VictorJuiz/thesis huggingface dataset:
Pressure Drop of a Boger Fluid in a Converging Channel

The pressure drop of viscoelastic fluids flowing through a converging channel was investigated and compared to Newtonian fluids under equivalent flow conditions. The channel shape was hyperbolic, so there was a constant extensional rate along the centreline. Three Boger fluids, one aqueous and two organic, with nearly constant viscosities were used to isolate elastic effects. The Boger fluids were fully characterised in shear and extension. The shear testing, in addition to results from literature, showed that the Oldroyd-B model does not model the first normal stress accurately. Elasticity was shown to increase the pressure drop, relative to a comparable Newtonian value. When the pressure drop was corrected for die swell, the change in pressure drop was comparable to the experimental error, suggesting that the major elastic effect is in shear, rather than extension. Unexpectedly, both hardy polymers showed signs of polymer degradation after flowing through the channel

Keywords: axisymmetric
Boger fluid
converging channel
dilute solution
hyperbolic
relaxation time
Advisor: James, David F.
Analyzing and Optimizing an Array of Low-Cost Gas Sensors for use in an Air Quality Measurement Device with Machine Learning

Low-cost gas sensors have been proposed in place of conventional expensive instruments however they have issues due to cross-sensitivity with other pollutants. Several different types of metal oxide and electrochemical sensors and machine learning methods were evaluated. The objectives were to determine which type of sensor, metal oxide or electrochemical, is better at measuring traffic-related air pollution and whether deep neural networks (DNN) and recurrent neural networks (RNN) improve sensor performance. Three devices were deployed across three sites, two in Toronto and one in Beijing to evaluate the performance of calibration. Calibration was performed with two weeks of data from only one site and evaluated with the remaining data. The combination of metal oxide and electrochemical sensors were more accurate when measuring NOx. When targets were normalized, the RNN performed better than DNN and linear calibration, however, not when applied to measuring data well outside the range for calibration.

Keywords: Air Pollution
Environmental monitoring
Low-cost sensor
Machine learning
Neural Network
Smart city
Advisor: Evans, Greg J
Custom Microporous Layers for Polymer Electrolyte Membrane Fuel Cells

Custom microporous layers (MPLs) were fabricated and designed to enhance fuel cell performance and water management at two specific operating conditions, operation without anode humidification and operation at high current densities. The two studies were aimed at addressing two challenges of water management, i.e., membrane dehydration and cathode liquid water flooding. The fuel cell performance and impedance measurements were paired with synchrotron X-ray visualization to quantify cell potential, membrane and mass transport resistances, and liquid water within gas diffusion layers (GDLs). The application of hydrophilic MPLs decreased the membrane resistance, and increased liquid water retention at the catalyst layer-MPL interface. MPLs with spatially graded PTFE content reduced the cathode GDL liquid water accumulation and oxygen transport resistance. Both MPLs led to increased fuel cell performance. The knowledge gained from this thesis can inform the design of next-generation fuel cell materials that further improve cell performance at desired operating conditions.

Keywords: Gas diffusion layer
Liquid water distribution
Microporous layer
Polymer electrolyte membrane fuel cell
Synchrotron X-ray radiography
Water management
Advisor: Bazylak, Aimy
Sodium Glucose Cotransporter-2 Inhibition and Renal Function

Sodium glucose cotransporter-2 inhibitors (SGLT2i) are approved therapies for renal decline in type 2 diabetes (T2D). Yet there is limited evidence on SGLT2i impact outside of T2D, which this thesis addresses. We hypothesized that 1) the SGLT2i empagliflozin would mediate intrarenal function in type 1 diabetes (T1D), 2) the SGLT2i canagliflozin would be tolerated in renal transplant populations and 3) the SGLT2i dapagliflozin would be protective in focal segmental glomerulosclerosis (FSGS), a subtype of non-diabetic renal disease. In the first study, we found intrarenal mediation upon SGLT2i therapy in T1D. In the second study, SGLT2i were tolerated in kidney transplant recipients. In the third study, SGLT2i imparted insignificant renoprotection in FSGS. Thus, despite the potential of SGLT2i as a renoprotective therapy outside of T2D, its efficacy may vary across disease subtypes, due to renal SGLT2 regulation. Larger clinical trials are needed to further characterize the renal impact of SGLT2i.

