VictorJuiz/thesis huggingface dataset:
Transient Receptor Potential Melastatin 7 Channel Affects Neurite Outgrowth of Hippocampal Neurons in vitro

Central Nervous System (CNS) neurons are highly specialized cells that assemble into functional networks by extending their axons and dendrites. Transient Receptor Potential Melastatin 7 (TRPM7) is a stretch-activated, calcium permeable non-selective cation channel that has previously been shown to be involved in cellular processes that are important for neurite elongation, such as vesicle fusion and cell adhesion by modulating cytoskeletal dynamics. The present study investigates the role of TRPM7 in neurite outgrowth using genetic and pharmacological approaches on cultured mouse hippocampal neurons. Both shRNA knockdown of endogenous TRPM7 expression and blocking of TRPM7 channel function using carvacrol resulted in enhanced neurite elongation, suggesting that TRPM7 may negatively regulate neurite outgrowth process during neuronal development. Co-immunoprecipitation data suggest that TRPM7 may be involved in neurite outgrowth process by modulating actin cytoskeletal dynamics via alpha-actinin-1.

Keywords: Neurite outgrowth
TRPM7
hippocampal neurons
neuronal development
Advisor: Sun, Hong-Shuo
Improving Hematopoietic Stem Cell Transplantation by Developing New Tools to Reduce Donor Cell Rejection

Patients undergoing hematopoietic stem cell transplantation (HSCT) face hurdles such as conditioning-related mortality, graft rejection and insufficient donor cell dose that impede recovery. To address these issues, we investigated the role of cell surface protein transfer in influencing graft rejection and the use of blood reprogramming intermediates as a novel source of donor cells, respectively. We found that the transfer of host MHC class I proteins onto donor cells protects the donor cells from NK cell-mediated and macrophage-mediated rejection. These results suggest that mild conditioning regimens that spare host NK cells and macrophages can be used on patients without compromising graft tolerance. Next, we attempted but failed to generate blood reprogramming intermediates using the non-viral piggyBac system. Moving forward, we should investigate the use of other methods to generate blood reprogramming intermediates. Altogether, our study provided novel insights and possible solutions to the aforementioned complications faced by patients receiving HSCTs.

Keywords: Hematopoietic stem cell transplantation
Trogocytosis
Graft rejection
NK cells
Macrophages
Immunocompromised mouse models
Donor cell
Reprogramming
piggyBac
Umbilical cord blood cells
Reprogramming intermediates
Bone marrow cells
Advisor: Rogers, Ian
Searching out Loud Together: Reflections from a Faculty Learning Circle

This qualitative study explored the experiences and reflections of nine part-time and newly hired College educators who agreed to participate in the development of a Faculty Learning Circle. A collective case study methodology was used to explore the emergent themes, responses and experiences of the participants who engaged with the FLC over the course of a year. Data was obtained by audio-recording the FLC sessions, participant reflections, as well as a group exit interview. The findings indicated that the FLC was an effective vehicle for sustained and meaningful informal professional development. The FLC allowed participants to explore their professional identities, garner peer support within a collegial community, and numerous opportunities to collaborate for professional learning that had benefits both within and outside the classroom. As a result, this thesis offers insights for both faculty and College administrators into the advantages of a collaborative, peer-led approach to professional development.

Keywords: college faculty
learning circle
professional development
teacher learning
professional growth
teacher identity
Advisor: Kooy, Mary
Superficial Zone Chondrocytes Modulate Polyphosphate Levels In Deep Zone Cartilage Which Correlate with Increased Tissue Formation And Decreased Mineralization By Deep Zone Chondrocytes

Loss of the superficial zone of articular cartilage is an early change in osteoarthritis and with disease progression the deep zone (DZ) of cartilage shows progressive mineralization. To date, the mechanism(s) regulating post-natal articular cartilage mineralization is poorly understood. Previously, we have shown that inorganic polyphosphate inhibits mineralization of in vitro-formed DZ cartilage. We developed an indirect co-culture method to investigate the effect of superficial zone chondrocytes (SZC) on mineralization in DZ cartilage. Our findings suggest that SZC suppress mineralization by modulating polyphosphate levels in DZ cartilage via FGF-18. Furthermore, SZC promote glycosaminoglycan and collagen accumulation in the extracellular matrix of cartilage formed by DZ chondrocytes. This study provides insight into the interaction between chondrocyte subpopulations and possible mechanism(s) controlling post-natal articular cartilage mineralization. Moreover, the results of this study establish polyphosphate and FGF-18, separately or in combination, as therapeutic candidates for articular cartilage repair and osteoarthritis prevention.

