VictorJuiz/thesis huggingface dataset:
Effects of Replacing Animal Protein with Plant Protein on Glycemic Control in Individuals with Diabetes

The objective was to conduct a systematic review and meta-analysis (SRMA) of randomized controlled trials (RCTs) to assess the effect of replacing animal with plant protein on glycemic control in diabetes and to perform a cross-sectional study using baseline data from 5 RCTs to assess the relationship between replacing animal with plant protein on HbA1c in type 2 diabetes. The SRMA of 12 trials (n=240) showed diets emphasizing replacement of animal with major plant protein sources significantly lowered HbA1c, fasting glucose and fasting insulin compared with control diets. Our cross-sectional study (n=627) showed substitution of animal with plant protein was not associated with HbA1c change. Overall, the results suggest that replacement of animal with plant protein leads to modest improvements in glycemic control in diabetes, however research is needed to address the limitations of our SRMA and lack of agreement with the associations seen in our cross-sectional study.

Keywords: Animal protein
Diabetes
Glycemic control
Plant protein
Advisor: Sievenpiper, John L
Jenkins, David JA
Hippocampal Neurogenesis Leads to the Erasure of a Cocaine Conditioned Place Preference

Newborn neurons are generated in the hippocampus during adulthood. Little is known however about the functional role of these new neurons. Previous research proposed that ongoing neurogenesis clears established memories from the hippocampus (Frankland et al., 2013). Consistent with this, we recently found that high rates of neurogenesis induce forgetting of hippocampus-dependent spatial and fear memories (Akers et al., 2014). These tasks were all aversively-motivated. To test whether neurogenesis-mediated forgetting generalizes to appetitively-motivated, hippocampus-dependent memories, here we used a cocaine place preference paradigm. We found that increasing neurogenesis (by voluntary exercise) before training did not impact the acquisition of cocaine place preference. However, increasing hippocampal neurogenesis after training weakened an established cocaine place preference memory. This series of studies provides insight to the temporal impact of neurogenesis and suggests a possible link between exercise and memory functioning.

Keywords: Addiction
Cocaine
CPP
Forgetting
Memory
Neurogenesis
Advisor: Frankland, Paul W
Structural Effects of Biodiesel on Soot Volume Fraction in a Laminar Co-flow Diffusion Flame

An experimental study was performed to determine the structural effects of biodiesel on soot volume fraction in a laminar co-flow diffusion flame. These include the effects of the ester function group, the inclusion of a double bond, and its positional effect. The soot volume fraction and temperature profiles of a biodiesel surrogate, n-Decane, 1-Decene, and 5-Decene fuels were measured. Improvements were made to existing laser extinction and rapid thermocouple insertion apparatus and were used to measure soot volume fraction and temperature profiles respectively. Flow rates of each fuel were determined in order to keep the temperature effects on soot negligible. Using n-Decane as a baseline, the double bond increased soot production and was further increased with a more centrally located double bond. The ester function group containing oxygen decreased soot production. The order of most to least sooting fuels were as follows 5-Decene > 1-Decene > n-Decane > Biodiesel Surrogate.

Keywords: biodiesel
double bond
laser extinction
methyl ester
soot
Advisor: Thomson, Murray J
Utilizing APEX2 to Identify Folding Factor Interactions in the Endoplasmic Reticulum

Protein (cargo) undergo folding and isomerization in the endoplasmic reticulum (ER) with help from various folding proteins and chaperones. There is little knowledge of the interactions between a cargo and its folding factors and even less is known about whether these folding partners change as a function of time and/or context or whether the folding factors differ from cargo to cargo. APEX2 is an engineered monomeric peroxidase reporter capable of catalyzing biotinylation of nearby proteins when activated using peroxide in the presence of biotin-phenol. APEX2’s activity has been established in the mitochondria, so we developed a molecular tool to help identify cargo-protein interactions in the ER. Preliminary labeling work was performed using a fusion protein of APEX2 and albumin that demonstrated robust biotinylation activity in the ER. Our data suggests APEX2 is highly active in the ER and with careful manipulation; this method has the potential to help fill the large gap in knowledge of protein folding.