Advisor: Cherney, David Z.I.
A Pathway to Interfacial Thermal Modeling for Electrochemical Devices

Interfacial thermal transport characteristics of electrochemical devices are an important aspect of modern device design. Through the Landauer approach, we have the means to model thermal transport for a wide range of materials and for a variety of operating conditions. In this work we present the building blocks towards the end goal of a complete thermal model for electrochemical devices. The focus of this thesis is on modeling the thermal transport in the bulk, and at interfaces for solids where phonons dominate as the carrier of thermal energy. We explicitly demonstrate the modeling approach for the case of bulk silicon, as well as for a silicon-germanium interface while also describing how the approach can be applied for an arbitrary choice of materials. Additionally, by applying concepts from the modern theory of liquid thermodynamics, we discuss how the approach can be extended to characterize thermal transport for liquid and solid-liquid systems.

Keywords: Electrochemical
Interface
Interfacial
Landauer
Modeling
Thermal
Advisor: Dawson, Francis P
Pugh, Mary
X-ray and Magnetic Resonance Imaging (MRI) Fusion to Guide Clinical Revascularization of Peripheral Chronic Total Occlusions (CTOs)

Percutaneous transluminal angioplasty (PTA) is a minimally invasive procedure used to revascularize blocked arteries of the heart and peripheries. However, endovascular approaches to treat chronic total occlusions (CTOs) of the superficial femoral artery (SFA) have proven challenging due to the presence of long and multiple occlusions, which cannot be visualized under x-ray fluoroscopy (XRF) alone. Devices can exit the artery leading to severe perforation. Magnetic resonance imaging (MRI) can produce three-dimensional vascular maps that are sufficient to identify the lesion extent and characterize the surrounding vasculature. Higher PTA success rates could be achieved for lengthy occlusions by merging 3D MRI data and XRF. This thesis develops a 3D MRI to 2D XRF registration method to guide revascularization of peripheral CTOs. The registration method utilizes bones in the MR and x-ray images as landmarks for registration. Furthermore, using an edge-based similarity measure the algorithm automatically maintains alignment together with C-arm tracking.

Keywords: Femur
MRI
Peripheral
Registration
Revascularization
X-ray
Advisor: Wright, Graham
Gestational Diet Folic Acid Content and Development and Function of Food Intake Regulation in Rats

High folic acid consumed during pregnancy promotes characteristics of metabolic syndrome in rat offspring. We hypothesized that folic acid alters the development of hypothalamic food intake pathways in utero, contributing to the metabolic phenotype of the offspring in later life. Pregnant Wistar dams were fed modified AIN-93G diets containing folic acid at: 0, 1.0 (control), 2.5, 5.0, or 10.0-fold of the recommended level. The folic acid content in the gestational diet was reflected in the expression of neuropeptide Y (NPY) neurons and body weight of the male offspring at birth. Low and high gestational folic acid led to higher food intake and weight gain in the offspring to 9 weeks post-weaning, consistent with decreased activity of pro-opiomelanocortin (POMC) neurons. The folic acid content in the gestational diet affects in utero development of hypothalamic feeding circuits and contributes to a phenotype that reflects characteristics of the metabolic syndrome in the offspring.

Keywords: Childhood Obesity
Fetal Programming
Folic Acid
Food Intake Regulation
Hypothalamus
Neurons
Advisor: Anderson, G. Harvey
An Immune-Deficient Prkdc Knockout Rat Model of Perinatal Hypoxic-Ischemic Brain Injury for Future Xenograft Studies

Perinatal hypoxia ischemia (HI) is a significant cause of brain damage leading to motor and cognitive impairments. There are no treatments that can repair the damage and improve outcomes, though preclinical research using neural precursor cell (NPC) transplantation as a therapy has shown promise. To promote clinical translation, it is essential that human-derived NPCs also be tested in animal models. To reduce the risk of xenograft rejection, we characterized a model of HI injury in immune-deficient Prkdc knockout rats. Knockout HI rats displayed sensorimotor deficits on the cylinder and pasta-handling tests, and reductions in size of and cellular loss in the hippocampus, cortex, and corpus callosum. Ventriculomegaly and grey matter gliosis were also prominent. Interestingly, knockout rats displayed overall more severe injuries than wildtype littermates. This model characterization will allow for future studies of human-derived NPCs in the rodent brain, paving the way for the clinical translation of this therapy.

