VictorJuiz/thesis huggingface dataset:
Subcellular Dynamics of RNAs and microRNAs in Mouse Embryonic and Trophoblast Stem Cells

Cell fractionation coupled to high-throughput RNA-sequencing allows for the identification of cytoplasmic and nuclear over-represented RNA populations. In mouse embryonic and trophoblast stem cells, an asymmetric distribution of protein coding RNAs were observed with respect to gene function. Cell lineage specific differences were found between population of nuclear over-represented messenger RNAs, such that embryonic stem cells showed an abundance of transcripts related to cell division, cell cycling, and DNA repair, whereas trophoblast stem cells showed an abundance of transcripts related to cell-cell adhesion, cell junction formation, and cell migration. Lineage specific processes were also found over-represented between nuclear enriched transcripts containing exon-intron junctions, suggesting intron retention may play a role in maintenance of cell identity in development. Small RNA-sequencing data showed microRNAs are related to embryonic and trophoblast lineages with association with signaling pathways. Presence of mature microRNAs in the nucleus was also identified.

Keywords: embryonic stem cells
intron retention
microRNA
RNA-seq
stem cell biology
trophoblast stem cells
Advisor: Cox, Brian
Global Climate Change Alters the Survival Potential of Freshwater Invasive Species

Global climate change is predicted to alter environments and allow some freshwater species to survive in new areas. Estimates of potentially invasive species’ survival probabilities provide valuable information for resource managers to develop effective invasion mitigation strategies. The probability of species’ survival is commonly estimated by quantifying the similarity in climates between species’ existing ranges (source region) and an area of introduction (recipient region). I quantified the climate similarity between all pairs of source-recipient global watersheds and freshwater ecoregions under historical and future climate scenarios. Results indicated climate change will alter climate similarities between source-recipient pairs with varying intensity depending on the pairing and, consequently, influence survival probabilities at a global scale. Moreover, estimates of climate similarity tended to be higher for larger spatial scales. Risk assessments of non-native species estimating survival probabilities would benefit from incorporating climate change and applying a multi-scale approach to better inform management decisions.

Keywords: Aquatic invasive species
Climate change
Climate similarity
Risk assessment
Advisor: Mandrak, Nicholas E
Drake, Andrew R
Working Memory in Action: Visual Field Differences in Transsaccadic Working Memory.

Hemispheric asymmetry has been observed in visual working memory with high levels of memory loads, specifically in that the left hemisphere is activated by memory items in the right visual field and the right hemisphere is activated by memory items in both hemifields. However, there has been prolonged deliberation as to whether there are any spatial differences, specifically in transsaccadic working memory. Recent research has argued for the presence or absence of visual field or saccade direction differences, however, because these studies do not probe working memory at minimum levels of load to see hemispheric differences, there remains a gap in whether spatial differences essentially exist. To adequately probe working memory, I employed a task that is sensitive to transsaccadic memory with a medium level of working memory load. Measures of response error were then submitted to a principal component analysis, revealing two components of transsaccadic memory and a left visual field disadvantage. My results additionally put an end to the debate, revealing that visual field differences exist across fixational as well as transsaccadic forms of working memory.

Keywords: remapping
saccade direction
saccade plane
transsaccadic memory
visual field
working memory
Advisor: Niemeier, Matthias
Hypothesis Testing in Joint Models for Longitudinal and Time-to-event outcomes

Many clinical studies collect longitudinal biomarkers known to be highly associated with a time-to-event outcome. Motivated by the problem of testing genetic association in this setting, we investigate joint models for the association of genetic variants with longitudinal measurements and time to event. We develop and validate a closed-form sample size formula for an overall genotype association in this setting, and conduct simulations to compare joint model approaches to test for direct/indirect/overall genotype associations with time to event. To improve robustness to model misspecification due to non-linearity of the longitudinal traits, we make use of spline functions to capture nonlinear subject-specific evolutions in the longitudinal process. In the simulation study, we also assess the sensitivity of inference to misspecification, and evaluate the validity and power of hypothesis tests in joint modelling. Different joint modelling approaches are implemented in an application to genetic data from the Diabetes Control and Complications Trial.