Keywords: albumin
APEX2
cancer
endoplasmic reticulum
protein folding
proximity dependent labeling
Advisor: Koritzinsky, Marianne
Development and Assessment of an Interactive Training Tool to Help Reduce Error Rate Associated With Shared Infusion Volume Management Tasks

Nurses often do not understand nor consider the presence of shared infusion volume (SIV) in their practice and there are currently no explicit training methods to address this issue. This research aimed to design and assess an effective interactive training tool (ITT) to help improve a clinician’s ability to deal with SIV management. Recommendations from a heuristic evaluation and two cycles of usability testing helped develop an ITT in the form of a computer-based module. A cognitive task analysis elicited knowledge behind the mental model that critical care nurses and anesthesiologists use when delivering intravenous (IV) infusions. In a high-fidelity simulation experiment, participants performed significantly better for both skill/rule-based and knowledge-based SIV tasks after using the ITT intervention in terms of theoretical comprehension and practical performance. Results of this work can help guide the development of ITTs to address medical administration errors in the context of multiple IV infusions.

Keywords: Cognitive Task Analysis
Human Factors
Interactive Training Tool
Multiple Intravenous Infusions
Shared infusion volume
Usability Testing
Advisor: Trbovich, Patricia
Quantification of Vertebral Trabecular Bone Strain Via Feature Based Image Registration

Image based strain measurement within whole bone structures can be used to better understand fracture risk under load. This project aims to apply feature registration algorithms to measure strain using µCT images of vertebral trabecular bone. It is hypothesized that the unique topology of the vertebral trabecular structure can be used to extract reliable feature points that can be registered to produce higher resolution strain fields compared to traditional digital volume correlation (DVC) techniques. A validation study comparing Scale Invariant Feature Transform and Skeletonization approaches for feature registration and Thin Plate Spline interpolation and Meshless Methods approximation for strain calculation was conducted. Using an ideal 2% linearly increasing strain field, the Skeletonization with Meshless Method approach yielded the best performance, with an accuracy of -405µstrain and a detection limit of 1210µstrain, similar to standard DVC performance. A hybrid feature/DVC registration algorithm may further improve the ability to measure vertebral strain.

Keywords: Feature Registration
Image Registration
Meshless Method
microCT
Strain
Trabecular Bone
Advisor: Whyne, Cari
Mechanical Properties of Graphene Oxide Infiltrated Carbon Nanotube Fibers

In this study, graphene oxide (GO) was infiltrated into the CNT fibers (i.e. voids infiltrated into the CNT fibers (i.e. voids infiltrated into the CNT fibers (i.e. voids within CNT bundles ~ 50 nm in diameter) to interlock and improve the interfacial shear strength of the fibers. GO was was selected instead of polymers due to its higher mechanical properties, similar carbon-based structures as the CNT fibers, and high temperature stability. GO particles with a diameter of approximately 50 nm, which match closely to the void size within fibers, have been found to be optimal for enhancing the mechanical properties of fibers. Tensile testing demonstrated that the optimized GO infiltrated CNT fibers exhibit improvement in stiffness, yield strength, ultimate tensile strength, and energy to failure of pristine CNT fibers of ~100%, ~110%, ~56%, and 30%, respectively.

Keywords: CNT
fiber
GO
Infiltration
Advisor: Filleter, Tobin
Linking the Teneurin-latrophilin Interaction with Glucose Metabolism: Role of the teneurin C-terminal Associated Peptide (TCAP)-1

