VictorJuiz/thesis huggingface dataset:
Towards a Chromatic Pupillometry Protocol for Assessing Melanopsin-driven Post-illumination Pupil Response in Basic Science and Clinical Investigations

The pupillary light reflex (PLR) is mediated by intrinsically photosensitive retinal ganglions cells (ipRGCs), a sub-group of retinal ganglion cells that contain photopigment melanopsin. Melanopsin activation drives a sustained pupil constriction after the offset of light stimulus, this so-called post-illumination pupil response (PIPR) is an in vivo index of melanopsin-driven ipRGC photoactivity. PIPR can be assessed by chromatic pupillometry, but consensus on a standardized PIPR testing protocol has not been reached yet. The purpose of this thesis is to develop an optimized PIPR testing methodology, and to use it to investigate clinical and basic science questions related to melanopsin and ipRGCs. Based on previous pilot work on full-field chromatic pupillometry, a new and repeatable method was developed to measure PIPR induced by hemifield, central-field and full-field light stimulation. This chromatic pupillometry system was then used to investigate a series of basic science and clinical questions related to melanopsin and ipRGCs.

Keywords: chromatic pupillometry
melanopsin
post-illumination pupil response
pupil light reflex
Advisor: Wong, Agnes M.F
Glotz, Herbert
Application of Nanofiltration for the Recovery of Phenolic Compounds from the By-product of Yellow Mustard Protein Isolation

Nanofiltration (MWCO 150-300 Da) was evaluated for the recovery of phenolic compounds from the wastewater of the production of yellow mustard protein isolates. High rejections were observed; however, under alkaline pH lower average rejections were shown (0.70) than acidic conditions (0.87). Fluxes of 51.3 L/hm2 and 28.8 L/hm2 were registered under alkaline and acidic conditions, respectively. At low pH, 77% of the phenolic compounds fed to the process were recovered in the retentate. Diafiltration was beneficial only when processing at low pH. The permeate from the nanofiltration process presented a total phenolic content of less than 100 ppm, which suggests the possibility of recycling these effluents to the production of yellow mustard protein isolates. p-Hydroxybenzoic acid was the major phenolic compound found in the waste effluent, and in the products of nanofiltration processing. Sinapic acid constituted a secondary fraction, and derivatives of quercetin and kaempferol were detected.

Keywords: Mustard
Nanofiltration
Phenolic compounds
Advisor: Diosady, Levente L.
X-ray and Electrochemical Impedance Spectroscopy Diagnostic Investigations of Liquid Water in Polymer Electrolyte Membrane Fuel Cell Gas Diffusion Layers

In this thesis, electrochemical impedance spectroscopy (EIS) and synchrotron x-ray radiography were utilized to characterize the impact of liquid water distributions in polymer electrolyte membrane fuel cell (PEMFC) gas diffusion layers (GDLs) on fuel cell performance. These diagnostic techniques were used to quantify the effects of liquid water visualized on equivalent resistances measured through EIS. The effects of varying the thickness of the microporous layer (MPL) of GDLs were studied using these diagnostic techniques. In a first study on the feasibility of this methodology, two fuel cell cases with a 100 µm-thick and a 150 µm-thick MPL were compared under constant current density operation. In a second study with 10, 30, 50, and 100 µm-thick MPLs, the liquid water in the cathode substrate was demonstrated to affect mass transport resistance, while the liquid water content in the anode (from back diffusion) affected membrane hydration, evidenced through ohmic resistance measurements.

Keywords: electrochemical impedance spectroscopy
liquid water visualization
mass transport resistance
microporous layer
Polymer electrolyte membrane fuel cell
synchrotron radiography
Advisor: Bazylak, Aimy
A Phenomenological Study of Loving Kindness Practice in Education Settings

This study uses Phenomenological research methods to explore the ways in which four teachers recited Loving Kindness Meditation for a three week period, particularly focusing on their students during the course of practice. Through personal reflection, journaling and interviews, the teachers describe how Loving Kindness Meditation affected their emotional life as teachers, their experiences of students and classroom dynamics, and the challenges experienced when reciting Loving Kindness Meditation to students. The study reveals a tendency for teachers to adopt a more yielding, less controlling orientation toward student encounters as their practice of Loving Kindness Meditation progressed. The study also hints at problematic limits to over-reliance on meditative imagery, redefining Eros in teacher-student dynamics as a surrender of idealistic expectations of student reciprocation. Future research could more deeply unpack the psychodynamic impacts of Loving Kindness on caregiver identities.

