VictorJuiz/thesis huggingface dataset:
Real-time Skin Analysis Filters

This thesis presents a framework for real-time skin analysis. Our system consists of two filters for skin redness analysis and pigmented skin lesions analysis. In skin redness analysis, we search for skin regions in video frames and assess size and degree of redness in skin regions. In order to analyze pigmented skin lesions, we localize potential moles of different sizes utilizing multiple difference of Gaussian filters and apply trained Support Vector Machine and K-Nearest Neighbours to eliminate non-mole candidates from the previous stage. After finding mole candidates, we present information about the symmetry, border irregularity and color variegation of detected moles. To test the real-time performance of our system, a prototype application on the iPhone 4S and iPhone 5S was implemented.

Advisor: Aarabi, Parham
The Relationship Between Markers of Oxidative Stress and Depressive Symptoms in Coronary Artery Disease Patients

Depression is highly prevalent and associated with worse prognoses in patients with coronary artery disease (CAD), but underlying mechanisms remain unclear. Oxidative stress, and ensuing lipid peroxidation, may be implicated in both depressive and cardiovascular pathologies but has yet to be assessed in CAD. This study investigated the relationship between depressive symptoms and the lipid peroxidation markers 8-isoprostane (8-ISO), 4-hydroxy-2-nonenal (4-HNE), and lipid hydroperoxides (LPH) in 204 CAD patients. Serum lipid peroxidation markers were analyzed using spectrophotometric assays. Higher concentrations of 8-ISO, a late-stage marker of oxidative damage to lipids, predicted greater depressive symptom severity measured by the Center for Epidemiological Studies Depression Scale (Î˛=0.265, p

Keywords: biomarkers
coronary artery disease
depression
depressive symptoms
lipid peroxidation
oxidative stress
Advisor: Lanctot, Krista L
Re-Imagining the Public Value of the Humanities: An Ecological Perspective

Much of the recent discussion regarding the humanities has been in response to the destabilizing effects economic pressures have on perceptions of their value. I explore the public value of the humanities in light of these contemporary challenges. Chapter One situates this approach in a public conception of the university. In Chapter Two I discuss how the aims of higher education are being reshaped, largely in response to an instrumentalist context that is framed by economic outcomes. In Chapter Three I review three defences of the humanitiesâ subjective, liberal, and democraticâ and how they address the question of public value, respectively. I conclude by arguing for an ecological approach to the humanities, grounded in the broader value of the university to the public it serves, and argue that working inwards from a situated position may provide a more robust account of public value than many of the previous attempts.

Keywords: Ecology
Higher Education
Humanities
Value
Advisor: Bialystok, Lauren
Slit2-Robo Signaling Pathway as a Potential Target for Attenuating Pathological Diabetic Glomerular Angiogenesis

A hallmark of diabetes, the leading cause of kidney failure, is glomerular endothelial cell injury, where pathological angiogenesis contributes to hyperfiltration, a common feature linked to progression of renal injury. No clinically available therapies safely target this process. Slit2 has emerged as a regulator of endothelial function, eliciting either pro- or anti-angiogenic effects through its Robo1 and Robo4 receptors respectively. Glomerular endothelial cells grown in high glucose medium expressed lower levels of Robo4, but not Robo1, and had greater response to vascular endothelial growth factor, while Robo1 knockdown inhibited VEGF-induced tube formation and migration. While healthy glomerular endothelial cell expressed high levels of Robo4 and low levels of Robo1 in vivo, Robo4 levels fell while Robo1 did not significantly change. Four weeks post-streptozotocin-induced diabetes, Robo4 knockout mice kidneys demonstrated increased glomerular endothelial cell density. Our observations suggest that diabetic glomerular angiogenesis is promoted by a reduction in anti-angiogenic Slit2-Robo4 activity.