A newly discovered neuropeptide called teneurin C-terminal associated peptide (TCAP) exists in four isoforms, and is functionally related to its proprotein ‘teneurin’. TCAP-1 is expressed as a separate mRNA distinct from teneurin-1 and its mature peptide binds to the latrophilin (LPHN) G-protein coupled receptors (GPCRs) and associates with β-dystroglycan, to activate a neurotrophic-like signal cascade, stimulating energy production and regulating cytoskeletal development. I found reduced levels of diacylglycerol (DAG), but not inositol triphosphate (IP3), in TCAP-1-treated hippocampal cells, indicating that TCAP-1 may downregulate the LPHN pathway. Immunocytochemical analyses show TCAP-1 co-localizes with LPHN-1 in hippocampal cells. I also confirm the endogenous mRNA expression of LPHN-1 and -3, and all four teneurins and TCAPs in mouse hippocampal and hypothalamic cells. An in vivo approach established that TCAP-1 significantly reduces serum glucose levels in diabetic rodents. Thus, the teneurin/TCAP-1-LPHN interaction may strengthen synapse formation and increase brain glucose utilization during stressful conditions.

Keywords: latrophilin
metabolism
neuropeptide
stress
synapse
teneurin
Advisor: Lovejoy, David A
Lines of Dissent: Representing Pipeline Resistance in Corporate Canadian Print Media

The Enbridge Line 9 reversal is part of a national development plan to expand Canada’s underground pipeline network that extends outward from Alberta’s tar sand epicentre, an industrial project dedicated to the extraction of the most carbon-intensive oil in the world. This research draws on insights gained from the fields of critical geography, political economy, and critical media studies to undertake a critical discourse analysis of the systemic articulations of grassroots Line 9 resistance generated by corporate Canadian print media, and the discursive regulation of political dissent. Representations are juxtaposed with insights offered by three key activists involved in anti-Line 9 campaigns in Toronto. I argue that the contestation of material forms of political engagement, the intersection of private property and embodied resistance, and the depoliticizing effects of militarized constructions of activism, operate as environmental governance technologies that may work to narrow or discourage civic participation in pipeline resistance efforts within a neoliberal state threatened by climate change.

Keywords: Anti-pipeline activism
Climate change
Environmental Justice
Neoliberalism
Political dissent
Print media
Advisor: Zoric, Terezia
Mathematical Modeling of the Solid-liquid Extraction of Phenolic-rich Compounds from Pinus contorta Bark

There is an ongoing effort to replace traditional wood adhesives with tree bark-derived resins that use an underutilized biomass residue (tree bark) to reduce the consumption of petroleum-derived chemicals for economic and environmental benefits. A key step in bark-to-resin conversion involves the reactive solid-liquid extraction of phenolic-rich compounds from bark by a caustic solvent. Despite significant work concerning bark conversion, efforts to understand this process were mostly empirical investigations. Therefore, this thesis focuses on developing mechanistic models for the solid-liquid caustic extraction and comparing theoretical predictions with experimental data. Among five types of kinetic behaviour models, it was found that the extended Fick’s law most accurately described the process. Isotherms were proposed to model equilibrium, which was found to have the best fit with the BET isotherm. This thesis work provided valuable insights into the extraction process mechanism that will help with future improvement in equipment design and scaling-up studies.

Advisor: Farnood, Ramin R.
Yan, Ning
Trends in Right Ventricular Dysfunction, Tricuspid Valve Regurgitation and their Differential Impact on Survival for Children with Single Right Ventricle Physiology: The Utility of Multiphase Mixed Model Regression

Objective: Single-ventricle palliation of hypoplastic left heart syndrome (HLHS) depends on right-ventricle (RV) and tricuspid-valve performance. We describe time-related trends in RV dysfunction, TR and their association with survival. Methods: RV dysfunction and TR were evaluated from postoperative echocardiograms (5450), for 515 children with HLHS. Nonlinear mixed-models characterized time-related prevalence of ≥moderate RV dysfunction and TR. Their impact on survival was determined via parametric-hazard models. Results: The peak-prevalence ≥moderate RV dysfunction was 11% 4-months post–stage-1. By 6-years,

