VictorJuiz/thesis huggingface dataset:
Mechanisms of Glucagon-like Peptide-2-mediated Effects on Intestinal Barrier Function in Health and Irinotecan-induced Enteritis

Glucagon-like peptide-2 (GLP-2) is an intestinal hormone that promotes gut growth through an insulin-like growth factor (IGF)-1 and intestinal epithelial (IE)-IGF-1 receptor (R)-dependent pathway. GLP-2 also promotes epithelial barrier function by as yet unknown mechanisms. I hypothesized that GLP-2-mediated effects on barrier function requires the IE-IGF-1R. Chronic GLP-2 treatment enhanced barrier function by decreasing gastrointestinal permeability in vivo and increasing jejunal resistance ex vivo. These responses were abolished in inducible IE-IGF-1R knockout (KO) animals. Additionally, epithelial sealing tight junctional proteins claudin-3 and -7 were upregulated by GLP-2 in control but not KO mice. Moreover, IE-IGF-1R deletion induced a shift in occludin localization from apical to intracellular domains. In contrast, in irinotecan-induced enteritis, GLP-2 normalized epithelial barrier function in control animals, but continued to be ineffective in KO mice. Collectively, the effects of GLP-2 on barrier function are dependent on the IE-IGF-1R and involve modulation of the tight junctional complex.

Keywords: GLP-2
Advisor: Brubaker, Patricia
Regression Modelling of Power Consumption for Heterogeneous Processors

This thesis is composed of two parts, that relate to both parallel and heterogeneous processing. The first describes DistCL, a distributed OpenCL framework that allows a cluster of GPUs to be programmed like a single device. It uses programmer-supplied meta-functions that associate work-items to memory. DistCL achieves speedups of up to 29x using 32 peers. By comparing DistCL to SnuCL, we determine that the compute-to-transfer ratio of a benchmark is the best predictor of its performance scaling when distributed. The second is a statistical power model for the AMD Fusion heterogeneous processor. We present a systematic methodology to create a representative set of compute micro-benchmarks using data collected from real hardware. The power model is created with data from both micro-benchmarks and application benchmarks. The model showed an average predictive error of 6.9% on heterogeneous workloads. The Multi2Sim heterogeneous simulator was modified to support configurable power modelling.

Keywords: Power Modelling
OpenCL
Simulation
Benchmarking
Advisor: Anderson, Jason
Jerger, Natalie Enright
Source and Carrier Effect on the Bioactivity of BMP Bio-implants

Bone morphogenetic protein-2 (BMP-2) plays a critical role in bone formation. The aim of this study was to compare the activity of the mammalian cell BMP-2 to the E-coli cell BMP-2. In vitro, the potency of mammalian and E-coli BMP-2 was compared by adding BMP-2 to C2C12 cells and measuring the level of alkaline phosphatase activity. In vivo, the activity was evaluated by placing the bioimplants in the thigh muscle of mice, and measuring the amount of bone induced. The in vitro assay clearly showed that mammalian BMP was significantly more potent than E-coli BMP. In vivo, on the calcium phosphate carrier, mammalian BMP produced more bone than E-coli BMP, but E-coli BMP produced higher density tissue than mammalian BMP. On both mammalian and E-coli BMP, the calcium phosphate carrier had a significant effect on the density but not the quantity of bone produced versus the absorbable collagen sponge carrier.

Keywords: BMP
Bio-Implants
Advisor: Peel, Sean
Clokie, Cameron
Novel Hydrogen Bonding Organocatalysts: Applications in the aza-Morita-Baylis-Hillman Reaction and Anion Sensing

Self-assembly is an efficient method for generating large numbers of structurally diverse catalysts for screening. In this work, the method of self-assembly was explored in the construction of bifunctional catalysts, from a chiral aminophosphine, 2-formylphenylboronic acid, and a (thio)urea-containing diol. These catalysts were evaluated by their effect on the asymmetric aza-Morita-Baylis-Hillman reaction. In the second half of this thesis, the hydrogen bonding abilities of different dithiosquaramides were analyzed. As thioureas have been shown to be stronger hydrogen bond donors than ureas, it was hypothesized that dithiosquaramides may also follow a similar trend. Affinities of corresponding squaramides and dithiosquaramides to chloride, sulfate, and tosylate were compared, as well as their abilities to catalyze the Freidel-Crafts alkylation between indole and trans-β-nitrostyrene.

