VictorJuiz/thesis huggingface dataset:
Exploring the impact of the ECHO model™ in Ontario on primary healthcare providers sharing of chronic pain knowledge: A qualitative study

ECHO Ontario Chronic Pain/Opioid Stewardship (ECHO Ontario Pain) is a telehealth platform, which supports healthcare providers (HCPs, spokes) to manage patients with chronic pain in their communities, using specialists (hub). ECHO Ontario Pain is using this model to address challenges, such as dealing with a lack of knowledge about chronic pain and inappropriate opioid prescribing practices. Thirteen qualitative semi-structured interviews were conducted with HCPs from the program. Four themes developed: (1) experiences with chronic pain management before joining ECHO, (2) learning and sharing in the program, (3) the use of technology, and (4) recommendations for improvements. ECHO Ontario Pain was a novel way to provide education by demonstrating the effectiveness of participating in an online learning model. The study highlights the value of different learning approaches and how they affect HCPs interactions with their patients, their practices, and their wider community. Overall, these findings complement and add to existing ECHO research.

Keywords: Chronic Pain
eLearning
Knowledge Dissemination
Online Learning
Primary Care
telehealth
Advisor: Stinson, Jennifer
Seto, Emily
MiR-139 is a Predictor of Prostate Cancer Recurrence and Regulates Cancer Aggressiveness by Targeting IGF1R

MiR-139 expression is significantly decreased in prostate tumours with an increased risk of recurrence and metastasis. We investigated the function and mechanism of miR-139 action in prostate cancer cells. Cell-based assays demonstrated that miR-139 decreased the proliferation and migration capabilities of prostate cancer cell lines. Luciferase assays indicated that miR-139 directly targeted IGF1R 3’UTR. This was confirmed through immunoblotting showing decreases in IGF1Rβ protein expression in miR-139 overexpressing cell lines. MiR-139 overexpressing cells exhibited a G2 cell cycle arrest and increased senescence. The induction of senescence was accompanied by decreased phosphorylated AKT and ERK proteins and increased p21 protein expression. Our results indicate that miR-139 decreases IGF1R expression, which prevents activation of downstream kinases AKT and ERK, leading to increased p21 expression concomitantly with senescence. This may represent a novel mechanism of growth suppression induced by miR-139 in prostate tumours.

Keywords: IGF1R
miR-139
miRNA
p21
prostate cancer
senescence
Advisor: Seth, Arun K
Development of a Single-Cell Optical Control Technique

Our brain encodes information via patterns of action potentials (APs) produced by neurons, referred to as the neural code. Studies of the neural code have shown two methods of information encoding: rate codes and temporal codes. Two of the major classes of interneurons in the neocortex, parvalbumin positive and somatostatin positive interneurons, have properties that may enable them to specialize in temporal and rate codes, respectively. However, the technology required to study neural code specializations has been out of reach until recently. In this thesis, I developed a system to use a digital multimirror device for patterned optogenetic stimulation. I demonstrate the system’s ability to control APs in individual neurons at physiologically realistic rates. Additionally, I demonstrate that in vivo-like patterns can be created for presynaptic activity in specific interneuron types in ex vivo brain slices. This system can be used in future studies of neural code specialization by interneurons.

Keywords: Digital Multimirror Device
Electrophysiology
Neural Code
Optogenetics
Patch Clamp
Single Cell Control
Advisor: Richards, Blake
Designing the HCI Living Curriculum

The Association for Computing Machinery (ACM) Special Interest Group on Computer-Human Interaction (SIGCHI) has been supporting research into Human-Computer Interaction (HCI) education for many years, most actively in the last six years. This thesis proposes the preliminary framework for a Community of Practice (CoP) of HCI scholars and educators, sharing and collaborating to develop teaching materials. Two studies were carried out. The first involved a set of 12 interviews with HCI educators and practitioners that examined requirements for the HCI Living Curriculum. The second study was a questionnaire with 28 respondents which carried out further requirements analysis. Based on the findings of the two studies, use cases and design requirements for the HCI Living Curriculum are presented. Guided by these use cases and design requirements, a prototype HCI Living Curriculum was then constructed. The thesis concludes with a discussion of lessons learned and prospects for future development of the Living Curriculum.