Keywords: Congenital heart surgery
critical left ventricular outflow tract obstruction
longitudinal data analysis
single ventricle
tricuspid valve regurgitation
ventricular dysfunction
Advisor: McCrindle, Brian W.
Caldarone, Christophder A.
The Impact of Collaborative Computer-mediated Communication on the Emergence of Voice and the Improvement of Overall Writing Quality of L2 Learners

This study explored the effects of collaborative Computer-mediated Communication (CMC) on acquiring voice and improving writing quality in English as a second language (L2) writing. This thesis is conceptually grounded in applications of socio-cultural theory to language learning (Vygotsky 1978, 1981). Data were collected from 35 L2 students studying English for Academic Purposes as part of a bridging program in an Ontario university. The data included writing samples over three iterations during 13 weeks of both face-to-face collaborative writing and collaborative CMC, interviews with a subsample of students, and a Technology Satisfaction Questionnaire. The focus of analysis was on changes in the quality of voice in the students’ English writing over time. There was a change in voice intensity in their writing over the course of the study; the use of the collaborative CMC was related to this change. Implications are recommended for teachers, students, and further research.

Keywords: Computer-mediated communication
educational technology
L2 learning
socio-cultural theory
voice
writing
Advisor: Cumming, Alister
Pass it On: An Evaluation of a Sexualized Violence Prevention Program for Middle School and High School Students

Sexualized violence is a growing problem among middle school and high school students, exacerbated by the proliferation of social media and technology. A group of community members and university researchers created the Pass it On program using feminist definitions and bystander frameworks to address this problem. This program was implemented in two waves, with three middle school and three high school male-only groups in the Thames Valley District School Board in London, Ontario, Canada. After the five-week program, high school participants showed significant positive change in both bystander and victim blaming attitude measurements. Both groups of participants showed significant positive change in knowledge about bystander intervention. Due to test version interaction, results about bystander beliefs could not be assessed. Results indicate that there were no significant changes in most attitude, knowledge, and belief measurements about sexualized violence in both age groups. Limitations and future directions of this program are discussed.

Advisor: Scott, Katreena
Forming Judgments and the Influence of Grouping Items

This study examined the judgment strategies used by doctoral students to self-assess their research skills, and the effects of questionnaire item grouping (thematic versus random) on the selection of those strategies. Self-identification of researcher type (quantitative versus qualitative) was also evaluated. A cognitive interview approach using “think aloud” and retrospective probing protocols were used with a two-group (control/random and item-grouped) design. Findings revealed participants used one main and at least one supporting judgment strategy to formulate their self-assessment. The authors found no evidence that item grouping affected strategy selection. Item grouping did seem to influence assessment accuracy on quantitative research skills, mediated by participants’ researcher type (qualitative or quantitative researcher)

Keywords: Cognitive interview
Item-grouping
Judgments
Self-assessment
Advisor: Lam, Tony C
Systematic Review of the Cost-effectiveness of Influenza Immunization Programs: A Canadian Perspective

In Canada, currently no national seasonal influenza immunization program exists. To better inform policy, the cost-effectiveness of influenza immunization programs was examined. Using a best-evidence synthesis approach, 31 economic evaluations were reviewed. Subgroups emerged from the literature, including pregnant and post-partum women, children, and healthy adults. Generally, from the societal and healthcare system perspective, vaccination was cost-effective. For pregnant and post-partum women, vaccinating all versus only high risk was cost-effective. For children (6 months to 18 years), vaccinating all versus only high risk was cost effective, especially for infants, toddlers, and adolescents. For healthy working age adults (19 to 64 years), results were mixed, and sensitive to vaccine efficacy, uptake, and productivity loss. For adults with co-morbidities and healthcare workers, vaccination was cost-effective. In Canada, six provinces (AB, SK, MB, ON, NS, NL) and all territories offer universal programs as of 2014. Three provinces (BC, QC, NB) offer programs targeting high risk groups only.