Keywords: hypoxia ischemia
model characterization
perinatal
prkdc knockout
rice vannucci
xenograft
Advisor: Fehlings, Michael G
Balance Control when Ascending and Descending Stairs of Different Architectural Designs

The purpose of this study was to understand differences in balance control during stair walking on stairs of different architectural designs under varying visual conditions and lighting conditions. An 8-step custom made staircase with removable covers permitted evaluation of stair ambulation. Individuals ascended and descended the staircase under two visual conditions (normal vision, and suboptimal vision), two lighting conditions (bright light and low light) and three architectural stair design conditions (glass treads, open wood risers, and closed wood risers). The main findings of the study showed that older adults positioned their centre of mass further back from the step edge and displayed larger margins of stability across all conditions. In addition, both young and older adults displayed larger margins of stability under the glass stair condition compared to the other stair designs and under the low lighting condition compared to the bright light.

Keywords: architectural designs
balance control
biomechanics
center of mass
stair walking
vision
Advisor: Fernie, Geoff
Novak, Alison
The Effect of Maternal Vitamin B12 Status in Combination with High Folate Status on Gene-Specific DNA Methylation in Cord Blood Mononuclear Cells

DNA methylation is an important epigenetic determinant in gene expression, with potential consequent effects on disease susceptibility. Maternal folate and B12 has the potential to modulate DNA methylation via the provision of S-adenosylmethionine. Using the Illumina Infinium MethylationEPIC array, we found lower genome-wide (-0.0059±0.0147, p=0.013) and gene-specific (p=0.007) DNA methylation in genes influenced by maternal low serum B12 and high RBC folate concentrations at early pregnancy. Analyses using Ingenuity Pathway Analysis and ddPCR determined that B12 and folate-induced DNA methylation changes altered expression of functionally relevant genes related to metabolism and development. Infants born to mothers with a low B12 status are shown to have larger infant anthropometric measures. Our data suggest that low B12 and high folate induced DNA methylation changes in the developing fetus. Given the potential for these changes to mediate disease risk later in life, future large-scale studies are warranted to confirm our exploratory findings.

Keywords: cord blood mononuclear cells
DNA methylation
folate
gene expression
pregnancy
vitamin B12
Advisor: Kim, Young-In
Hyperphosphorylated Tau as a Novel Biomarker for Traumatic Axonal Injury in the Spinal Cord

The tau protein is a focus of biomarker research for spinal cord injury (SCI). Brain injury studies have demonstrated that hyperphosphorylation of tau (p-tau) occurs within injured axons and can be used as a biomarker; however, the potential of p-tau as a biomarker for SCI is not yet known. Therefore, the present study determined whether tau is hyperphosphorylated within injured spinal cord axons and whether p-tau levels increase in cerebrospinal fluid (CSF) and serum after an experimental SCI in rats. Severe SCI at T8 showed the presence of p-tau in damaged axons with a similar time-course and distribution pattern to β-amyloid precursor protein, a biomarker of axonal injury. CSF levels of p-tau and total-tau significantly increased at 1 day post-SCI, however, only serum p-tau levels were significantly elevated in SCI rats compared to naïve rats. These results suggest that CSF and serum p-tau may be a useful biomarker for severe traumatic SCI.

Keywords: Axonal injury
Biomarker
Hyperphosphorylation
Spinal cord injury
Tau
Trauma
Advisor: Tator, Charles H
Analysis of Drosophila Nervous System Development Following a Brief Exposure to Ethanol

Improper neuronal mapping predisposes many of the neurodevelopmental deficits that arise in patients of Fetal Alcohol Spectrum Disorders (FASD). Here I used Drosophila embryos as a model to investigate the neuronal defects that arise after exposure to ethanol. Drosophila is an excellent model for studying the mechanisms underlying FASD due to their vulnerability to the toxic effects of alcohol and the ease of manipulating their development. Using this model, I was able to provide detailed morphological analyses of the effects of a brief ethanol exposure on Drosophila neural development. I also examined the mechanisms that may regulate the FASD phenotype, specifically the serum response factor (SRF) signalling pathway. SRF signalling regulates numerous functions in the nervous system, including neuronal growth and migration. Through SRF manipulation in Drosophila, I was able to show that SRF is necessary for proper Drosophila axonogenesis, and that it may contribute to the FASD phenotype.