Keywords: HCI
HCI education
living curriculum
Advisor: Chignell, Mark H
Mortality and Morbidity in Office-Based Deep Sedation and General Anaesthesia for Dentistry in Ontario

Objectives: To estimate the prevalence of mortality and serious morbidity for office-based deep sedation and general anesthesia (DS/GA) for dentistry in Ontario from 1996-2015. Materials Methods: Data were collected retrospectively in two phases. In Phase I, cases involving injury or death for dentistry under DS/GA, sourced from the Chief Coroner of Ontario and the Royal College of Dental Surgeons of Ontario were reviewed. Phase II involved a survey of all registered providers of DS/GA where they estimated the number of DS/GA administered. Prevalence was calculated using Phase I and Phase II findings. Results: The estimated prevalence of mortality is 0.8 deaths per 1 million cases, and the estimated prevalence of serious morbidity is 0.25 per 1 million cases. Conclusions: The mortality and morbidity rates found in this study fit within the lower end of the range of mortality and morbidity reported by similar studies for office-based DS/GA in dentistry.

Keywords: dental anaesthesia
dental anesthesia
mortality and morbidity
office-based anesthesia
Advisor: Quiñonez, Carlos R
How Sequencing Affects Remembered Technical Quality for Viewed vs. Visualized Video Impairments

In this thesis I examine how memories of experience affect overall ratings of technical quality (TQ) for groups of videos. Observations of experience are time consuming, and the effects of TQ are difficult to entangle from content quality. Thus an experiment was carried out to examine how well visualized (vs. actually viewed) presentations uncover expected memory effects associated with retrospective ratings of experiences. In the within-subjects experiment, participants viewed actual videos in some blocks of trials, and visualizations in other blocks. The experimental results showed a significant effect of negative ends and effects of linear trend. Similar sequencing effects were obtained with visualized videos as with viewed videos, although the size of sequencing effects was generally smaller with the visualized videos. These results are discussed in terms of their implication for future research on how QoE accumulates over time and ultimately shapes attitudes towards a service.

Advisor: Chignell, Mark
Mapping and Characterization of the Interaction Network of ALK Receptor Tyrosine Kinase using the Mammalian Membrane Two-Hybrid (MaMTH) Assay

Anaplastic Lymphoma Kinase (ALK) which belongs to the Receptor Tyrosine Kinases (RTKs) play a critical role in development and progression of many type of cancers. To design new treatments for ALK associated human diseases, it is essential to study the interactions of the protein to better understand the biological significance of its protein-protein interactions (PPIs) and how they contribute to ALK regulation and function. Novel high-throughput technology, the Mammalian Membrane Two-Hybrid (MaMTH), was used in this study to generate a targeted protein-protein interaction map (interactome) of full length ALK. Biased screening of 150 predicted and previously known ALK interactors were performed and 34 identified as novel ALK interactors. The active mutant cells stably expressing ALK F1245C, F1245I and L1196M have been generated which showed more phosphorylation of ALK (pALK1604) as compared to wild type. Moreover, these active mutants exhibited more phosphorylation of downstream signaling ERK1/2 as compared to wild type.

Advisor: Stagljar, Igor I
Establishing Performance Limits at Ages that Are Appropriate for SCM Concretes

Early-age transverse cracking of High-Performance Concrete (HPC) bridge decks has become of a major concern to the Ministry of Transportation Ontario (MTO). However, the MTO’s early-age performance requirements result in suppliers and contractors using silica fume and increasing the total cementitious materials contents, making the HPC mixtures more susceptible to cracking problems. Also, the MTO’s 28-day performance limits do not provide an appropriate indication of the quality of these concretes which contain supplementary cementitious materials (SCMs). Therefore, this study investigates the statistical relationship at 28 and 56 days of age for concrete strengths and permeability ratings to determine the minimum 28-day values that would meet the MTO HPC design properties at 56 days. The results show the possibility to predict 56-day performance results based on conservative statistical analysis based on prequalification data. All test results are well within the MTO’s requirements.