Keywords: Diabetes
Endothelial Cellular Biology
Murine Models of Diabetes
Renal Injury
Slit-Robo Signaling
VEGF Signaling
Advisor: Yuen, Darren A
Multidentate Iodoalkyne Receptors as Halogen Bond Donors

Halogen bonding is an expanding area in supramolecular chemistry. Previously, the Taylor group has reported a series of multidentate iodoperfluoroarene based receptors that displayed strong halogen bonding with anions in solution. Recent computational studies have shown that iodoalkyne based halogen donor exhibit comparable positive character of Ď -hole to perfluoroiodoarene donors. As iodoalkynes remain unexplored as halogen bond donors, numerous multidendate iodoalkyne based receptors were developed. Preliminary investigations involved obtaining thermodynamic data, in order to understand their binding behavior with anions in solution. These studies are imperative to further understand processes of self-assembly based on halogen bonding, for applications in wide range of areas, including molecular recognition, biomedical applications and crystal engineering. Chapter 1 describes the synthesis and development of various multidentate iodoalkyne based halogen bond donors, with discussions of their binding properties in solution-phase. Chapter 2 discusses crystal design employing tetrakis(4-(iodoethynyl)phenyl)methane, for understanding structure design by halogen bonding and for future applications in materials engineering.

Keywords: Halogen bonding
Iodoalkyne
Advisor: Taylor, Mark S
Development and Evaluation of Dry Electroencephalography (EEG) Systems Towards Applications in Remote Patient Monitoring

The primary objectives of this project were to evaluate the signal quality of dry electroencephalography (EEG) electrodes, and to develop an EEG headset that optimized usability and electrode performance. Two iterations of adjustable headsets were designed and tested using a side-by-side comparison method between wet (Ag/AgCl) and dry electrodes. The overall performance of the dry electrodes varied between participants and electrode sites, but high signal quality was demonstrated under ideal conditions. The major design outcome from the first round of testing involved adding the ability to independently adjust the angle of each electrode on the headset. Design recommendations from the second round of testing included increasing the range of the applied force on each electrode. A series of additional recommendations and guidelines were created for future headset development in order to promote consistently high signal quality from dry electrodes.

Keywords: Dry Electrodes
Electroencephalography
Advisor: Cafazzo, Joseph
Determining the Effects of an Acute Bout of Exercise on Executive Function among Individuals with Schizophrenia

Objective: To investigate whether one bout of exercise can improve executive function among individuals with schizophrenia. Methods: In this within-subject, counterbalanced experiment, participants with schizophrenia (n=36) either completed a 20-minute bout of moderate intensity exercise on a cycle ergometer or, passively sat for the same time period. Participants completed the Wisconsin Card Sorting Test (WCST) before and after the condition to measure changes in executive function. All participants returned one week later to complete the arm of the study that they did not complete. Results: Due to a significant practice effect, only the WCST scores from the first condition completed by participants were analyzed. There was a significant time by session interaction effect for non-perseverative errors. Post-hoc analyses revealed a significant reduction in non-perseverative errors among the exercise group. Conclusions: An acute bout of exercise may be able to help patients with schizophrenia with select working memory tasks.

Keywords: Acute
Cognition
Executive Function
Exercise
Schizophrenia
Wisconsin Card Sorting Test
Advisor: Faulkner, Guy
Evolution of Arabidopsis thaliana Flowering Time in Response to Water Availability Post-introduction

Flowering is one of the most influential events in the life history of a plant â its beginning and duration are two main determinants of reproductive investment and lifetime fitness. Understanding the selective pressures influencing time to flowering and being able to reliably predict how it will evolve in novel environments is an unsolved challenge for plant evolutionary geneticists. Using naturalized lines of Arabidopsis thaliana from across the eastern North American range, I examined the impact of simulated winter precipitation levels on flowering time and the fitness consequences of early versus late flowering. Flowering time was significantly genetically correlated across two environments â in common gardens outdoors and in environmental chambers set to mimic mid-range photoperiod and temperature conditions â suggesting that flowering time rank between lines remains consistent. The interaction between flowering time and water treatment for fitness indicates that water availability contributes to differential selection on flowering time in introduced populations

Keywords: Flowering time
Introduced species
Life history
Selection gradients
Selective agents
Water relations
Advisor: Stinchcombe, John R
Modular Synthesis of Chiral beta-Aminophosphine P,N-Ligands and Their Applications in Asymmetric Catalysis

A series of chiral beta-aminophosphine ligands bearing different carbon backbones and electronically differentiated diarylphosphino groups were prepared using a modular approach. These P,N-ligands were found to induce a modest level of enantioselectivities in the Pd-catalyzed asymmetric decarboxylative allylation reaction. Thiourea-phosphine bifunctional catalysts derived from the chiral beta-aminophosphine building blocks were prepared and applied to the asymmetric Morita-Baylis-Hillman (MBH) reaction of methyl acrylate and 4-nitrobenzaldehyde. The electronically unmodified diarylphosphino-thiourea was found to be optimal for achieving high activity and enantioselectivity in this particular MBH reaction. We also reported the synthesis of a P-chiral C2-symmetric bisphosphine ligand. However, the utility of this Trost-type ligand remains to be explored in the future.