Advisor: Kandel, Rita
Nitrate-Dependent, pH Neutral Bioleaching of Ni from an Ultramafic Concentrate

This study explores the possibility of utilizing bioleaching techniques for nickel extraction from a mixed sulfide ore deposit with high magnesium content. Due to the ultramafic nature of this material, well-studied bioleaching technologies, which rely on acidophilic bacteria, will lead to undesirable processing conditions. This is the first work that incorporates nitrate-dependent bacteria under pH 6.5 environments for bioleaching of base metals. Experiments with both defined bacterial strains and indigenous mixed bacterial cultures were conducted with nitrate as the electron acceptor and sulfide minerals as electron donors in a series of microcosm studies. Nitrate consumption, sulfate production, and Ni released into the aqueous phase were used to track the extent of oxidative sulfide mineral dissolution; taxonomic identification of the mixed culture community was performed using 16S rRNA gene sequencing. Nitrate-dependent microcosms that contained indigenous sulfur- and/or iron-oxidizing microorganisms were cultured, characterized, and provided a proof-of-concept basis for further bioleaching studies.

Keywords: bioleaching
pentlandite
denitrification
nitrate
iron sulfide
ultramafic
nickel
neutral pH
Advisor: Papangelakis, Vladimiros G.
Track Changes: Identity in Version Control

The growing sophistication of version control systems, a class of tools employed in tracking and managing changes to documents, has had a transformative impact on the practice of programming. In recent years great strides have been made to improve these systems, but certain stubborn difficulties remain. For example, merging of concurrently introduced changes continues to be a labour-intensive and error-prone process. This thesis examines these difficulties by way of a critique of the conceptual framework underlying modern version control systems, arguing that many of their shortcomings are related to certain long-standing, open problems around identity. The research presented here casts light on how the challenges faced by users and designers of version control systems can be understood in those terms, ultimately arguing that future progress may benefit from a better understanding of the role of identity, representation, reference, and meaning in these systems and in computing in general.

Keywords: Version Control
Identity
Git
Software Development
Advisor: Smith, Brian Cantwell
Slotta, James
Hockema, Steven
Optimal Pairs Trading: Static and Dynamic Models

Pairs trading has been a popular statistical arbitrage strategy among hedge funds. One important research field in pairs trading is to maximize the return under differential constraints and assumptions. In this thesis, we develop two models to optimize the performance of pairs trading. In the static model, we find the analytic solution of optimal thresholds for pairs trading to maximize the long run profit per unit time. Comparison is made between the optimal rules we developed and the common practice. To overcome limitations of the static model, we extend our research to dynamic pairs trading, where a continuous time Markov chain is used to model the change of parameters. Our objective is to maximize the expected return in the finite horizon under the Constant Relative Risk Aversion (CRRA) utility. Numerical examples are presented to illustrate the impact of price limits, risk aversion rate and regime switching on consumers' investment decision.

Keywords: Pairs Trading
Stochastic Control
Advisor: Chi-Guhn, Lee
Feasibility and Simulation Study of DC Hybrid Circuit Breakers

Interruption of DC is more challenging than that of AC because of the absence of DC zero-crossings. This thesis proposes an alternative counter-voltage (ACV) DC hybrid circuit breaker (DC-HCB). This DC-HCB can interrupt the DC up to 5 kA with the source voltage of up to 1 kV and it can meet the general requirements i.e., interrupting the DC within 5ms, and limiting over-voltages due to the CB operation. The existing/investigated DC circuit breakers, i.e., active mode DC-HCB and the traditional counter-voltage (TCV) DC-HCB are also investigated and compared with the proposed DC-HCB. The investigations are based on the time-domain simulation studies in the PSCAD/EMTDC. The studies show that the ACV DC-HCB is the preferred option to both the existing DC-HCBs. The main features of the proposed ACV DC-HCB include lower capacitance in the commutation path and the need for a smaller dielectric strength for the primary-path circuit breaker.

Keywords: Hybird Circuit Breakers
Electric Arc Model
Advisor: Iravani, Reza
Layer-by-layer Electrode Modification for Electrochemical Capacitors - Alternative Cations and Process Optimization

Layer-by-Layer (LbL) deposition of electrochemically active materials on porous carbon electrodes is a proven method to leverage both electrochemical double-layer capacitance and pseudocapacitance for charge storage on the same electrode. LbL coatings are held together by electrostatic attraction between adjacent layers of oppositely charged molecules. Previous studies have used Keggin polyoxometalates to great effect as the anionic layer in LbL electrode modification, but little effort has been devoted to cationic material selection and LbL process optimization. This work investigated alternatives to the conventional, electrochemically inert polydiallyldimethylammonium (PDDA) cation. The use of fuchsin molecular cations in LbL deposition improved the specific energy and specific power of modified electrodes. Fuchsin cation also rendered the environmentally harmful oxidative surface activation step unnecessary for LbL deposition. Process parameters were optimized for MWCNT/Fuchsin/POM samples, and post-LbL electrochemical polymerization was found to further improve the performance of these electrodes.