Keywords: Age limits for concrete performance
concrete performance
High-Performance concrete
Permeability prediction
Resistivity correlation
Advisor: Hooton, Douglas R
Sensorimotor Integration during Rubber Hand Illusion in Normal Subjects and Subjects with Parkinson’s Disease

Rubber hand illusion (RHI) measures visuo-tactile multisensory integration. Non-motor symptoms are well recognized in Parkinson’s disease (PD) and PD patients have impaired sensation and sensorimotor integration. We hypothesized that 1) RHI decreases sensorimotor integration in healthy subjects 2) PD patients will show reduced RHI and less modulation of sensorimotor integration by RHI. We used transcranial magnetic stimulation to examine short- and long-latency afferent inhibition (SAI and LAI), which measures the influence of sensory input on the primary motor cortex (M1), and the posterior parietal cortex (PPC)-M1 interactions during RHI. In healthy subjects, we found reduced SAI and LAI during RHI, and stronger RHI correlated with greater inhibitory PPC-M1 interactions. PD patients showed normal RHI, but had no correlation between RHI strength and PPC-M1 interactions. Our results show that RHI modulates both early and late stages of sensorimotor integration in healthy subjects and this effect of RHI is altered in PD.

Advisor: Chen, Robert
Investigation of the influence of heterogeneous and anisotropic nature of rock mass on blast-induced outcomes - a case study at Detour Lake mine

Blasting is the initial stage of comminution in mining. It has significant influence on the cost and efficiency of downstream operations. A highly heterogeneous orebody requires control and minimization of blast-induced rock movement to reduce ore-loss and dilution. The objective of this study is to characterize the influence of rock mass properties on blast-induced rock movement and fragmentation. Statistical analysis of rock mass geological and geomechanical data as well as multi-year blasting data collected from Detour Lake mine, indicate that both intact rock strength and RQD can influence blast-induced rock fragmentation, however, blast-induced rock movement is only influenced by the intact rock strength. Using predictive analytics the blast-induced outcomes (fragmentation and movement) were modeled by incorporating rock mass properties and blasting parameters. Decision trees were developed which can help to achieve the desired blast-outcomes by changing the blasting parameters.

Keywords: blast-induced fragmentation
blast-induced rock movement
blasting
data analytics
rock mass characteristics
statistical analysis
Advisor: Esmaeili, Kamran
Mohanty, Bibhu
‘Get Out’ White Supremacist Projects: Racialization and Anti-Blackness

For my thesis, I will be using Jordan Peele’s movie, ‘Get Out,’ as the centre for my analysis on Anti-Black racism and racialization. I will discuss the ways in which the processes of racialization mask/masquerade as an intended politicalized method for perpetuating the continuity of racist violent representations of Blackness. Following this, I will highlight how this process works as an intended tool for controlling/possessing the Black body, and therefore serves as another form of colonization. To conclude, I will speak to the idea of White “injury,” which Wiegman (2007) refers to in Whiteness Studies and the Paradox of Particularity and the disavowal of White supremacy in regard to its responsibility/perpetuation and removal/negation of complacency in the project/perpetuation of Anti-Black racism.

Advisor: Wane, Njokie
Dei, George
Successive Cancellation List-Based Latency and Computational Complexity Reduction for Polar Codes

Polar codes provide a promising new direction in channel coding that is expected to play a vital role in 5G wireless cellular communication systems. Successive cancellation list (SCL) decoding, as a widely adopted decoding scheme for polar codes, sacrifices decoding complexity and latency to improve error performance. To address the shortcomings of SCL, a decoding complexity and latency reduction technique, denoted bit skipping and verified to be applicable for most list decoders, is proposed in this thesis. By bypassing unnecessary sorting operations, bit skipping reduced the decoding complexity, for a half rate code, by 27.2% while increasing throughput by 19.1%. A hybrid decoder for decoding complexity reduction was also proposed and was shown to reduce the decoding complexity by up to 97.8% under favorable channel conditions.

Keywords: bit skipping
hybrid decoding
list decoding
polar codes
successive-cancellation decoding
Advisor: Sousa, Elvino S
Nicotinamide Mononucleotide in the Context of Elevated Plasma Levels of Free Fatty Acids Improves Glucose Tolerance by Decreasing Insulin Clearance

The NAD-dependent deacetylase SIRT1 has been shown to be beneficial to beta cell function. Nicotinamide Mononucleotide (NMN), the product of the rate-limiting enzyme in NAD synthesis, has recently been shown to have positive effects on glucose tolerance in mice fed a high fat diet. This is the first study to examine the effects of NMN on insulin clearance and FFA-induced beta cell dysfunction. NMN was i.v. infused, with or without oleate, in C57BL/6 mice over 48h in order to elevate intracellular NAD levels and consequently increase SIRT1 activity. We demonstrated that administration of NMN in the context of elevated plasma FFA levels results in a significant decrease in insulin clearance as well as partial protection against FFA-induced beta cell dysfunction in vivo. This culminated in a large improvement in glucose tolerance. In summary, NMN may have a therapeutic potential to improve glucose tolerance in conditions of increased plasma FFA levels, which is typical in patients with type 2 diabetes mellitus.

