VictorJuiz/thesis huggingface dataset:
Borophene and Carbon Nitride Nanosheets for Energy Storage Applications

Borophene phases are a set of two-dimensional (2D) allotropes of boron that are excellent candidates as cathode materials in lithium sulphur (Li-S) batteries. Ab initio calculations were performed to determine stripped borophene and β12-borophene’s applicability as Li-S battery cathode materials. The calculations suggest β12-borophene would sufficiently inhibit the dissolution of lithium polysulphides into the electrolyte, preventing the “shuttle effect”. 2D carbon nitrides including tg-C3N4, hg-C3N4, C2N, and C3N were investigated as potential photocatalyst for solar water splitting, through first principles calculations. Band engineering via n-type, p-type, and isoelectronic doping was demonstrated for tuning the electronic structure, optimizing solar absorption and band alignment for photocatalysis. Among the dopants, Si and Ge dopants can narrow the band gap of carbon nitrides and increase their optical absorption in the visible spectrum. This work expands on the surface chemistry of borophene and comments on the complexities of substitutional doping with group IV elements.

Keywords: energy storage
hydrogen
lithium sulphur battery
photocatalysis
surface chemistry
two dimensional materials
Advisor: Singh, Chandra Veer
CFD Modeling and Measurements of Jet Properties and Mixing Chamber Flow in a High-pressure Abrasive Slurry Jet

Techniques to enhance the performance of a high-pressure abrasive slurry jet micro-machining process (HASJM) were investigated by altering the conditions within the nozzle. The slurry flow rate was controlled using inlet tubes of various diameters, and computational fluid dynamic (CFD) modeling was used to simulate the slurry entrainment process between the high-velocity water from the orifice and low-velocity slurry that occurred within the mixing chamber and mixing tube. The models correctly identified flooding conditions in which there was an increase in the net mass flow rate in the nozzle. Flooding was found to significantly reduce the jet velocity, thus diminishing its erosive efficacy which was assessed by machining blind holes and channels in aluminum 6061-T6. Differences in the centerline erosion rates of holes and channels for a given jet showed clear evidence of incubation and stagnation zone effects.

Keywords: Abrasive slurry jet
Aluminum 6061-T6
Computational fluid dynamics (CFD)
Erosion
Micro-machining
Slurry entrainment
Advisor: Spelt, Jan K.
Papini, Marcello
Biomarkers of Ceramide Accumulation and Decline in Verbal Memory in Coronary Artery Disease

Background: Biomarkers in cognitively vulnerable populations like those with coronary artery disease (CAD) may inform earlier intervention in vascular neurodegeneration. Circulating ceramide C18:0 (CerC18:0) is associated with cognitive changes in early neurodegeneration and CAD progression. Objective: To investigate whether plasma CerC18:0 accumulation is associated with longitudinal declines in verbal memory in CAD. Methods: In addition to CerC18:0, we assessed its relative abundance to its precursors as ratios: to monohexosylceramide C18:0 (CerC18:0/MHxCer18:0), to sphingomyelin C18:0 (CerC18:0/SM18:0), and to sphingosine-1-phosphate (CerC18:0/S1P). In 60 CAD participants, we evaluated associations between baseline CerC18:0 and its ratios to changes in verbal memory, adjusted for potential confounders. Results: Increased baseline CerC18:0 (b[SE]=-0.91[0.30], p=0.003), CerC18:0/MHxCerC18:0 [(b[SE]=-0.90[0.40], p=0.03)], CerC18:0/SM18:0 (b[SE]=-1.11[0.36], p=0.004) correlated with steeper declines in verbal memory. Conclusions: Aberrant CerC18:0 metabolism may be an early neurobiological change in vascular neurodegeneration. Future studies should measure enzymatic activity responsible for conversion of precursors into CerC18:0.