Keywords: asymmetric catalysis
organocatalysis
P
N ligands
transition metal catalysis
Advisor: Taylor, Mark S.
Exploring Evolution: I. Directing Evolution of Proteins with Phage, II. Examining the Effects of Toxic Quantum Dots on the Yeast Genome

This thesis comprises two separate directed evolution studies. Part I describes the optimization of a reporter construct for the protein evolution tool, PACE. Myc is a transcriptional activator and oncoprotein associated with more than half of all human cancers. Our aim is to use PACE to develop DNA-binding proteins that compete with Myc binding to E-box DNA and inhibit Myc-mediated activation. We employed a bacterial one-hybrid system to test E-box reporter constructs and identified seven constructs that could serve as potential PACE precursors. Part II explores the effects of toxic nanoparticles on the yeast genome. We showed that Saccharomyces cerevisiae populations evolve to survive chronic exposure to CdSe quantum dots (QDs). Genetic analysis of evolved cells confirmed one mutation in bul1 that was implicated in increased tolerance for QDs. This is the first demonstration that chronic QD exposure can lead to irreversible genetic changes and adaptation.

Advisor: Shin, Jumi A.
The Within- and Cross-language Role of Syntactic Awareness in Reading Comprehension Among French Immersion Students

Two related studies examining the within- and cross-language transfer of syntactic awareness (SA) to concurrent measures of reading comprehension (RC) between English and French are reported. Participants were first- and third-grade Canadian French immersion students. Results indicated that Grade 1 English SA significantly predicted French RC after cognitive and within-language controls, while Grade 1 French SA did not. In Grade 3, by contrast, English SA was unrelated to either English or French RC, while French SA was predictive of both. In all cases, SA was indirectly related to RC both within and across languages. Adding to the limited research on metalinguistic transfer, these results support hypotheses for the transferability of SA and provide preliminary evidence for its crossover role in reading across languages. The findings call for increased theoretical and academic attention to, and pose educational implications for, the involvement of SA in models of within- and cross-language RC.

Keywords: Curriculum Development
Foreign Language Education
French immersion
Metalinguistic Awareness
Reading Comprehension
Syntactic Awareness
Advisor: Chen, Xi
Phosphorylation-dependent structural changes in the N-terminal extension of SUR2A NBD1

ATP-sensitive potassium (KATP) channels are involved in many biological processes and play an important role in sustaining healthy functioning organs. KATP channels are composed of four copies of a pore-forming Kir6.x protein that is surrounded by four copies of regulatory sulfonylurea receptor (SUR) proteins. SUR proteins are members of the ATP-binding cassette (ABC) superfamily. Nucleotide binding and hydrolysis at the SUR proteins results in channel opening, which is potentiated by SUR protein phosphorylation. The studies conducted during this thesis aimed to understand how phosphorylation of the N-terminal extension (N-tail) of the first nucleotide binding domain (NBD1) of SUR2A alters its structure and influences the N-tailâ s interaction with the core NBD1. This biophysical study utilizes nuclear magnetic resonance (NMR) and other biophysical techniques to understand these structural and dynamic changes in N-tail with phosphorylation which will allow us to further understand ATP-binding at NBD1 and control of KATP channel conductance.