Keywords: Electrochemical Capacitors
Supercapacitors
Layer-by-Layer
Polyoxometalate
Fuchsin
Luminol
Electrode Modification
Advisor: Lian, Prof. Keryn
Informed Consent for Chiropractic Care: Comparing Patients’ Perceptions to the Legal Requirements

Purpose: Patients’ perspectives of informed consent for chiropractic care have not been investigated. This study explored how patients of chiropractors perceived the exchange of risk information during informed consent. Methods: Interviews were conducted with 26 participants, recruited from chiropractic clinics. Interview transcripts were analyzed using a constant comparative method of analysis. Findings: Participants experienced informed consent as an on-going process where risk perceptions were shaped throughout four distinct stages. In the first stage information acquired prior to arriving at the clinic for treatment shaped perceptions of risk. In the second stage participants assessed the perceived competence of the practitioners. Participants then signed the consent form and discussed the risks with t heir practitioner. Finally, they communicated with their practitioners during treatment to ensure their pain threshold was not crossed. Conclusion: These findings suggest that patients perceive informed consent as a social process involving on-going communication with their practitioners.

Keywords: Informed Consent
Chiropract*
Qualitative
Patient Safety
Spinal Manipulation
Adverse Events
Advisor: Boon, Heather
Epigenetic Alterations Associated with Uropathogenic Escherichia coli (UPEC) Infections in the Bladder

Infection of the human urinary tract is one of the commonest bacterial infections, with uropathogenic E.coli (UPEC) being responsible for 90% of the diagnosed cases, with significant morbidity and mortality. The urinary bladder is a remarkable autonomic musculomembranous organ under conscious control. Its two main functions are, storage and voiding of urine. Any disturbance to normal urination leads to various clinical conditions, such as urinary incontinence, bladder retention, overactive bladder syndrome, prostatitis in men and urinary tract infections (UTI). Determining the predisposition of an individual to UTI by discovering a biomarker would allow for a more rational selection of patients who might best benefit from either antibiotic prophylaxis or preemptive surgical intervention. The purpose of this study was to examine the epigenetic effects of UPEC infection directly, or indirectly in the bladder. The study also identified potential gene candidates, such as TLR4 and CTCF, for development of DNA methylation biomarker targets.

Keywords: Bladder
Epigenetics
Uropathogenic Escherichia coli
Advisor: Bagli, Darius J
The Role of Gap Junctions in Brain Glucose Deprivation and Glucose Reperfusion

Hypoglycemia is a severe side effect of insulin overdose in the diabetic population and can result in various neurological sequalae including seizures, coma, and brain death. There is still a limited understanding of the generation and propagation of hypoglycemic seizures, which may exacerbate hypoglycemia-induced neuronal damage. Moreover, glucose reperfusion after a period of transient hypoglycemia has been shown to cause neuronal hyperexcitability which can have further damaging effects. Gap junctional communication can be involved in the spread of hypoglycemic injury in two ways: 1) by providing a cytoplasmic continuity in which seizures can easily propagate and 2) by engaging the astrocytic network in metabolic compensation as well as enhancing astrocytic buffering of K+. This study aims to investigate the role that gap junctions play during brain energy deprivation. Results from these experiments show that gap junction blockade can have a neuroprotective role during hypoglycemia and glucose reperfusion.

Keywords: Hypoglycemia
Seizure
Gap Junction
Glucose Reperfusion
Advisor: Carlen, Peter
Trunk Muscle EMG in a Specially Designed Virtual Reality Motion Simulator

Virtual reality (VR) has become an important tool in the study of human balance. It has also been used as a training tool for seated balance and assistive mobility devices. The objective was to design a system that can be used to investigate the effect of VR on trunk muscles during perturbed sitting and perform a preliminary study with two subjects. A spherical system was designed that rotated 26º in the pitch and roll plane at three speeds. The corresponding muscle activity was recorded using EMG in the presence and absence of VR during perturbed sitting. The design was capable of performing the required motions. The results showed a maximum of 31.8% and a minimum of 3.66% muscle activity, relative to maximum voluntary contraction. Our findings suggested that our developed system was successfully able to detect a noticeable effect of VR under perturbed sitting on the subjects’ EMG responses.