Advisor: Ungar, Wendy
A Qualitative Investigation into the Decision Making Patterns of Community Pharmacists

Abstract Context: There is a lack of literature describing the reasoning strategies utilized by pharmacists. Given the increasing complexity of pharmacists’ work this is a concern for pharmacy educators, regulators, employers and other stakeholders, including patients. Purpose: The purpose of this study was to undertake preliminary research into clinical problem solving strategies utilized by pharmacists. Design, Setting and Participants: 12 pharmacists were studied who had experience in community pharmacy in the Greater Toronto Area. Methods: Using qualitative data collection and analysis techniques, participants’ responses to clinical case studies involving professional practice situations were evaluated. Results: Managing cognitive dissonance between pharmacists’ conflicting identities was a primary motivation for responses to clinical cases. Participants predominantly relied upon three specific reasoning/problem-solving tactics: educating/relationship building, seeking advice/deferring to other professionals, and “following the rules”. Conclusion: The data suggest that there is value to further education in the area of clinical reasoning and problem solving.

Keywords: clinical reasoning
decision making patterns
pharmacy
qualitative research
think aloud
Advisor: Austin, Zubin
A Dynamic Approach to Sensor Network Deployment for Target Detection in Unstructured, Expanding Search Areas

This thesis presents a novel dynamic deployment strategy for a network of static sensors using a probability model of target motion to detect un-trackable targets. The focus herein is on the dynamic and optimal deployment of the static sensor network. The network nodes are determined at regular time intervals throughout the search based on available real-time information. Optimality is achieved based on maximizing the probability of finding the target through the use of the novel iso-cumulative curve. It is adaptable to terrain variation, presence of obstacles, and can be re-calculated whenever target information, like a clue, is found to re-locate search effort. Simulations showed that the proposed methodology increases the success rate of target interception and reduces the mean detection time compared to uniform coverage-based approaches. In addition, the methodology was applied to a wilderness search and rescue scenario, where static sensors assisted mobile sensors in intercepting a target.

Keywords: Deployment
Static Sensors
Target Detection
Advisor: Benhabib, Beno
Nejat, Goldie
Does Conservation Account for Splicing Patterns?

A computational model is presented that predicts absolute (though not tissue-differential) percent-spliced-in of cassette exons more accurately than previous models. Nearly identical performance is achieved using only the conservation score (mammalian phastCons) of each splice junction normalized by average conservation over 100 bp of the corresponding flanking intron. Evidence is provided that splicing regulation occurs predominantly in these averaging regions, and that conserved elements there are splicing regulators, predominantly inhibitors. Among conserved cassette exons, increased conservation of flanking introns is associated with reduced inclusion, suggesting one mechanism for the evolutionary transition from constitutive to alternative splicing is the emergence of cis-acting splicing inhibitors. A new definition is proposed for intronic splicing regulatory elements (ISREs) that is independent of conservation. Most ISREs do not match known binding sites or splicing factors despite being predictive of percent-spliced-in, suggesting the existence of novel RNA-binding proteins and novel splicing roles for known RNA-binding proteins.

Keywords: alternative splicing
evolutionary conservation
neural networks
Advisor: Frey, Brendan
Comparing Techniques for Classifying Patients with Schizophrenia and Healthy Controls using Machine Learning and Magnetic Resonance Imaging

Schizophrenia and related psychoses are debilitating mental illnesses that are associated with an abnormal neuroanatomical phenotype on magnetic resonance images. Machine learning is a powerful statistical tool that can recognize unique feature patterns in data and use this information to perform class separation in unseen instances. This study explores the effect of machine learning algorithm selection, dataset characteristics, and feature choice on classification performance within a rigorous validation framework. Specifically, penalized logistic regression, support vector machines, and linear discriminant analysis are compared using three large, independently-collected datasets with multiple neuroanatomically-based features. This study replicates existing studies in the literature, and provides a direct comparison of techniques within a systematic structure. Additionally, this study illustrates many of the challenges inherent to performing patient classification, and aims to establish a benchmark for future studies in the field.

Keywords: Classification
Cortical thickness
Machine learning
Magnetic resonance imaging
Schizophrenia
Voxel-based morphometry
Advisor: Chakravarty, Mallar