Keywords: hypothesis testing
joint modelling
longitudinal data
power determination
sample size
survival analysis
Advisor: Bull, Shelley B.
Ferric Leaching of Pyrrhotite Tailings under Controlled PH and ORP Conditions

This work investigates the direct ferric sulfate oxidative leaching of pyrrhotite tailings under controlled pH and redox potential (ORP) conditions in order to dissolve the mineral matrix, release Ni2+ into the solution, and convert the sulfide to elemental sulfur. It was found that with every 5 wt% increase in solids loading, nickel extraction kinetics and final nickel extraction levels were decreased by 5 to 10%, while 65% to 92% of the sulfur in the tailings were converted to elemental sulfur. It was concluded that hydrogen peroxide performed better than potassium permanganate in maintaining constant ORP. The effects of pH, temperature, ORP and solids loading were also studied using a two-level fractional factorial design method, from which ORP and temperature were found to have the most beneficial effects on leaching kinetics and elemental sulfur production, respectively.

Keywords: Ferric Leaching
Hydrometallurgy
Nickel
Pyrrhotite
Tailings
Advisor: Papangelakis, Vladimiros G
Evaluating the Role of Selective Daily Mobility Bias in Retail Food Environment Research

Global positioning system (GPS) devices are increasingly being used to provide insight the into retail food environment and how it might be contributing to the ongoing obesity epidemic. Concern has recently been raised about the potential for GPS-based research to over-estimate the impact that exposure to food retailers has on food behaviour. This phenomenon, where it is difficult to discern using GPS data whether an individual is passively exposed or actively seeking a space out, is referred to as a ‘selective (daily) mobility bias’ (SDMB). Using GPS-generated activity spaces from the Canada Food Study, this thesis investigates whether or not including activity locations where food purchases occur changes the association between exposure to restaurants and self-reported consumption of fast food. No significant associations were found in any of the models, but suggestions are made for adopting a biopsychosocial approach in future work that aims to address SDMB within the context of food behaviour.

Keywords: Biopsychosocial Approach
Built Environment
Food Behaviour
Geographical Information Science (GIS)
Global Positioning Systems (GPS)
Obesity
Advisor: Widener, Michael J
Investigating the Role of CDK11 in Animal Cytokinesis

Finely tuned spatio-temporal regulation of cell division is required for genome stability. Cytokinesis constitutes the final stages of cell division, from chromosome segregation to the physical separation of cells, abscission. Abscission is tightly regulated to ensure it occurs after earlier cytokinetic events, like the maturation of the stem body, the regulatory platform for abscission. Active Aurora B kinase enforces the abscission checkpoint, which blocks abscission until chromosomes have been cleared from the cytokinetic machinery. Currently, it is unclear how this checkpoint is overcome. Here, I demonstrate that the cyclin-dependent kinase CDK11 is required for cytokinesis. Both inhibition and depletion of CDK11 block abscission. Furthermore, the mitosis-specific CDK11p58 kinase localizes to the stem body, where its kinase activity rescues the defects of CDK11 depletion and inhibition. These results suggest a model whereby CDK11p58 antagonizes Aurora B kinase to overcome the abscission checkpoint to allow for successful completion of cytokinesis.

Keywords: abscission
cancer
CDK11
cell cycle
cell division
cytokinesis
Advisor: Wilde, Andrew
Antimicrobial Efficacy and Physical Properties of Root Canal Sealers loaded with Drug-silica Co-assembled Particles

Background: Endodontic sealers are intended to entomb residual bacteria and prevent reinfection of the root canal system. However, current endodontic sealers either have no antimicrobial properties or lose their antimicrobial activity after setting. Objective: To assess the effect of incorporating a novel highly-loaded antimicrobial drug-silica co-assembled particles (DSPs) on the flow and antimicrobial properties of root canal sealers. Materials: DSPs were mixed homogenously with either epoxy-resin sealer or calcium silicate-based sealer. The sealers’ antimicrobial activity against planktonic and biofilms of Enteroccocus faecalis ATCC 47077 infected dentin was investigated using in vitro tooth model. Results: DSPs had no effect on the antimicrobial properties of epoxy-resin sealer; however, it improved the antimicrobial performance of calcium silicate-based sealer throughout the 30-day experiments while maintaining the flow compliant with the ISO parameters. Conclusion: Depending on the sealer, DSPs could potentially prevent interfacial biofilm formation and proliferation, potentially decreasing the risk of persistent/secondary endodontic infections.