Advisor: Lanctôt, Krista L
Herrmann, Nathan
Engineered Protein Scaffolds as Tools for Studying Intracellular Proteins

Molecules that bind to targets with high specificity and affinity are used as therapeutic and diagnostic agents in medicine and research. Protein and non-protein ligands are used for introduction of mutations within the binding region to increase the binding affinity. Phage-display technology is used to screen multiple scaffolds against target proteins to select for high affinity binders. Scaffolds are displayed on phage particles and can be tested for binding to targets with standard binding assays. Various target proteins are encoded by essential genes to disrupt cellular proliferation and were identified as fitness genes in CRISPR screens. Altogether, utilizing the two technologies facilitates making and screening of binders to intracellular targets and accelerates the production of highly efficient synthetic binders. To develop and optimize the technique, the Sidhu lab generated 27 protein scaffold libraries that were tested against 25 target proteins and selected several variants for further analysis in mammalian cells.

Advisor: Moffat, Jason
The Performance of a Zirconium-based Root-Filling Material with Artifact-Reduction Properties in the Detection of Artificially Induced Root Fractures Using Cone Beam CT Imaging

Objectives: To describe a novel technique for characterizing beam hardening artifact (BHA) using cone-beam computed tomography (CBCT); and to evaluate the influence of the Zirconium-based (Zr) root filling material using CBCT in the detection of artificial root fractures (RF). Material and Methods: The palatal root canals of three phantom teeth were root-filled and subjected to CBCT imaging. The light and dark components of the BHA were quantified. 176 mandibular premolar teeth were divided between Zr and GP. RFs were induced in 44 teeth of each group. All samples were subjected to CBCT images. The images were evaluated by 6 examiners. Results: GP showed a significantly higher measurement of the ‘dark’ artifact (p

Keywords: Beam hardening artifact
Cone beam CT
Gutta percha
K absorption egde
Zirconium
Advisor: Lam, Ernest WN
Identifying Factors Which Influence Medication Adherence in a Cardiac Rehabilitation Population

Nonadherence to cardiovascular disease medications is a health-related behaviour which increases adverse patient outcomes and healthcare costs. Identification of factors which impact adherence levels in those undergoing cardiac rehabilitation may reduce cardiovascular mortality rates. We hypothesized that use of a greater number of medications and use of acetylsalicylic acid (ASA), beta-blockers and statins would result in lower medication adherence levels. A Poisson regression showed that those who were adherent were taking 1.15 (95% CI, 1.03-1.28, p=0.014) times more medications than those who were nonadherent. An analysis of covariance found the combined use of ASA, beta-blockers and statins was associated with higher adherence levels (F1, 242=5.76, p=0.017). Furthermore, lower cardiopulmonary fitness levels, increased depressive symptoms and forgetfulness were all associated with lower medication adherence levels. These findings suggest that factors other than polypharmacy and medication class – such as cognitive function, depression, or fitness – may negatively influence adherence rates in this population.

Keywords: Cardiac Rehabilitation
Cardiovascular Disease
Cardiovascular risk factors
Medication Adherence
Polypharmacy
Advisor: Lanctot, Krista L
Development of a real-time algorithm for the detection of physiological arousal in the presence of motion among children with autism

Anxiety is a clinical concern among some children with autism, for whom such an emotional onset may exacerbate core symptoms. Current treatment options are challenged as many of these children are unaware of their emotional state, and due to autism some children also have difficulties with language and communication which further complicates anxiety diagnoses. In this thesis, we proposed a novel automated anxiety detection algorithm capable of interpreting heart rate arousal in the presence of physical movements , and intuitively notifying the user to engage in anxiety management techniques. The novelty of our proposed algorithm is based on its ability to detect anxiety in presence of motion; this is a challenge as motion and anxiety influence the heart rate similarly. This algorithm was able to account for the changes in heart rate due to motion and detection anxiety with an accuracy, specificity and sensitivity of 92.7% in children with autism.

Keywords: anxiety detection
autism
kalman filter
multimodal kalman filter
presence of motion
Advisor: Kushki, Azadeh
The Role of Perineuronal Nets in Learning and Memory

The balance between stability and plasticity in the brain determines our ability to learn. A key molecular regulator of this balance includes perineuronal nets. Perineuronal nets are specialized extracellular matrix structures surrounding neurons, and have a presumed function in promoting stability within neural circuits. We investigated the effects of disrupting perineuronal nets, thereby enhancing plasticity, on learning and memory in mice. We found that perineuronal net disruption in the hippocampal CA1 region is associated with faster water maze reversal learning, and increased contextual fear generalization. Moreover, the population of active neurons is larger at retrieval of a contextual fear memory. These results demonstrate that perineuronal nets are important for learning and memory, and that shifts in perineuronal nets is associated with altered circuit level activity.