Keywords: Eros
Imagery
Loving Kindness
Meditation
Phenomenology
Teacher Emotional Life
Advisor: Miller, John P
Community composition and Biogeography of northern Canadian Ephemeroptera, Plecoptera and Trichoptera

Climate change has a disproportionately effect on northern ecosystems. To measure this impact we need to understand the structure of northern communities and the influence of current and historical climate events. Insect of the orders Ephemeroptera, Plecoptera and Trichoptera (EPTs) are excellent subjects for study because they are widespread and good bioindicators. The objectives of this study are: (1) Determine patterns of distribution and community composition of northern EPTs. (2) Understand the role of historical events (i.e., Pleistocene glaciations). We found that northern EPT communities are influenced by temperature and precipitation. Also, community composition and population structure of EPT exhibit a similar geographical pattern, with differences on either side of Hudson Bay, suggesting the influence of glaciations in shaping communities of EPTs in northern Canada. The COI barcode approach provided a reliable means for identifying specimens to produce the first wide-scale study of community structure and biogeography of northern EPTs.

Keywords: Aquatic insects
Arctic
Barcode COI
Biogeography
Community composition
Advisor: Currie, Douglas C
Characterization of Hot Surface Ignition in a Direct Injected Natural Gas Combustion Apparatus

The process of hot surface ignition of direct injected natural gas using a shielded glow plug was studied in an optically accessible combustion apparatus by varying combustion chamber design and operational parameters. Parameters studied were glow plug temperature, relative angle of the fuel injector and the glow plug shield, and the fuel injector nozzle orifice size, shape, and angular spacing. Results were analyzed using ignition delay time, fuel utilization, rate of heat release, and acquired high speed combustion images. Glow plug temperature had a dominant effect on ignition delay in comparison to all other parameters. Fuel injector nozzle design, along with the geometric interaction between the fuel injector and the glow plug shield, had a strong effect on the air fuel mixture available for ignition in the vicinity of the glow plug. Results will be used to inform the design and operation of a hot surface assisted natural gas engine.

Keywords: Diesel
Direct Injected
Engine
Glow Plug
Hot Surface Ignition
Natural Gas
Advisor: Wallace, James S
Socio-demographic and Health Factors Associated with Vulnerability to Food Insecurity in Social Assistance Recipients

While recipients of social assistance have been consistently identified as highly vulnerable to food insecurity, there is still variation in food security status among this population. Our objective was to examine how provincial social assistance policies, recipients' socio-demographic characteristics, and their chronic disease status relate to their food security status. We used logistic regression models to determine these relationships in a sample of single social assistance adults in the 2011-2012 Canadian Community Health Survey.The odds of food insecurity were higher in Nova Scotia and Saskatchewan compared to Ontario, controlling for socio-demographic factors. Homeowners and respondents with higher incomes appeared to have lower odds of food insecurity. Independent of these effects, having 2 or more chronic conditions, hypertension, or a mental health condition indicated an increased vulnerability. These findings suggest that the needs of social assistance recipients, particularly those chronically ill, are not being adequately met through current benefit structures in order to maintain food security.

Keywords: Chronic Health
Food Insecurity
Provincial Social Assistance Policy
Social Assistance
Advisor: Tarasuk, Valerie
Exploring New Synthetic Methodologies using Organoboron Catalysts

Organic molecules as reaction catalysts (organocatalysts) has represented a major direction of research over the past 10-15 years. Organoboron compounds possess many advantageous features of organocatalysts, including their relatively low cost and toxicity, their high functional group tolerance and ease of structural modification. 2H-Chromenes have been studied extensively as a consequence of their widespread natural occurrence, diverse biological properties and photochromic behaviour. They have been employed as useful intermediates in the synthesis of many natural products, pharmaceuticals and photochromic ophthalmic plastic lenses. Chapter 1 describes the optimization and initial substrate scope of an arylboronic acid-catalyzed synthesis of 2H-chromenes from the condensation of various phenols and aldehydes. Chapter 2 explores the utility of borinic acid catalysts in a Conia-Ene reaction. Finally, Chapter 3 discusses the synthesis of homobarrelenones, attractive building blocks for organic synthesis, via a Diels-Alder cycloaddition reaction using catalytic boronic acids.