Keywords: beta cell dysfunction
insulin clearance
lipotoxicity
nicotinamide mononucleotide
SIRT
type 2 diabetes
Advisor: Giacca, Adria
Once Daily Aminoglycoside Pharmacokinetics and Optimal Tobramycin Dosing in the Burn Population: A Prospective Study

Background. Once-daily aminoglycoside (ODA) dosing is not commonly recommended in burn patients due to altered pharmacokinetics (PK). The objective was to determine the ability of ODA dosing to achieve target concentrations in burn patients. Methods. A single dose of tobramycin 10 mg/kg was given to patients with a total burn surface area (TBSA)

Keywords: burn
once daily aminoglycoside
pharmacokinetic
tobramycin
Advisor: Walker, Sandra
Walker, Scott
The Impact of Adult Heatlh Care Model (Academic versus Community) on Emergent Health Resource Utilization in Patients with Pediatric-onset Inflammatory Bowel Disease

Background: Patients diagnosed with Inflammatory Bowel Disease (IBD) during childhood require transfer to an adult gastroenterologist. Purpose: The purpose of this study was to determine the impact of post-transfer health care setting (academic vs. community) on emergent health resource utilization. Methods: This was a population-based retrospective cohort study using health care administrative data from Ontario, Canada. Patients with PO-IBD were identified and health resource utilization during a 2-year pre-transfer period, transfer of care period and 2-year post-transfer period was analyzed. Comparator groups included academic vs. community vs. loss-to-follow-up. The primary outcome comprised Emergency Department (ED) utilization. Secondary outcomes included hospitalizations, surgeries, ambulatory visits, endoscopic and radiological investigations. Results: There were no significant differences found in ED use, ambulatory care visits (aside from the lost to follow-up group), hospitalizations, endoscopic or radiological procedures. Conclusion: Post-transfer healthcare setting does not impact emergent health resource utilization in the post-transfer period..

Keywords: Health Resource Utilization
Inflammatory Bowel Disease
Transition
Advisor: Nguyen, Geoffrey C
The Development and Characterization of VX-770 Molecular Probes

Cystic fibrosis is the most common genetic disease affecting the Canadian population. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, and there is currently no cure. In 2012, VX-770 became the first FDA approved drug targeting the genetic defects of CF; its binding site and mechanism of action are currently unknown. In the present study, we studied the structure-function relationship of VX-770. We determined the structural components that are critical for activity and identified a position on the structure that could be modified without compromising its effects. These findings led to the generation of VX-770-Biotin and VX-770-Rhodamine. Subsequent testing of the two molecular probes suggests that they both retain properties of the parental drug VX-770. Hence, VX-770-Biotin and VX-770-Rhodamine may be used to provide further insight into the VX-770 binding site and mechanism of action, enabling the design of more effective drugs for CF therapy.

Keywords: CFTR
cystic fibrosis
potentiator
Advisor: Bear, Christine E
Design & Validation of a Hybrid-capture Next-generation Sequencing-based T-cell Clonality Assay

This project details the development of a novel NGS-based T-cell clonality assay, incorporating all four TcR loci. The assay was both analytically and clinically validated. For the former, a series of idealized specimens was used, with combined PCR/Electrophoresis and Sanger Sequencing to confirm NGS-data. The latter validation compared NGS results to the current gold standard for clinical T-cell clonality testing (i.e. the BIOMED primer PCR-based method) on an appropriately-sized minimally-biased sample of hematopathology specimens. In the latter dataset, the patterns of T-cell clonality were also correlated with clinical, pathologic, and outcome data.