Keywords: generalization
hippocampus
memory
plasticity
Advisor: Frankland, Paul
COMBINATORIALLY CONSTRAINED PORTFOLIO OPTIMIZATION USING MESSAGE PASSING ALGORITHMS

Portfolio optimization aims to find the optimal investment strategy for a series of assets that results in a minimization of the portfolio's variance. Real life portfolio considerations like limiting the number of assets or limiting assets to be traded in lots add combinatorial constraints to the original problem that are computationally expensive for commercial solvers. The aim of this thesis is to explore the use of message passing approaches to solve the portfolio problem with these hard constraints. Message passing represents a class of algorithms used to solve inference problems in graphical models. They are known to recover good sub-optimal solutions and we test this for the posed problem by comparing with branch-and-bound exact methods. Computational results for the portfolio problem with varying cardinality, target return and portfolio size confirm that message passing is a viable method for finding sub-optimal solutions and can return tight bounds around the exact solution.

Keywords: Mixed Integer Programming
Portfolio Optimization
Probabilistic Graphical Model
Advisor: Kwon, Roy H
Characterizing contrast origins and noise contribution in spin-echo BOLD at 3 T

Spin-echo (SE) EPI is generally associated with lower BOLD sensitivity than its gradient-echo (GE) counterpart, limiting the use of SE-BOLD. However, SE-BOLD is less sensitive to physiological noise than GE-BOLD. Yet, unlike for GE, SE-BOLD signal origins and noise contributions haven’t been investigated empirically. In this work, we introduce a two-compartment SE-BOLD model that integrates a physiological-thermal noise model. We fit this model to SE-BOLD fMRI data acquired during hypercapnic manipulations at various echo times (TE) at 3 T in order to characterize SE-BOLD contrast and noise behaviour, and identify optimal contrast-to-noise (CNR) settings for SE-EPI. Our results quantitatively demonstrate that the physiological noise contribution in SE-BOLD signal is lower than that of GE. Importantly, we demonstrate that CNR for SE is maximized at TEs lower than the typically used tissue T2. These findings will lead to improved SE-BOLD sensitivity, making it a more attractive choice for fMRI studies.

Keywords: Echo-time optimization
Spin-echo BOLD signal
Spin-echo physiological noise contribution
Advisor: Chen, Jean
Prophylactic Bisphosphonate Therapy to Reduce Glucocorticoid-Induced Osteoporosis in a Mouse Model of Duchenne Muscular Dystrophy

Glucocorticoids (GCs) is a standard therapy to prolong muscle function in Duchenne Muscular Dystrophy (DMD) but induce osteoporosis. Bisphosphonates are used prophylactically in adults starting chronic GC treatment but are not in DMD patients until after they sustain fractures. C57BL/10ScSn-mdx mice, a common DMD animal model, was treated with prednisone (0.083 mg/day) from 5-10 weeks of age. Prophylactic pamidronate (8 mg/kg) was administered over 2 or 6 weeks starting at 4 weeks of age to assess the two dosing regimens in ameliorating GCinduced osteoporosis. Pamidronate did not attenuate GC’s improvement on muscle function. GC caused cortical bone loss and decreased cortical bone strength. Two- and 6-week pamidronate treatment improved bone architecture but only 2-week pamidronate improved cortical bone strength. The improvement of bone strength seen only with 2-week pamidronate highlights the importance of when and how much bisphosphonate is administered prior to glucocorticoid exposure, rather than the total cumulative dose.

Keywords: Bisphosphonate
Duchenne Muscular Dystrophy
Glucocorticoid
mdx
mouse model
Osteoporosis
Advisor: Mitchell, Jane
Grynpas, Marc
Compressed Sensing for Diffusion MRI of the Mouse Brain: A Trade-off of Spatial and Directional Information

Diffusion magnetic resonance imaging (MRI) uses loss of signal coherence caused by movement of water molecules to determine how water diffuses in tissue. These scans are known to take a significant amount of time owing to the repeated acquisition of images, each measuring diffusion for a particular direction and weighting. Emerging methods based on collection of increasingly large numbers of diffusion directions and/or weightings promise to provide a more detailed characterization of brain microstructure than previously possible. However, because the time required for these methods can render them impractical, I present a method of acquiring and reconstructing diffusion MRI data based on compressed sensing (CS) that enables flexible trade-off between spatial sampling and diffusion direction/weighting sampling. This method enables the collection of more diffusion data in a given scan time at the cost of extended reconstruction time.