Keywords: Catalyst
Organoboron
Organocatalyst
Advisor: Taylor, Mark S
The Role of the Progesterone Receptors in Mammary Stem and Progenitor Cell Regulation

Increased exposure to ovarian hormones is strongly linked with breast cancer risk, however, the molecular mechanisms underlying this phenomenon remain poorly understood. The steroid hormone progesterone is highest during the luteal phase of the menstrual cycle and exerts mitogenic effects within specific mammary epithelial cell populations. Specifically, an induction of mammary stem cells (MaSCs) is observed although hormone receptors have not been detected in the MaSC-enriched basal compartment. The progesterone receptor (PR) has two main differentially regulated isoforms, PR A and PR B, but most studies do not distinguish between isoforms. This study identifies a unique PR+ population within the MaSC-enriched basal fraction following progesterone treatment. Further, it is shown that functional PR signaling enriches for HR+ progenitors (CD49b+Sca-1+) within the luminal compartment in addition to inducing total luminal, total basal, and alveolar progenitor activity. Finally, we also identify a previously uncharacterized luminal population (CD49b-Sca-1-) that is progesterone sensitive.

Keywords: Breast Biology
Hormone Signaling
Mammary Biology
Mammary Progenitor Cell
Mammary Stem Cell
Progesterone Receptor
Advisor: Khokha, Rama
Improving Cancer Radiotherapy Outcomes with Vasculotide, an Angiopoietin-1 Mimetic

Most cancer patients are treated with radiotherapy, but the treatment can also damage the surrounding normal tissue. Radiotherapy side-effects diminish patients' quality of life, yet effective biological interventions for normal tissue damage are lacking. Protecting microvascular endothelial cells from irradiation is emerging as a targeted damage-reduction strategy. Therefore, this dissertation centers on Vasculotide, an angiopoietin-1-based mimic that signals through the Tie2 receptor on endothelial cells to stabilize diseased vasculature. To address the need for skin-protecting agents, the present work investigates Vasculotide as an endothelial cell-targeting agent in a mouse model of acute skin radiation damage.

Keywords: acute skin toxicity
angiopoietin-1
athymic mouse
endothelial cells
radiotherapy
Tie2
Advisor: Liu, Stanley K
A Surrogate mRNA-based Single Cell Assay for Rapidly Enumerating Rare Long-Term Hematopoietic Stem Cells

Long-term hematopoietic stem cells (LT-HSCs) exist at a frequency of 1 in 20,000 nucleated murine bone marrow cells. LT-HSCs sustain hematopoiesis lifelong. Their numbers in the donor samples determine the long-term efficacy of hematopoietic cell transplants. Additionally, there are ongoing efforts to identify conditions that expand LT-HSC numbers ex vivo, or to derive LT-HSCs from pluripotent sources. Accordingly, the ability to enumerate LT-HSCs rapidly would be valuable. Here, I developed a surrogate mRNA marker-based single cell assay to enumerate LT-HSCs rapidly. The combined presence or absence of EPCR, Gata3, and IL-7R transcripts was found to mark LT-HSCs independent of their cell cycle state. A microfluidic system was developed to encapsulate single cells with qRT-PCR reagents into nanolitre microdroplets. QRT-PCR parameters were adapted to quantify the three targets simultaneously across a broad dynamic range, and were subsequently used in the microdroplets for single mRNA molecule and single cell analyses.

Advisor: Iscove, Norman N
Effects of Long-acting Insulin Analogues on Breast and Colon Cancer Promotion

Insulin glargine, a long-acting insulin analogue, has been implicated in increased cancer risk by epidemiological studies and has been reported to increase mitogenicity in in vitro studies. However, studies in preclinical models confirming the tumor promoting effect of glargine are lacking. Methylnitrosourea and azoxymethane treated female Sprague-Dawley rats were randomly assigned to receive saline, neutral protamine Hagedorn (NPH, unmodified insulin), glargine, or detemir (long-acting insulin analogues) for 6 weeks (30/group). Rats treated with NPH had significantly higher mammary tumour multiplicity and a tendency to increased tumour incidence. Mammary tumour burden tended to increase in all insulin-treated rats compared to control. There was no effect of insulin on aberrant crypt foci, a precursor of colon cancer, compared to control. These data suggest that glargine does not promote breast or colon cancer to a greater extent than unmodified insulin. This is important information in the management of patients with diabetes.