Keywords: Bioceramic
Endodontics
Enteroccocus faecalis
Epoxy resin
Nanoparticles
root canal sealer
Advisor: Finer, Yoav
Levesque, Celine
Investigation of Monoamine Oxidase-B Status in Alcohol Use Disorder using PET Radiotracer [C-11]SL25.1188 during Early Abstinence

Background: The dopaminergic system has been implicated in alcohol use disorder (AUD), however there is a lack of in vivo studies examining monoamine oxidase-B (MAO-B), an enzyme involved in dopamine metabolism. Based on some post-mortem brain and preclinical studies, we hypothesized that MAO-B levels would be elevated in AUD. Methods: MAO-B positron emission tomography (PET) radiotracer [C-11]SL25.1188 binding was measured in 13 AUD participants during early abstinence and 14 controls. Results: [C-11]SL25.1188 binding was not significantly different in AUD prefrontal (-13%; p=0.14) and cingulate (-16%; p=0.13) compared to controls. However, AUD subjects who smoked cigarettes (n=5) had lower [C-11]SL25.1188 binding in the prefrontal (-40%; p

Keywords: Addiction
Alcohol Use Disorder
Dopamine
MAO-B
PET
[C-11]SL25.1188
Advisor: Kish, Stephen J
Boileau, Isabelle
A Novel Polypyrrole-polyurethane Patch for Cardiac Electric Signal Restoration

Myocardial fibrosis (MF), an event that follows myocardial infarction (MI), generates fibrotic scar tissue with significantly altered electrophysiological properties. As the scar tissue matures, its resistance to incoming action potentials increases, leading to irregular cardiac arrhythmia and, eventually, sudden cardiac death. We hypothesized that a conductive acellular epicardial patch made from biomaterials would electrically synchronize isolated cardiomyocytes in vitro; an observation that is critically important to proceed to in vivo treatment applications for MF-associated arrhythmia. To address the issue, we present a novel biomaterial referred to as PPy-PCNU. The material was synthesized in a uniquely defined route, whereby solid-state conductive nanoparticles of polypyrrole (PPy) were uniformly distributed inside electrospun aliphatic polycarbonate polyurethane (PCNU) nanofibers in a controlled manner. The resulting epicardial patch was biocompatible, conductive, accelerated cellular alignment, and promoted synchronous contraction of isolated neonatal rat cardiomyocytes in vitro.

Keywords: Arrhythmia
Cardiac Fibrosis
Conductive Biomaterials
Electrophysiology
Materials Science and Engineering
Tissue Engineering
Advisor: Li, Ren-Ke
Santerre, J. Paul
Musculo-Aponeurotic Architecture of the Human Masseter Muscle: An In Vivo Study of Architectural Changes during Mandibular Protrusion and Lateral Excursion

Temporomandibular joint disorders (TMD) affect 5% to 12% of the population. Architectural changes may occur in the masticatory muscles; notably the masseter muscle (MM) in TMD. Without an understanding of the normal architecture of MM, it may be difficult to understand such changes in disease. Studies investigating the in vivo multilaminar MM architecture are scarce. The aim of this study was to evaluate the in vivo musculo-aponeurotic architecture of the superficial head of MM in asymptomatic individuals with ultrasound in excursive movements of the mandible. An ultrasound protocol was developed, and twenty-four participants’ MMs were scanned bilaterally. On protrusion and contralateral excursion, superficial laminae showed significant changes compared to the relaxed state; no significant difference was found in the deep lamina. On ipsilateral excursion, superficial and deep laminae showed significant changes. These findings suggest there are differential changes to the laminae of MM during mandibular protrusion and lateral excursion.