Keywords: Electromyography
EMG
Perception
Roll and Pitch
Seated Balance
Virtual Reality
Simulation
Phasic and Tonic activity
Trunk Muscles
Abdomen and Back Muscles
Seated Posture
Advisor: McConville, Kristiina M. Valter
Investigating the Mechanisms of Intrinsic Specificity Achievement in SH3 Domains

Protein-protein interactions are an integral part of virtually all aspects of cellular function. Many of these interactions are mediated by small modular units called protein interaction domains (PIDs). We do not yet understand, however, how much functional information is encoded in these modules. It has previously been shown that Nbp2SH3 and Bem1SH3b domains in S. cerevisiae bind several target peptides with the same consensus sequence, yet display finely tuned affinities for each. In this study, I have shown that there exists an evolutionarily conserved ability of orthologous fungal Nbp2SH3, Bem1SH3b, and Abp1SH3 domains to discriminate between target peptides within the same species. In addition, I have developed a method to quantitatively probe SH3 domain specificity using purified SH3 domains and naturally occurring proline-rich constructs (PRRs) in the context of cell lysate from S. cerevisiae. Expansion of this work may yield valuable insights into intrinsic SH3 domain specificity.

Keywords: SH3 Domain
Intrinsic Specificity
Advisor: Davidson, Alan R
The Hawthorne Effect in Hand Hygiene Compliance Monitoring

Introduction: The Hawthorne effect, or behaviour change due to awareness of being observed, is believed to inflate directly observed hand hygiene compliance rates, but evidence is limited. Methods: A real-time location system tracked hospital hand hygiene auditors and recorded alcohol-based hand rub and soap dispenses. Rates of hand hygiene events per dispenser per hour within sight of auditors were compared to dispensers not exposed to auditors. Results: The event rate in dispensers visible to auditors (3.75/dispenser/hour) was significantly higher than unexposed dispensers at the same time (1.48) and in prior weeks (1.07). The rate increased significantly when auditors were present compared to five minutes prior to arrival. There were no significant changes inside patient rooms. Conclusions: Hand hygiene event rates increase in hallways when auditors are visible and the increase occurs after the auditors’ arrival, consistent with the existence of a Hawthorne effect localized to areas where auditors are visible.

Keywords: Hand hygiene
Hawthorne effect
Hospital epidemiology
Advisor: Baker, G. Ross
Phenotypic and Genetic Differentiation Between Sex Chromosome Races of Rumex hastatulus (Polygonaceae)

Wind-pollinated plants often have little genetic structure owing to high gene flow. However, sex chromosomes evolution promotes divergence, potentially leading to population subdivision. Rumex hastatulus (Polygonaceae) is a wind-pollinated, dioecious coloniser of open disturbed land with two sex chromosome races (SCRs), which occupy different parts of the species’ range in the southern USA. My thesis investigated phenotypic and genetic differentiation between the SCRs, based on a study of 28 populations sampled throughout the range. A glasshouse experiment demonstrated significant differentiation between the SCRs in several life-history traits, several of which exhibited clinal variation. Analysis of population genetic structure, based on 13 nuclear loci, revealed two distinct clusters corresponding to the two SCRs, with an estimated origin of the North Carolina SCR from the Texas SCR between ~5000–15000 generations ago. My results indicate that the SCRs have developed a moderate degree of phenotypic and genetic differentiation despite ongoing gene flow.

Keywords: Rumex hastatulus
ecological genetics
population structure
wind pollinated
phenotypic differentiation
Advisor: Barrett, Spencer
Fuel Moisture and Sustained Flaming in Masticated Fuelbeds

Mastication is a fuel management technique that disrupts the vertical continuity of forest fuels by mechanical shredding of trees and understory vegetation into a highly-compacted surface fuelbed. The particle size distributions, bulk density and arrangements differ from natural and slash fuel types, thus resulting in fuelbeds with potentially different moisture dynamics and fire behaviour. We conducted three experiments, the first of which examined differences in in-stand micrometeorology and fuelbed moisture content between differing levels of stand thinning via mastication. In the second experiment, a fuel moisture model was created, validated with an independent dataset, and compared with pre-existing models that are incorporated in the Canadian Forest Fire Danger Rating System. In the third experiment, we compared the results of standard ignition tests performed on masticated fuelbeds in the laboratory and field to determine probability of sustained flaming, and compared our findings with pre-existing models of ignition for other forest fuels.

Keywords: fuels management
mechanical fuels treatment
chipping
Advisor: Wotton, Brian Michael
Object-based Image Analysis for the Delineation of Canopy Gaps and Individual Tree Crowns using Multi-source Data: A Case Study in Haliburton Forest, Ontario

This thesis assessed object-based image analysis techniques using multi-source remote sensing data in order to automatically delineate canopy gaps and individual tree crowns (ITCs). Image segmentation is much more complex when conducted on data covering deciduous, un-even aged forests like those in Central Ontario. To delineate canopy gaps high spatial resolution multispectral ADS40 aerial imagery and a LiDAR CHM were assessed both separately and jointly. To delineate ITCs two commonly used segmentation approaches were assessed – region growing and watershed segmentation. