K and OBGSH with K. The highest OP and OB values were seen in the East Central airshed, while the lowest were in the Southern Atlantic and Northern airsheds. AA and DTT activity are associated with coal combustion and combustion emissions while GSH activity is associated with anthropogenic metals.

Keywords: Canada
OPERA
Oxidative Burden
Oxidative Potential
PM2.5
Advisor: Evans, Greg
Safety in Construction: Connecting Safety Climate, Safety Performance, and Leading Indicators

Due to the injury-prone nature of the general construction industry, identifying the sector as the better performer in safety would provide insights on aspects requiring further improvement, and determining the leading indicators of injury can help companies develop preventive measures towards increasing injury reports. The two objectives were achieved into two sub-studies. Based on self-administrated survey data, comparisons on workers’ demographic information, their safety perception, and safety performance were conducted between the nuclear sector and the general construction industry through Mann-Whitney test. The nuclear sectors was found to have better safety performance, and factors where the nuclear sector is the better performer were also identified. Besides, based on a 2019 incident dataset, time-dependent relationships between injuries and near miss events were developed using time series analysis. It was found that near miss and physical injuries are interacting with each other closely with lag-time of 1 or 2 weeks.

Keywords: Construction management
Leading indicators
Near misses
Safety
Time series analysis
Advisor: McCabe, Brenda Y
Resting-state fMRI Activity within the Semantic Network Associated with Changes in Verbal Fluency after Anterior Temporal Lobe Resection

The aim of this study was to examine the impact of disruption of the semantic network, including the ATL, on performance in fluency tasks considered to be differentially dependent on the integrity of this amodal hub. We studied 17 patients who underwent surgical resection of the left ATL to improve seizures. We collected pre-surgical resting-state fMRI data as well as pre- and post-surgery performance on verbal fluency tests. A correlation value representing the similarity between the network resting-state connectivity pattern of each patient and that of a healthy control template was calculated. We found a significant positive correlation between this matrix similarity score and pre- to post-surgical change in both unique and general semantic fluencies, indicating that a more ‘normative’ network is protective. The connections driving that effect were those outside the to-be-resected ATL. Overall, our findings indicate that network integrity is key in predicting post-operative changes in semantic processing.

Keywords: fMRI
Matrix Similarity
Semantic memory
Temporal Lobe Epilepsy
Advisor: McAndrews, Mary Pat MPM
Novel Porous Transport Layers with Through Pores for Polymer Electrolyte Membrane Electrolyzers

Development of cost-effective porous transport layers (PTLs) for polymer electrolyte membrane (PEM) electrolyzers is crucial for the implementation of clean energy systems. In this thesis, novel PTLs with through pores have been investigated. Limited mass transport in the in-plane direction was observed in through pore PTLs, using in operando synchrotron X-ray radiograph. Furthermore, the limited in-plane mass transport led to dehydration of the catalyst layer (CL). Therefore, the placement of through pores play a critical role in the performance of PEM electrolyzers. Next, through pore PTLs consisting of woven meshes were studied. The contact resistance between the woven mesh PTL and the CL dominated performance losses, and smaller pore sizes improved the contact resistance. Stacking meshes with different pore sizes resulted in inhomogeneous compression of the CL, significantly degrading the PEM electrolyzer performance. The results from this thesis contribute to the development of cost-effective PTLs for next generation PEM electrolyzers.

Keywords: Mass transport losses
PEM electrolyzer
Porous transport layer
Synchrtron X-ray radiography
Advisor: Bazylak, Aimy