Advisor: Kanelis, Voula
The Role of the Ventral Tegmental Area and Nucleus Accumbens in Nicotine-induced Enhancement of Responding for Conditioned Reinforcement

Nicotine enhances the reinforcing properties of reward-paired cues but little is known about neural mechanisms mediating this enhancement. We hypothesized that nicotine enhances responding for conditioned reinforcement through nAChRs in the VTA but not the NAcc. Thirsty male Long-Evans rats underwent Pavlovian conditioning sessions where a 5-sec CS was paired with water. Next, responding for conditioned reinforcement was tested. The effects of α4β2 nAChR antagonist DHβE infusion into the VTA or NAcc on nicotine-enhanced responding for a CRf were assessed. The effects of nicotine infusion into the VTA or NAcc on responding for a CRf were also examined. Results indicated that nicotine enhanced responding for a CRf and this effect was attenuated following DHβE infusion into the VTA or NAcc. Nicotine infused into the VTA, but not the NAcc, enhanced responding for a CRf. These data suggest that nAChRs in the VTA primarily mediate the reinforcement enhancing actions of nicotine.

Keywords: Conditioned reinforcement
Environmental cues
Nucleus accumbens
Rats
Ventral tegmental area
α4β2 nicotinic receptors
Advisor: Fletcher, Paul
We Are What We Eat: Cultivating Well-being and Happiness through Sustainable Food Systems

If the systems that we build, including food systems, are meant to support and reflect our ideologies and theories, then contemporary interest in well-being and happiness cannot be ignored. If we want well-being to flourish and to be happy then the foods we eat must also be produced, processed and consumed in this way. This thesis critically examines if and how well-being and happiness are being facilitated through food systems driven by neoliberalism, food security and food sovereignty. This thesis uses systems thinking to identify the elements and relationships within each food system and applies a critical theory lens to delineate the power within those relationships. Each system is then evaluated using Dr. Jennifer Sumner’s theoretical model of sustainability to understand if and how they promote the three building blocks of sustainability – counter-hegemony, dialogue and life values – and thus well-being and happiness.

Keywords: Food security
Food sovereignty
Food systems
Happiness
Sustainability
Well-being
Advisor: Sumner, Jennifer
Treatment with the α-Synuclein Oligomer Prone Mutants E35K and E57K Leads to Significant Intracellular Aggregation and Inclusion Formation

Alpha-synuclein (α–syn) is a key neuronal protein that undergoes pathogenic conformational changes and accumulates in Parkinson’s disease. Currently α–syn oligomers have gained a lot of attention as being a particularly toxic version of the protein. This work aims to characterize the aggregation seeding properties of these oligomers. Cells were treated with either oligomeric (E35K or E57K) or fibrillar versions of α–syn. Intracellular changes were assessed using cellular fractionation, fluorescent imaging, and in vitro protein fragment complementation assays. The results from this study highlight the ability of the E35K and E57K treatments to induce changes in α–syn solubility to a greater extent than fibrillar forms of the protein. Exposure to either E35K or E57K also caused the formation of α–syn inclusions that appeared to be transmissible to naïve neighbouring cells. This study highlights interesting properties potentially attributable to α–syn oligomers that merit further investigation.

Keywords: Aggregate
Alpha-Synuclein
Parkinson's Disease
Prion-like Propagation
Advisor: Tandon, Anurag
Microfluidic Analysis of Pore-scale Petroleum Recovery in Steam Assisted Gravity Drainage

Steam Assisted Gravity Drainage (SAGD) is an in-situ method of extracting bitumen and involves the injection of steam into the oil sands reservoir through a horizontal well pair. The formation of a steam chamber and heat transfer to the bitumen allows gravity drainage and production. There is presently a lack of understanding concerning the specific mechanisms of bitumen mobilization and drainage at the pore-scale within the SAGD process. This thesis focuses on developing and utilizing microfluidic platforms to allow the experimental observation and characterization of the interface morphology at the edge of the steam chamber.

Keywords: Microfluidics
Petroleum
Pore-Scale
SAGD
Advisor: Sinton, David
Pharmacogenetic Analysis of Glutamate System Gene Variants and Clinical Response to Clozapine

Altered glutamatergic neurotransmission is implicated in schizophrenia etiology and response to the atypical antipsychotic clozapine. Response to clozapine is highly variable and partly depends on genetic factors as indicated by twin studies. The association of 17 glutamate system gene variants and clinical response to clozapine was investigated in a sample of European schizophrenia/schizoaffective patients deemed resistant/intolerant to previous pharmacotherapy. Categorical and continuous response measures were assessed following six months of clozapine treatment using change in Brief Psychiatric Rating Scale Scores, and were analyzed using Pearsonâ s chi-squared test or analysis of covariance, respectively. No significant associations were observed for all analyses after correction for multiple testing. Prior to correction, several nominally significant associations were observed, the most notable being between the SLC6A9 rs16831558 variant and change in positive symptoms (puncorrected=0.008, pcorrected=0.08). This finding warrants further investigation in larger well-characterized samples to clarify the role of SLC6A9 in clinical response to clozapine.

Keywords: Clozapine
Glutamate
Pharmacogenetics
Schizophrenia
Treatment Response
Advisor: Kennedy, James L
Quantitative Trait Loci and Candidate Genes for Neutrophil Recruitment in Sterile Inflammation Mapped in AXB-BXA Recombinant Inbred Mice

Neutrophil recruitment (NR) to sterile inflammation (SI) sites play a key role in tissue damage and healing potential of non-infectious inflammatory diseases. NR was quantified in 16 AXB-BXA recombinant inbred strains and their progenitors, A/J(A) and C57BL/6J(B). A continuous distribution of NR was found, with parent B showing higher NR than parent A (3.0-fold difference, p=0.05). Within the progeny strains, a 5.5-fold difference in NR was observed between the lowest, BXA1, and the highest responders AXB19 (p

Keywords: innate immunity
Neutrophil recruitment
QTL
sterile inflammation
Advisor: Glogauer, Michael
RIBI (Radiotherapy Induced Bone Injury) as a Late Side Effect in Patients Treated with Stereotactic Lung Radiotherapy

Abstract The standard treatment for patients with early stage non-small cell lung cancer is a surgical approach; however inoperable patients may be treated with stereotactic body radiotherapy (SBRT) with an excellent local control rate of 80 to 90%. Although the majority of patients tolerate this treatment reasonably well, some may experience side effects such as chest wall pain and rib fracture. In this study several potential dosimetric and clinical factors related with rib fracture were evaluated and a nomogram estimating the risk of rib fracture based on the most relevant risk factors was created. Our study supported the relationship between dosimetric-clinical factors and rib fractures in patients with lung cancer treated with stereotactic radiotherapy. Based on our findings and supported published data, we have modified our radiotherapy dose in high risk patients for rib fracture.

Keywords: late toxicity
lung cancer
radiotherapy
rib fracture
side effect
stereotactic radiotherapy
Advisor: Bezjak, Andrea
Response of Annealed Glass Windows to Blast Loads

This thesis presents the comparison of experimentally collected data on the response of monolithic annealed glass windows to blast loads with the output of several predictive software packages. Experimental data was gathered from two full-scale field arena blast testing series, during which 34 glass panes were subjected to explosive blast waves of varying intensity. The setups tested in the field were modelled using three blast analysis programs. A series of small- and large-scale laboratory tests was carried out to investigate the material properties of the glass and the load-displacement behaviour of the field-tested window systems, to refine the model predictions. By comparing software-predicted window behaviour with the observed response, the accuracy and applicability of the various modelling techniques and glass failure criteria employed by the software packages were evaluated.

Keywords: Annealed Glass
Blast testing
Finite Element Analysis
Glazing
Single Degree of Freedom Analysis
Advisor: Packer, Jeffrey
Seica, Michael
The Effect of Orifice Flow Treatment on Biosludge Dewaterability

This research assessed the potential for orifice flow treatment to improve biosludge dewaterability by disintegrating the flocs, thereby releasing the interstitial water trapped within them. Pulp and paper waste activated sludge, municipal waste activated sludge, and municipal anaerobically digested sludge samples were orifice flow treated at strain rates up to 29,280 ± 1060 s-1, 34,540 s-1, and 34,090 s-1, respectively, and their particle size distribution, water distribution, and dewaterability were assessed. Although orifice flow treatment disintegrated the biosludge flocs, it did not significantly affect the interstitial water content. Overall, orifice flow treatment worsened filterability. Orifice flow treatment did, however, increase the centrifuge cake solids content of pulp and paper and municipal waste activated sludge by 10 and 15 % respectively, showing the potential to improve biosludge centrifugability. Additionally, orifice flow treatment was more effective in disintegrating pulp and paper waste activated sludge flocs than sonication at the same energy output.

Keywords: biosludge
centrifugability
dewaterability
filterability
hydrodynamic
orifice-flow
Advisor: Farnood, Ramin
Allen, Grant