Keywords: Insulin analogues
Breast Cancer
Colon Cancer
Advisor: Giacca, Adria
Investigating Surface Lipoprotein Translocation in Neisseria meningitidis

Neisseria meningitidis infections are a major cause of bacterial meningitis cases around the world. During an infection, Neisseria meningitidis employs surface lipoproteins in nutrient acquisition and host immune system evasion. The Moraes lab identified an outer membrane protein, 5H3 that was required for TbpB, a surface lipoprotein, to be expressed on the cell surface. My goal was to functionally characterize this outer membrane protein and to gain insight into its role in surface lipoprotein translocation. I found that other surface lipoproteins were dependent on 5H3 for surface translocation. I was also able to reconstitute this system in E.coli. While I was unsuccessful at obtaining a crystal structure of 5H3, I was able to identify potential interacting proteins through a pull down and mass spectroscopy experiment. These findings indicate that 5H3 is a non-specific surface lipoprotein transporter and could prove to be a valuable therapeutic target against pathogenic Neisseria.

Keywords: Surface Lipoproteins
Neisseria meningitidis
Advisor: Moraes, Trevor
Uncovering the Cause of A Novel Neurological Syndrome: Autosomal Recessive Non-progressive Dystonia-myoclonus with Sensorineural Hearing Impairment

Mitochondrial disorders manifest with a spectrum of presentations, most of which are progressive. Mitochondrial and nuclear DNA encode proteins that regulate mitochondrial functions; genetic defects in these proteins cause human diseases. A combination of dystonia, sensorineural hearing impairment, and progressive encephalopathy is described in mitochondrial depletion syndrome V, where a nuclear DNA encoded SUCLA2 gene mutation leads to a mitochondrial depletion phenotype. We describe a family manifesting autosomal recessive congenital sensorineural hearing impairment, with a non-progressive childhood-onset movement disorder. In this thesis, I identify a novel mutation in SUCLA2 causing a unique phenotype. The disease is allelic to mitochondrial depletion syndrome type-V but is associated with normal mitochondria as evidenced by muscle histology and biochemical testing. I describe the clinical features and elucidate the pathological basis of this genetic disorder. Then, I explore and implement a rational therapy. The knowledge gained from this study affords significant insights into mitochondrial function.

Keywords: SUCLA2
Dystonia and deafness
Novel neurologic syndrome
Advisor: Minassian, Berge
The Axial Spray Mode I as a Solution for Miniaturized Ion Mobility Spectrometry

Miniaturized ion mobility spectrometers present several advantages as portable chemical detection tools. They are fast, simple and inexpensive. However, they still suffer from low resolving power and hard implementation of ion gates in micro scale designs. Even in examples where they are successfully combined, ion gates cause dispersion, compression, and depletion effects that result in ion packets than are wider than desired. This thesis describes an alternative gating method that is free of ion gates and that can be used in liquid phase ion mobility spectrometry (LPIMS), a technique where conventional ion gates are currently unsuitable. A parametric study shows that the method proposed has the potential to achieve resolving powers comparable to macro scale designs if successfully coupled to LPIMS. Observations relating the maximum meniscus height to current measurements are presented and are of particular interest to E-jet printing and similar techniques.

Keywords: ion mobility spectrometry
chemical detection
Lab-on-a-chip
e-jet printing
electrospray
electrohydrodynamic jet
Axial spray mode
spindle mode
Advisor: Sullivan, Pierre E.
Mrad, Ridha Ben
Properties, Dimensions, and Heritability of Obsessive-Compulsive Symptoms in a Community Sample of Children and Adolescents

Obsessive-compulsive disorder (OCD) is a debilitating neuropsychiatric disorder commonly seen in children and adolescents. The etiology of OCD remains elusive mostly due to its complex, heterogeneous phenotype and genotype. Increasing evidence support a multidimensional model of OCD and a continuous nature of obsessive-compulsive (OC) symptoms in the general population. However, there is limited understanding of OC symptoms in pediatric populations. Using a novel questionnaire, the Toronto Obsessive Compulsive Scale, we investigated properties, dimensions, and heritability of OC symptoms in a community sample of 16,380 children and adolescents, and a sub-sample of 220 twin pairs, respectively. We identified six distinct OC symptom dimensions in our study that parallel those identified in previous studies: (1) Superstition, (2) Cleaning/Contamination, (3) Hoarding, (4) Symmetry/Ordering, (5) Checking/Counting, (6) Rumination. Phenotypic and heritability characteristics of overall and dimensions of OC symptoms are reviewed in detail. Research and clinical implications of the current study are also discussed.

Keywords: obsessive-compulsive disorder
child and adolescent psychiatry
heritability
quantitative trait approach
psychometrics
Advisor: Arnold, Paul
Design and Evaluation of an Improved Mixer for a Selective Catalytic Reduction System

More stringent environmental regulations have created a requirement for Selective Catalytic Reduction (SCR) after-treatment technology on stationary Diesel engines. In this work, Computational Fluid Dynamics (CFD) is used in conjunction with a separate 1-D catalyst reaction model to evaluate the overall performance of the combined High Efficiency Vortab (HEV) mixer and U-bend design. This model yielded mixing results with a Uniformity Index (UI) of 97% while generating less than 10 ppm of NH3 slip. The compact nature of the combined design creates an SCR that is easy to install and manufacture. Pressure drop, was also determined to be less than 10” of water (WC) over the range of operating conditions. The performance from this design will assist engineers in meeting current and next generation environmental regulations.

Keywords: SCR
Advisor: Wallace, James
Sullivan, Pierre E.
Mechanisms of Atrial Fibrillation in Mice with Genetic Ablation of the α1D L-type Calcium Channel

Atrial fibrillation (AF) is the most common supraventricular arrhythmia with a multifactorial pathophysiology. Reductions in α1 L-type calcium channel (LTCC) current (ICaL) and action potential duration is commonly observed in human AF patients. As expected, mice lacking the α1D (Cav1.3) LTCC gene are more susceptible to inducible AF, albeit without a reduction in atrial refractoriness. Despite increased fibrosis and delayed conduction velocity in Cav1.3-/- mice, spectral analysis of AF revealed a highly disorganized pattern consistent with electrical remodeling. Conforming to electrical remodeling, Cav1.3-/- atrial myocytes displayed increased sensitivity to calcium alternans, which was alleviated with inotropic agents and absent in α1C LTCC heterozygous atrial myocytes. In addition, we observed increased electrical alternans in Cav1.3-/- atria, which coupled positively to voltage. These electrical alternans were in-turn associated with AF in Cav1.3-/- atria. Our findings support the conclusion that preferential loss of Cav1.3 promotes calcium alternans, resulting in arrhythmogenic electrical alternans.

Keywords: atrial fibrillation
cav1.3
arrhythmia
atria
alternans
electrophysiology
heart
L-type calcium channel
Advisor: Backx, Peter H
Design and Fabrication of Micro-structured Surfaces for Algal Biofilm and Human Cell Migration Studies

Cells have been reported to respond to structured surface cues that are on the micro and nanometer scale. In this work, widely known semiconductor fabrication processes such as lithography, etching along with hot embossing methods were utilized to fabricate consistent micro-patterns in polymethyl methacrylate (PMMA) substrate in order to grow algal biofilms in a photo bioreactor. Results show an increase in productivity of biomass on deep (~20 µm) V-grooved PMMA surfaces compared to smooth and shallow (~1.5 µm) grooved PMMA surfaces. The hot-embossing parameters such as force, temperature and wait-time settings in Jenoptik HEX 02 hot embosser were tested and optimized for an efficient pattern transferring process using PMMA sheets and PMMA resist. Furthermore, micro-structured surfaces on silicon substrates were fabricated with distinct flat-groove interface for guided cell migration study and the custom-made Si stamp design helped in concluding that cells were guided on the interface through mechanical exclusion interaction.

Advisor: Aitchison, Stewart