Keywords: aponeuroses
fiber bundle length
masseter
muscle architecture
ultrasound
Advisor: Agur, Anne MR
Dental Anatomy, Development, and Replacement in the Early Permian Hyper-carnivorous Synapsid Mesenosaurus

Pelycosaur-grade synapsids represent the first amniotes to successfully adapt to a wide range of feeding strategies, reflected by their dental morphologies. The present study investigates the dental anatomy, development, and replacement of the highly carnivorous, early Permian varanopid Mesenosaurus efremovi using morphometric, computed tomographic, and histological analyses. This study describes the level of heterodonty present in the marginal dentition of M. efremovi, confirms the presence of true ziphodonty, and demonstrates the preservation of lines of von Ebner that reflect daily dentine formation, used to estimate tooth replacement rates. Replacement rates for this varanopid synapsid are surprisingly high, ranging from 30 to 46 days, higher than in most carnivorous dinosaurs, and the first such evaluation for a Paleozoic tetrapod. This dental specialization and high replacement rate may have contributed to this taxon’s ability to be a successful mid-sized predator in the taxonomically diverse community of the early Permian carnivores. extended ecological resilience across major faunal and environmental transitions.

Keywords: Mesenosaurus
Permian
Varanopidae
Advisor: Reisz, Robert R
X-ray Imaging Practices of General Dentists in Ontario, Canada

The objective of this thesis is to determine how general dentists in Ontario currently practice oral and maxillofacial radiology. In this cross-sectional study, an email survey was sent to all general dentists in Ontario; 1,330 dentists responded (14.7% response rate). There is widespread adoption of 2D and 3D digital imaging technologies. Approximately 42.8% of dentists take an individualized approach to ordering images for new adult dentate patients. When dentists are presented with clinical case scenarios and asked to make decisions about imaging, between 18.8% and 57.2% of dentists make decisions that do not conform with established guidelines (depending on the scenario), and over-prescribe x-ray imaging far more commonly than they under-prescribe. Numerous dentist and practice factors correlate significantly with over-prescription of imaging. Changes in dental education, continuing education course offerings, and possibly regulatory requirements are needed to ensure that ionizing radiation is used appropriately in general dentistry in Ontario.

Keywords: dental radiography
radiation dosage
radiation protection
x-ray imaging technology
x-ray prescription
Advisor: Lam, Ernest WN
Environmental Sampling and Next-generation Sequencing as a Novel Approach for the Detection and Characterization of Influenza A Virus (IAV) in Swine

Current influenza surveillance systems detecting zoonotic sources such as swine, are costly and labour-intensive. The genetic diversity due to reassortment of influenza A virus in swine underscores the need for a non-invasive, population based surveillance approach to improve pandemic preparedness. Aggregate, environmental samples from agricultural settings can be analyzed using high-throughput sequencing (HTS) techniques, providing an alternative approach to classic surveillance methods for influenza viruses of public health importance. We collected environmental samples from a swine barn in Southern Ontario, Canada. All samples were analyzed by RT-PCR for detection of the matrix gene. A subset of samples were sequenced using two HTS techniques for comparison. We derived viral genomic sequence from environmental samples and identified segment diversity of IAV of swine origin. We also demonstrated that personal samplers retained IAV from the breathing zone of personnel working with swine. The feasibility of environmental sample collection underscores its utility in IAV surveillance in swine production facilities.

Keywords: Influenza
Sequencing
Swine
Advisor: Mubareka, Samira
Does the Local Application of Teriparatide Prevent Medication-related Osteonecrosis of the Jaw after Tooth Extraction in Rats?

Systemic Teriparatide treatment in patients with medication-related osteonecrosis of the jaw (MRONJ) has shown promising results in clinical studies. I hypothesized that local application of PTH (1-34) on an acellular collagen sponge (ACS) following tooth extraction would lower the incidence of MRONJ. In rat model of MRONJ, the maxillary molars were extracted then the extraction sockets were filled with ACS+PTH (1-34), ACS or left unfilled. The extraction sites were assessed clinically for bone exposure, and then underwent analysis by microCT and histology. The ACS+PTH (1-34) group had a significantly lower incidence of bone exposure and less exposed bone area (0. p

Keywords: Animal Model
bisphosphonates
MRONJ
Osteonecrosis
Parathyroid Hormone
Tooth Extraction
Advisor: Peel, Sean
A Model Predictive Control-based Motion Drive Algorithm for Driving Simulators with Adaptive Motion Scaling and Actuator Based Constraints

Model predictive control offers numerous advantages over conventional motion drive algorithms, primarily the ability to predict the future state of a simulator and simulated vehicle. Although several model predictive control-based motion drive algorithms have been developed for use in real-time applications, they often aggressively scale down inputs to avoid simulator excursion limits. This thesis develops a new model predictive control-based algorithm, introducing the motion gain as an optimization variable so the controller has separate penalties on the scale and overall profile of the simulator driver’s and simulated vehicle driver’s motion perception. A paired comparison study was undertaken to compare the new algorithm with filter-based algorithms. Participants were asked to rank which algorithm felt more realistic after each of a series of maneuvers. Driving performance metrics and simulator performance are also compared. The new algorithm ranked similarly to conventional algorithms, performing best when it had accurate prediction of the simulated vehicle.

Keywords: driving simulator
model predictive control
motion drive algorithm
Advisor: Grant, Peter R
Haycock, Bruce
Optimization of 2×2 Couplers for Optical Frequency Domain Reflectometry

This thesis demonstrates broadband, low-loss 2×2 couplers on a silicon photonics platform for chipscale implementations of optical frequency domain reflectometers (OFDRs). Silicon nitride curved directional couplers and multimode interference couplers were designed, optimized, and evaluated for the O-band near a wavelength of 1310nm. Both types of couplers achieved a 1dB imbalance bandwidth of >100nm around 1310nm in both candidates. However, the curved directional coupler had negligible loss, while the multimode interference coupler had a 1dB excess loss bandwidth of >40nm around 1310nm. The results demonstrate the suitability of the silicon nitride-on-silicon platform for optical frequency domain reflectometry applications and builds a foundation towards a fully integrated photonic OFDR circuit.

Keywords: 3dB coupler
broadband coupler
directional coupler
OFDR
optical frequency domain reflectometry
Advisor: Poon, Joyce K.S
Experiences of Institutional Racism: Black Graduate Students Navigating Higher Education

There is an educational problem that is ongoing and evident – namely, the paucity of Black students in higher education across Canada. Black students who are enrolled in these institutions experience challenges navigating them. The purpose of this qualitative study is to gain deeper insights into the experiences of Black students in predominantly White higher education institutions. Data were obtained through in-depth semi-structured interviews with five Black students, who attended a predominantly White institution in the Greater Toronto Area. Critical Race Theory, which validates the narratives and counter narratives of marginalized groups, framed this research. The following themes emerged as impacting Black students: a) issues of degree attainment, b) navigating campus climate and, c) impact of ongoing activism and burnout. It is hoped that this research will assist post-secondary institutions in implementing programs not only to attract and retain Black students, but offer supports to serve their needs and academic success.

Keywords: Activism and burnout
Black students
Campus climate
Canadian education
Institutional racism
Predominantly White Institutions
Advisor: Lopez, Ann
Building Information Modeling in Canada: Benchmark Development and Future Directions

Building information modeling (BIM) has recently aroused significant attention in the architecture, engineering, construction, and facility management industries (AEC/FM). However, Canada lags behind other developed countries in nationwide adoption of BIM. The main objective of this research is to fill this knowledge gap by benchmarking the current state of BIM adoption in Canada and identifying the barriers against accelerating this effort. To this aim, nationwide surveys were conducted, and the results were analyzed and compared with other countries. Moreover, a review of existing studies and technologies to facilitate onsite implementation of BIM is provided. This is accompanied by a case study to evaluate the feasibility and potential applications of BIM on a construction site. This research contributes to the body of knowledge by establishing a benchmark for evaluating and tracking the state of BIM adoption in Canada, as well as identifying the potential applications of BIM to improve field workflows and coordination.

Keywords: Augmented Reality
Benchmark
BIM
Building Information Modeling
Construction
Virtual Reality
Advisor: McCabe, Brenda Y