Keywords: hydrogen bonding
organocatalysis
anion sensing
self assembly
squaramides
Advisor: Taylor, Mark S.
Effect of Gtf2i Gene in Anxiety

Duplication and deletion of a common interval spanning 26 genes on chromosome 7q11.23 cause Dup7q11.23 Syndrome and Williams-Beuren Syndrome, neurodevelopmental disorders with contrasting anxiety phenotypes. The General Transcription Factor 2 I (GTF2I) gene has been implicated in separation anxiety, common in people with Dup7q11.23, and we studied the effects of commonly used anxiolytics on maternal separation-induced USV in mouse models with copy number changes in Gtf2i. Subcutaneous injection of saline affected both USV production and plasma corticosterone levels in a Gtf2i gene-dosage dependent manner. Drugs acting on the glutamate receptors were most effective at attenuating USVs in all genotypes, compared to GABAergic and serotonergic modulators. Brain c-fos expression after separation was reduced by a GABAA agonist, but not a glutamate antagonist. Collectively, these results suggest a potential difference in pain sensitivity based on Gtf2i copy number and implicate the glutamatergic and GABAergic systems in anxiety phenotypes in these two disorders.

Keywords: anxiety
Williams Beuren Syndrome
Dup7q11.23
Gtf2i
Advisor: Osborne, Lucy
The Mineralogy and Geochemistry of the Green Giant Vanadium-graphite Deposit, S.W. Madagascar

The purpose of this project was to determine the vanadium bearing ore minerals present at the Green Giant vanadium-graphite deposit in the S.W. of Madagascar owned by Toronto based Energizer Resources Inc. The rocks are mainly quartzofeldspathic gneiss, with alternating bands of hornblende biotite gneiss, marble, granitoid, and amphibolite. Using X-ray diffraction, electron microprobe analysis, and Raman spectroscopy, the vanadium bearing minerals were identified as vanadium bearing rutile, schreyerite, berdesinskiite, karelianite, a member of the karelianite-eskolaite solid solution, V-bearing phlogopite, V-bearing pyrrhotite, V-bearing pyrite, goldmanite, dravite, uvite, actinolite, and unidentified V-sulphide 1, V-sulphide 2, and V-silicate 1. The mineral assemblage present at Green Giant deposit is quite similar to that at Lake Baikal, Russia. Vanadium-bearing phlogopite is primary vanadium host in the deposit, although V-bearing oxides contribute substantially to the total V concentration, even where present in very trace amounts.

Keywords: Vanadium
Geology
Mineralogy
Geochemistry
Madagascar
Advisor: Spooner, Edward
The Effects of Event Properties on Age-related Differences in Episodic Memory

Episodic memory (EM) is disproportionately impaired in normal healthy aging. However, experimental comparisons and literature reviews of the neural correlates of EM across lab-based and naturalistic paradigms reveal significant differences. The current study systematically manipulated the degree of naturalism by testing memory for the same content encoded in a naturalistic vs. laboratory context in order to investigate how memory performance interacts with the properties of the encoding context in younger and older adults. We found that the naturalistic event was subsequently associated with greater overall recognition accuracy, specifically for sequence information, and was associated with a greater contribution of re-experiencing to recognition. We found no significant interaction of normal aging with the event manipulation, but our older sample is currently too small to draw definitive conclusions. Overall, our results suggest that the experimental manipulation of a controlled real-life event is a viable method for studying naturalistic episodic memory.

Keywords: episodic memory
autobiographical memory
hippocampus
aging
Advisor: Levine, Brian
Slips During Gait on Winter Surfaces: Evaluation of Ice Cleat Design and Slip Definition

Current winter footwear provides inadequate protection from slip-related injuries on ice, and there is limited research investigating the optimal design of anti-slip devices. This study examined how ice cleat spike height and position in the heel affect slipping. No differences could be observed between spike conditions, but results demonstrated that heel spikes may prevent slips initiated between heel contact and foot-flat and forefoot spikes may be necessary to prevent foot-flat slips. Further analysis compared slip outcomes measured using two slip onset definitions: 1) heel contact, and 2) the first point of increasing positive heel acceleration. Slip onset defined as time of heel contact overestimated the number of slips and slip distances. These results demonstrate that ice cleats have the potential to protect pedestrians from slipping but some styles available to consumers (i.e. heel spikes only) may not be adequate. Choice of slip definition in footwear evaluations can significantly influence study outcomes.