Keywords: compressed sensing
conjugate gradient
diffusion mri
DTI
HARDI
Advisor: Nieman, Brian J
The Antioxidant Status of Breast Milk in Women with and Without Gestational Diabetes Mellitus

Gestational diabetes mellitus (GDM) is associated with reduced total antioxidant capacity (TAC) in blood, but association of GDM with breast milk (BM) TAC and antioxidants is unknown. Therefore, BM TAC, α-tocopherol, ascorbic acid, and β-carotene concentrations were compared in GDM (n=8) and normoglycemic (NG) women (n=10) in a cross-sectional study. This study found no differences between BM TAC and antioxidant concentrations in women with GDM versus NG. BM α-tocopherol correlated significantly with TAC (p = 0.011) in NG and ascorbic acid correlated significantly with TAC (p = 0.040) in GDM. BM β-carotene in the combined group (p = 0.005) and in NG (p = 0.003) correlated significantly with β-carotene consumption. The results suggest that GDM has no association with BM TAC and antioxidant concentrations. The correlations between BM TAC and antioxidants differed in GDM versus NG for α-tocopherol and ascorbic acid suggesting that unmeasured antioxidants differ in GDM versus NG.

Keywords: Antioxidants
Breast milk (BM)
Gestational diabetes mellitus (GDM)
Normoglycemic (NG)
Pregnancy
Total antioxidant capacity (TAC)
Advisor: Wolever, Thomas M.S.
Validation of Sirtuin 3 as a Neuroprotective and Neurorestorative Target in the Mutant Human A53T α-synuclein Rat Model of Parkinson’s Disease

Mitochondrial dysfunction plays a major role in the progressive and pathological development of Parkinson’s disease (PD). Mitochondrial protein deacetylase sirtuin 3 (SIRT3) assists in controlling bioenergetic and antioxidation processes by regulating mitochondrial enzyme acetylation levels. Based on this, overexpression of SIRT3 in the substantia nigra pars compacta (SNc) was assessed for its disease-modifying and cytoprotective effects in a well-accepted, adeno-associated virus (AAV) model of PD. SIRT3-myc AAV was infused into the SNc before or after A53T AAV induction of parkinsonism and analyzed at three and six-week time points. Results suggested that at six weeks, SIRT3 overexpression significantly reduced parkinsonian deficits, localized to the mitochondria, and displayed deacetylase function. Overall, the beneficial effects of SIRT3 demonstrate its disease-modifying implications for PD.

Keywords: Adeno-associated virus
Mitochondria
Neuroprotection
Parkinson's Disease
Sirtuin 3
Substantia Nigra
Advisor: Nash, Joanne
The Use of High-Dose Riboflavin to Limit Topotecan Efflux in Milk: A Proof-of-Principle Study in Mice and Cells

Various mechanisms mediate transport of compounds into milk throughout lactation. Breast cancer resistance protein (BCRP) is one of the apically expressed transport proteins in mammary epithelial cells and it extrudes vitamins, like riboflavin, and many xenobiotics, including topotecan, into breast milk. The purpose of this project was to determine whether using pharmacological doses of riboflavin can limit xenobiotic accumulation into milk. By elucidating the mechanisms of milk production, mothers could continue drug therapy while reducing risk to suckling infants. Mouse models with adequate riboflavin levels showed that topotecan-riboflavin interactions at Bcrp were not associated with significant changes in topotecan accumulation in milk. Two cell models were optimized and ultimately one of the two cell lines exhibited significantly higher topotecan retention when treated with the known, chemical Bcrp inhibitor Ko143. This proof-of-principle study indicates that riboflavin administration does not significantly interrupt extrusion of the potent Bcrp substrate topotecan into breast milk.