Keywords: Axon Guidance
Drosophila
Fetal Alcohol Spectrum Disorders
Serum Response Factor
Advisor: Stewart, Bryan
A Low-Power Sub-GHz RF Receiver Front-End With Enhanced Blocker Tolerance

Sub-GHz wireless systems have become a popular choice for Internet-of-Things (IoT) applications due to their lower cost, lower power consumption and longer transmission range compared to their 2.4 GHz counterpart. This thesis presents a class-AB sub-GHz RF receiver front-end for low power IoT applications. By exploiting transistors' class-AB operation in both the RF and baseband sections, the receiver front-end achieves a very low sensitivity and an elevated blocker tolerance while keeping a low power consumption. Such performance makes the receiver fully compliant with the short-range (e.g. IEEE 802.15.4) application and also suitable for the emerging long-range (e.g. LoRa) application. The proposed RF receiver front-end has been implemented in 0.13um CMOS technology, operates in the 868/915MHz ISM bands, and exhibits an in-band gain of 50dB, noise figure of 2.7dB, out-of-band IIP3 of +2dBm, out-of-band IIP2 of +37dBm, out-of-band P1dB of -10.5dBm, while draining 2.1mA from a 1.2V supply.

Keywords: Blocker Tolerance
Class-AB
IEEE 802.15.4
Low-power
RF Receiver
Sub-GHz
Advisor: Johns, David A
Liscidini, Antonio
Population Genomics of Transposable Elements and their Effect on Gene Expression Variation

Transposable elements (TEs) make up a significant portion of eukaryotic genomes, and thus are important drivers of genome evolution. The forces controlling TE copy number and the extent to which TEs affect phenotypic variation genome-wide are still unclear. I characterised TE insertion polymorphism in 124 whole genome sequences from a single population of Capsella grandiflora. The frequency of insertions is negatively correlated with distance to genes, as well as density of non-coding conserved elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their spread throughout the population. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. Contrarily, rare single nucleotide polymorphisms (SNPs) contribute equally to upregulation and downregulation, but have a weaker overall effect. Taken together, these results imply that TEs contribute significantly to gene expression variation and can be more likely than rare SNPs to cause extreme changes in gene expression.

Keywords: Gene expression
Genomics
Population genetics
Transposable elements
Advisor: Wright, Stephen I
The Spatiotemporal Distribution of SPARC and Collagen IV in the Secretory Pathway and Evidence of a Functional Relationship During Extracellular Collagen IV Polymerization

Basement membranes (BMs) are a hallmark feature of multicellular organisms and support essential developmental events. Collagen IV is the major structural component of BMs, however, its spatiotemporal assembly into stereotypic lattice networks is poorly understood. SPARC, a collagen IV-binding glycoprotein, is enriched in BMs of Drosophila melanogaster. SPARC is hypothesized to be an extracellular chaperone-like protein, whereby it prevents premature collagen IV polymerization. In this study, I demonstrate that SPARC and collagen IV co-localize primarily in the trans-Golgi network prior to secretion. Moreover, SPARC reduces premature nucleation of collagen IV molecules in cultured hemocytes seeded on a laminin matrix, but is not required for the establishment of collagen IV-rich BMs in the embryo. To gain further insight on the functional relationship between SPARC and collagen IV, CRISPR/Cas9 sparc mutants were generated. This genetic tool will be used to unmask SPARC structural domains responsible for collagen IV assembly and BM homeostasis.