Keywords: winter footwear
slips
falls
ice cleats
Advisor: Fernie, Geoff
Investigation of Molecular and Cellular Mechanism of Myelin – Induced Axonal Degeneration

Axon degeneration is a selective elimination of axons, which plays a crucial role during development, injury, and maintenance of neuronal connections. The p75 neurotrophin receptor (NTR) is responsible for maintaining the specificity of neuronal connectivity in parts of the adult brain by inducing the degeneration of aberrantly growing axons into myelinated tracts. The objective of this study is to identify and characterize the signaling pathways used by p75NTR to mediate axon degeneration on myelin. Since p75NTR signals via JNK/Bax/caspase pathway to cause apoptosis, I asked whether this pathway might also be involved in axon degeneration. I observed that inhibition of JNK or Bax significantly decreased myelin-induced axonal degeneration, while depolarization of axons with potassium chloride prevented axonal degeneration on myelin. Together, these results suggest that p75NTR-dependent, myelin-mediated axon degeneration occurs via JNK/BAX signaling, and that neural activity is important for the prevention of myelin-induced axonal degeneration.

Keywords: Myelin
Axonal Degeneration
JNK
Bax
Neuronal activity
Advisor: Kaplan, David R.
Copying Canada - A Critical Analysis of the Barbados Bankruptcy And Insolvency Act

Barbados enacted the Bankruptcy and Insolvency Act in the year 2001. This Act is based entirely on the Canadian Bankruptcy and Insolvency Act. Barbados reformed its bankruptcy and insolvency laws in order to offer greater protection to debtors while simultaneously protecting creditors from fraud. Additionally, the new reforms were designed to remove the stigma that attaches to insolvent and bankrupt individuals and businesses and to make Barbados a more attractive destination for the creation of and investment in new businesses. Despite the existence of a legislative framework designed to assist debtors and creditors only five matters have been initiated under the Barbados Act. In this thesis I examine why there has been reluctance to rely on the Act. Ultimately, I conclude that the bankruptcy and insolvency regime that exists in Barbados is ineffective and lacks many of the features that are necessary for the efficient administration of bankruptcies and insolvencies.

Keywords: Bankruptcy
Insolvency
Advisor: Duggan, Anthony
Alkaline Pressure Oxidation of Pyrite in the Presence of Silica – Characterization of the Passivating Film

Alkaline pressure oxidation, particularly in the presence of trona as additive, can be used to oxidize high carbonate refractory gold ores as it prevents the formation of CO2 in the autoclave. However, the presence of silica in the ore can lead to the encapsulation of pyrite due to the formation of a passive layer. This phenomenon occurs due to the high solubility of silica in alkaline solutions and its subsequent re-precipitation on the reacting pyrite surface. The present study investigated the chemical composition and thickness of the passive layer on a rotating pyrite surface in an aqueous slurry containing silica sand, sodium carbonate and calcium carbonate at 230°C and under 7 bar of oxygen overpressure. Results obtained from XPS and SEM show that a concentration of 2.5 g/L sodium carbonate gave the maximum thickness of passivation on pyrite and that the passive layer consisted primarily of silicates and aluminosilicates.

Keywords: Pressure Oxidation
Pyrite
Advisor: Papangelakis, Vladimiros G.
"A Beautiful Picture of Chaos": La Vía Campesina and the Convergence of Food Sovereignty and Climate Justice

La Vía Campesina is an international network of peasant farmers that, since 1996, has promoted the concept of food sovereignty. More recently, this collection of over 160 groups worldwide has been connecting this concept with climate justice issues. Drawing on interviews conducted during the 2012 People’s Summit that took place in Rio de Janeiro, and an analysis of the network’s documents, I consider its work in relation to its member organizations and a broader movement tackling the systemic issues that are driving a range of social, economic and ecological crises. I contend that, while many of Vía Campesina’s proposals will require the establishment of intricate processes and systems depending on the geographic, political and cultural context in question, the network is demonstrating that its radical critiques, proposals and decision-making processes may help contribute to a larger counter-hegemonic narrative as a force to counteract global capitalism.