Keywords: Breast cancer resistance protein
Drug transfer
Lactation
Riboflavin
Riboflavin transporter
Topotecan
Advisor: Ito, Shinya
Long-Term Perceived Engagement and Research Priorities Among Chronic Kidney Disease Stakeholders: A Qualitative Study

Despite increasing engagement of patients and other stakeholders in the research process, little is known about its impact, particularly over the long term. In this qualitative descriptive study, we sought to explore how stakeholders who participated in a chronic kidney disease (CKD) research prioritization exercise two years earlier viewed their engagement experience and the research priorities. Through thematic analysis of interviews with 23 participants across stakeholder groups (patients, caregivers, healthcare providers and policymakers) and levels of engagement (steering committee, workshop and wiki), we identified four themes related to perceived engagement and three themes related to views on the CKD research priorities and prioritization process. Our findings highlight important considerations to support meaningful engagement in research prioritization, including roles and expertise, representation, and communication, and characterize ways in which individual priorities can change over time. Findings may contribute toward optimizing the design and conduct of future research engaging patients as stakeholders.

Keywords: Chronic kidney disease
Patient engagement
Patient-oriented research
Qualitative research
Advisor: Straus, Sharon
Has De-listing Routine Eye Examinations Increased the Use of Primary Care Providers for Ocular Diagnoses?

Purpose: In 2004, Ontario de-listed routine eye examinations for individuals aged 20-64. Post-delisting, affected individuals pay out-of-pocket or have the costs covered by private insurance for eye care. To avoid payments, patients with eye problems may visit a government-insured primary care provider (PCP) for help and/or for a referral to see a government-insured optometrist/ophthalmologist. We investigated if PCP utilization for eye diagnoses increased among affected Ontarians post- versus pre-delisting. Methods: PCP utilization for eye diagnoses from 2000-2014 was assessed using administrative data and interrupted time series analysis. Eye diagnoses were identified using ICD-9 diagnostic codes. Results: Post-delisting, PCP utilization for eye diagnoses significantly increased among affected Ontarians (20-39 group: 30%, p

Keywords: Health Policy
Primary Care
Routine Eye Examinations
Advisor: Jin, Ya-Ping
Trope, Graham E
MiRNA-106a is a Novel Regulator of Radiation Resistance through Targeting LITAF and ATM in Prostate Cancer

Prostate cancer (PCa) recurrence is a major clinical problem after radiotherapy, particularly in high-risk disease. MicroRNAs are small non-coding RNAs that regulate gene expression and are involved in many aspects of cancer. We hypothesize that miR-106a confers radioresistance in PCa. MiR-106a was significantly overexpressed in prostate tumours relative to normal prostate samples, and in high-grade tumours compared to low- and intermediate-grade specimens. MiR-106a overexpression increased survival and proliferation after radiation compared to control cells, by reducing senescence. Tumour xenograft experiments confirmed that miR-106a increases tumour growth after radiation compared to control tumours. LITAF was identified as a target of miR-106a. LITAF knockdown recapitulated miR-106a-induced radioresistance. MiR-106a overexpression and LITAF knockdown led to ATM promoter activation, with increased transcript and protein levels. ATM inhibition using KU-55933 resensitized miR-106a cells to radiation by inducing senescence. This work identifies miR-106a and LITAF as novel modulators of PCa radioresistance, through upregulation of ATM.

Keywords: ATM
LITAF
miR-106a
Prostate cancer
Radiation resistance
Advisor: Liu, Stanley K
Species Diversity and Preferred Attributes of Trees: A Case Study of the Private Urban Forest in the Greater Toronto Area

Healthy urban forests should have a diverse, native assemblage of species to support ecological integrity and reduce vulnerability to stressors. Since most urban trees are located on private property, landowner preferences for urban trees have a significant impact on the urban forest. Recent studies indicate that landowners select tree species based on aesthetic or functional attributes, without considering species diversity or ecological integrity. To examine the impact of landowner decisions, this study explores the relationship between property-level diversity metrics and aesthetic and functional attributes. Field inventories of trees on residential properties were conducted in Oakville and Markham, Ontario, and the results were analyzed along with residents’ knowledge, attitudes, and corresponding household characteristics gathered through a written survey. Few significant relationships were found in the statistical analysis, indicating that the residents’ decision-making process is complicated and requires further study.

Keywords: Ecological integrity
Residential landscapes
Socio-ecological relationships
Species diversity
Tree attributes
Urban forest
Advisor: Conway, Tenley