Keywords: Collagen IV
Drosophila
Extracellular matrix
SPARC
Advisor: Ringuette, Maurice
Quantum Mechanical Characterization of Substrated Bilayer Graphene for Future Supercapacitor Applications

Energy storage is one of the most crucial ingredients of a sustainable energy future. The safety, reliability, and performance of storage devices present a number of design challenges that require developing accurate predictive models capable of representing the most relevant physical phenomena at various spatial and temporal scales and a reasonable computational cost. Moreover, the current trend of decreasing the device size and the advent of low-dimensional nanomaterials have increased the dominance of interfacial physics that cannot be accurately modelled as a continuum within the device. This thesis is a first step towards developing a methodology for characterizing interfaces in capacitive energy storage devices based on insights from Density Functional Theory. Monolayer and bilayer graphene electrodes, attached to nearly lattice-matched conducting substrates, are then modelled as case studies. Graphene is one of the most promising materials for future supercapacitors due to its high specific surface area and unique electronic properties.

Keywords: Density Functional Theory
Electrochemistry
Energy Storage
Graphene
Interfacial Physics
Supercapacitors
Advisor: Dawson, Francis P
Huzayyin, Ahmed
Jet Oscillation in Abrasive Slurry-Jet Machining as a Function of Polymer Concentration and Nozzle Geometry

This thesis investigated the effects of polymer concentration and nozzle design on jet stability for polymeric abrasive slurry-jet channel machining in glass. Conical nozzle contractions, having angles of 180°, 60°, 30°, and 20°, were used with aqueous polyethylene oxide (PEO) polymer solutions, having concentrations of 100, 200, and 300 ppm. Channels were machined in glass using slurries containing 1 wt% of 10 μm aluminum oxide particles, made from the same four working fluids used to study jet oscillation. Jet oscillation was found to increase nonlinearly with polymer concentration for all contraction geometries. As a result of the effect of the varying degrees of jet oscillation, a clear relationship was found between the polymer concentration and the channel width. Flow visualization within the nozzle confirmed the presence of vortices that have been associated with jet instability, but did not reveal a clear reason for the changes in jet stability.

Keywords: Jet Oscillation
Machining
Viscoelasticity
Advisor: Spelt, Jan K
Papini, Marcello
Participants’ Perspectives on Ethical Issues in Arts-Based Health Research: A Qualitative Study

Arts-based health research (ABHR) is a novel qualitative approach that uses different art forms to conduct health research. Despite the growth of ABHR, ethical consideration has been significantly lacking. More importantly, participants’ perspectives on ethical issues in this co-constructive and collaborative approach are absent. From a constructivist-interpretivist stance, factors incorporated in participants’ decision-making concerning ethical issues in ABHR were investigated to construct their perspectives on ethical issues in ABHR. Using constructivist grounded theory, 10 participants from an urban arts charity organization were interviewed, and three major factors were constructed: identities as artists, art is a story, and art is to express. An overarching theme called respect for the artist was also constructed to illustrate how these factors influence participants’ perspectives on ethical issues in ABHR. Findings of this study contribute to informing researchers, REBs, and guideline development for ABHR to better meet the needs of participants as they articulate them.

Keywords: arts-based health research
arts-based methods
constructivist grounded theory
participant perspectives
qualitative research
research ethics
Advisor: Parsons, Janet
Kirsh, Bonnie
1,1-Hydroboration and Borane Adduct of Diphenyldiazomethane

The advent of frustrated Lewis pair chemistry has demonstrated unique reactivity with a variety of small molecules. This thesis explores related chemistry with reactions of diazomethanes and highly electrophilic boranes. Diphenyldiazomethane Ph2C(N2) reacts with HB(C6F5)2 resulting in 1,1-hydroboration via a concerted reaction involving initial formation of the Lewis adduct, yielding the robust amino-borane product Ph2CN2BH(C6F5)2. Alternative synthetic routes to this product are detailed, as well as a related salt. Conversely, Ph2C(N2) reacts with B(C6F5)3 to form a highly sensitive adduct Ph2CN2B(C6F5)3. This product liberates N2 and is proposed to generate Ph2CB(C6F5)3. DFT calculations reveal that formation of this product is thermodynamically favourable from the starting compounds of carbene, N2 and borane. The isolation of this latter species opens the possibility that judicious choice of a Lewis acid and base could provide an avenue to metal-free fixation of N2.

Keywords: Diazomethane
Dinitrogen
Frustrated Lewis Pair
Hydroboration
Main Group Chemistry
Nitrogen Fixation
Advisor: Stephan, Douglas W.