Keywords: food sovereignty
climate change
social movements
hegemony
peasants
La Vía Campesina
climate justice
system change
Advisor: Prudham, W. Scott
Kumar, Kundan
Inter-Strain Differences in Responses to Subarachnoid Hemorrhage in Mice

Spontaneous subarachnoid hemorrhage (SAH) is a form of hemorrhagic stroke that accounts for approximately 7% of all strokes worldwide. Recently, researchers have gained insight into some possible genetic influences involved in the response to SAH. The goal of this study was to investigate the potential contribution of different mouse genetic backgrounds to brain injury after SAH. SAH was induced in 7 inbred strains of mice, and the degree of large artery vasospasm and brain injury was assessed. After 48 hours, SAH mice showed a significant reduction in middle cerebral artery diameter and increased neuronal injury in the cerebral cortex compared to sham controls. The degree of vasospasm and brain injury varied across strains. This data suggests that vasospasm and neuronal injury may not correlate, and that different genetic factors may influence each one. Future investigations may provide invaluable insight into the causes of these inter-strain differences and potential genetic contributors.

Keywords: subarachnoid hemorrhage
vasospasm
brain injury
mouse
Advisor: Macdonald, Robert Loch
Ectopic Eruption of the Maxillary First Permanent Molar: Rate and Predictive Factors of Self-correction and Survey of Specialists Attitudes Regarding Intervention

Purpose: To retrospectively assess the incidence and predictive factors for self-correction of ectopic eruption of maxillary permanent first molars (EE) and the prevailing attitudes amongst surveyed specialists regarding intervention in cases of EE. Methods: Charts of patients diagnosed with EE were assessed for predictive clinical and radiographic factors. An online survey was sent to pediatric dentists and orthodontists. Results: The rate of self-correction was 71%. One third of self-corrections occurred after age 9. Increased amount of impaction (r(43)=0.59, p<.001) and degree of resorption (r(57)=0.41, p=.001) were positively correlated with irreversibility. Orthodontists estimated the spontaneous self-correction rate to be lower (t(1178)=19.2, p<.001) than pediatric dentists. Conclusions: One third of self-corrections occurred after 9 years of age and delaying treatment of EE may be a viable option when uncertain of the outcome. Reliable predictive factors of irreversibility of EE were identified. Differences exist between pediatric dentists and orthodontists regarding management of EE.

Keywords: ectopic eruption
survey
predictive factors
self-correction
Advisor: Andrews, Paul
Assessing Patients' and Radiation Therapists’ Perceptions of Safety in Radiation Therapy and Using a Patient-provider Collaborative Checklist to Engage Patients

Approximately 52% of cancer patients require radiation therapy during the progression of their illness. Radiation therapy is a safe procedure; however, errors may occur and have the potential to harm patients. Recent studies have looked at patient engagement as a means of preventing errors in healthcare. Through interviews and focus groups, this study looks at patients’ and radiation therapists’ current perceptions of safety in radiation therapy and whether they feel that patient engagement in the form of a patient-provider collaborative checklist can improve its safety or the perception of safety. Through workflow observations and literature reviews, a patient-provider collaborative checklist was developed. Furthermore, STAI surveys were conducted to document the progression of patient anxiety through treatment. Feedback from radiation therapists demonstrated their opinions on the usability of the final iteration of the patient-provider collaborative checklist and how it could fit into the clinical setting.

Keywords: checklist
checklist design
patient safety
radiation therapy
radiotherapy
patient engagement
anxiety
patient anxiety
STAI
clinical engineering
safety
quality assurance
qualitative analysis
thematic analysis
state trait anxiety inventory
Advisor: Milosevic, Michael
Determining the Factors Contributing to Electronic Referral System Adoption by Radiation Oncologists through User-centred Design

This study aimed to utilize usability engineering methods in order to identify facilitators and barriers to electronic referral system adoption by radiation oncologists at Princess Margaret Cancer Centre, and provide recommendations for electronic referral system design. Analyses included workflow analysis of radiation oncologists reviewing referrals, belief elicitation interviews with radiation oncologists, a heuristic evaluation of an existing electronic referral system interface, and cognitive walkthrough of that interface with radiation oncologists. Based on these findings, the system interface was redesigned using mock-up software to address identified usability issues. The existing and redesigned interfaces were compared using observational usability testing with radiation oncologists. The redesigned system interface yielded reduced task times and enhanced user satisfaction as compared to the existing interface. Thus, user-centred design was useful in determining facilitators and barriers to e-referral adoption.