Keywords: bioinformatics
clonality
gene rearrangement
lymphoma
t-cell receptor
validation
Advisor: Kamel-Reid, Suzanne
Characterization of Voltage-gated Calcium Channel CaV2.1 in the Chicken Nervous System

Transmitter release is gated primarily by P-type voltage-gated calcium channels (CaV2.1) at most mammalian synapses, while N-type (CaV2.2) channels play a lesser role. While this is also true in some lower vertebrates curiously in synapses in the chicken transmitter release appears to be gated almost exclusively by CaV2.2 channels (Stanley and Goping, 1991). Our objective is to resolve this dichotomy and in this study we have used a cloning approach to look for, and characterize the primary molecular structure of chick CaV2.1. RT-PCR applied to chick whole brain cDNA generated a full length CaV2.1 sequence. Interestingly, while the channel includes the transmembrane domains, the C-terminal is truncated and lacks a typical DxWC terminus. While we cannot as yet conclude any functional details about the channel, we do show that it is expressed in the chicken nervous system in some capacity.

Advisor: Stanley, Elise
Integrated Asymmetric Hybrid Plasmonic Waveguides and Devices

Long-range hybrid plasmonic modes with optimal loss-confinement trade-off are enabled in asymmetric waveguides irrespective of material or structural symmetry by engineering conditions for electric field matching. A field-symmetric superposition of coupled hybrid and SPP modes enable the design of asymmetric hybrid-SPP plasmonic waveguides with 0.021dB/Îźm propagation losses and 0.15Îźm^2 mode area confinement across telecom-wavelength range. Moreover, a highly efficient junction coupling of 71% between hybrid-SPP waveguides and silicon nanowires allows integration of compact plasmonic devices such as microring resonators and photodetectors into conventional silicon technologies. The performance for these passive devices are experimentally verified in samples that can be reproducibly fabricated thanks to improvements in the latest nanofabrication techniques. The unique properties of the coupling mechanism asymmetry between hybrid and SPP modes allow the potential to explore the design of both low loss optical circuits, as well as enhanced absorption for photodetection on the same platform.

Keywords: Integrated circuits
Nanofabrication
Optoelectronics
Photonics
Plasmonics
Semiconductors
Advisor: Helmy, Amr S
Survival, Treatment Patterns, and Identifying Predictors of Receipt of Adjuvant Therapy and Survival for Curative-intent Pancreatic Adenocarcinoma: A Population-based Analysis

Introduction: Pancreatic adenocarcinoma (PC) is a leading cause of cancer-related mortality in North America. Methods: This study was conducted as a retrospective observational cohort trial of patients undergoing resection of PC in the province of Ontario, Canada between 2005-2010. The study involved linkage of administrative datasets, and abstraction of resection specimen pathology reports. Overall survival (OS) and receipt of adjuvant treatment were the primary outcomes in this study. Adjuvant treatment was classified as chemotherapy (CT) or chemoradiation therapy (CRT). Results: While adjuvant CT or CRT were not associated with improved OS, those with node-negative disease benefited from adjuvant CT. Histopathologic factors were the strongest prognostic factors. Substantial variation in the likelihood of receiving adjuvant treatment between different institutions treating PC was identified. Residential instability, material deprivation, rurality, and median income were associated with receipt of surgery among PC patients. Conclusions: Outcomes following resection are primarily determined by tumour biology.

Keywords: Adjuvant treatment
Marginalization
Outcomes
Pancreatic cancer
Population
Advisor: Coburn, Natalie
Expression of Clostridium acidurici 9a Glycine Cleavage System in Escherichia coli for Formatotrophic Growth via Reductive Glycine Pathway

There has been a marked increase in carbon dioxide levels in the atmosphere over the years, presenting countries with the task of reducing the emissions. This drives the motivation of discovering methods to fix carbon dioxide into valuable commodities. Microorganisms can be engineered to express pathways that do not exist naturally, and more efficient at providing high yields and titre of a particular product. This principle serves as the basis for this research project. A computationally designed carbon fixation pathway for growth on formate, known as the reductive glycine pathway, can theoretically produce pyruvate, a central to E. coli metabolites, through the expression of recombinant genes. The goal of the project is to test the expression of a bidirectional glycine cleavage system that has been cloned from C. acidurici 9a in E. coli, which is predicted to be a major pathway expression challenge for the reductive glycine pathway.

Keywords: Biofuel
Escherichia coli
Formate
Glycine Cleavage System
Advisor: Mahadevan, Radhakrishnan
Savchenko, Alexei