Keywords: eHealth
referral
e-health
eReferral
e-referral
healthcare
clinical engineering
TAM
DOI
user centered design
UCD
usability
usability engineering
technology adoption
Advisor: Urowitz, Sara
Cafazzo, Joseph
Risk Tolerance, and the Impact of Central Executive Abilities on Dual-task Performance

Multiple Resource Theory (Wickens, 1980) has evolved over the past three decades into a four dimensional multiple resource model. Separately, central executive functioning has been investigated. Other research has examined the relationship between risk taking and behaviour. The research in this thesis aimed to address questions arising out of these theoretical approaches. An experiment was carried out to explore the impact of executive abilities, risk perception, and risk-taking behaviour on multitasking performance. Using a novel methodology it was found that executive functioning, and the way that information is presented, were each significantly related to task performance and eye gaze in a dual-task setting. Statistically significant relationships were also found between independently developed instruments of risk perception and of risky driving behaviour. The implications of these findings for theories of attentional resources, executive functions, and mental workload are discussed.

Advisor: Chignell, Mark
Design, Fabrication, and Testing of an Integrated Optical Hydrogen and Temperature Sensor

In this thesis, the details of the design, fabrication, and characterization of an optical, integrated hydrogen gas and temperature sensor are explored. The hydrogen sensor is implemented by coating a ridge waveguide with a thin layer of palladium and shows very good response time and detection response for hydrogen concentrations ranging from 0.5-4%, both of which compare very favourably to similar existing technologies. Multiple film thicknesses were tested and it was found that thinner films give a faster response time at the expense of a reduced detection response. The temperature sensor is implemented with a multi-mode interferometer coupled ring resonator and has a sensing range of 100 K with good sensitivity. Both sensors are fabricated on a silicon-on-insulator platform and could easily be integrated together onto a single chip as part of an optical nose technology that would have the ability to sense multiple environmental factors simultaneously.

Keywords: Hydrogen Sensor
Palladium
Temperature Sensor
Optical Nose
Advisor: Aitchison, J. Stewart
The Role of Amygdala Cholecystokinin and Parvalbumin Expressing Neurons in the Acoustic Startle Reflex in Mice

Parvalbumin (PV) and cholecystokinin (CCK) proteins are found in the basolateral amygdala nuclei, particularly in gamma-aminobutyric acid (GABA) interneurons. PV+ neurons were localized to the basolateral amygdala and they expressed the GABA neuron marker glutamic acid decarboxylase (GAD). Here, we used Cre recombinase mouse lines to induce expression of mutant muscarinic inhibitory (hM4D) and excitatory (hM3D) receptors on PV+ or CCK+ neurons. Activation of the mutant receptors with clozapine-n-oxide (CNO) was used to measure how amygdala neural changes affect the acoustic startle reflex (ASR). Excitation of amygdala PV+ neurons potentiated the ASR. Activation of basolateral amygdalar CCK+ neurons potentiated the ASR and caused seizures, possibly by activating glutamate CCK+ neurons. The CCK+ subset of GAD neurons were targeted with a new triple transgenic mouse line (Dlx5-flpe/CCK-Cre/FrePe) to show that most CCK+ neurons were GAD negative. These findings are compared with optogenetic approaches to target specific neuronal populations.

Keywords: acoustic startle
parvalbumin
cholecystokinin
pharmacogenetics
Advisor: Yeomans, John S.
Identifying Novel MicroRNA Enhancers of Somatic Cell Reprogramming

In addition to the well-characterized Induced Pluripotent Stem cells (iPSCs) that closely resemble Embryonic Stem cells (ESCs), a recent study has proven the existence of a stable state, resembling partially reprogrammed cells, termed F-class iPSCs. To study these distinct iPSC states, a reprogramming dataset has been generated, featuring the parallel analysis of multiple molecular platforms. MicroRNAs (miRNAs) are small RNA regulators of gene expression whose critical role in reprogramming is now being realized. In the present study, small RNA deep sequencing data from this novel reprogramming dataset was used to identify miRNAs that are likely to enhance reprogramming by detecting significantly up-regulated miRNAs in ESC-like iPSCs versus F-class iPSCs. These candidate miRNAs were cloned and overexpressed in reprogramming mouse embryonic fibroblasts and their effect on reprogramming efficiency was measured. miR-214 was discovered to increase iPSC generation efficiency, marking the first reprogramming-related role for this microRNA.

Keywords: Induced Pluripotent Stem Cell
MicroRNA
iPSC
Reprogramming
miRNA
miR-214
Advisor: Nagy, Andras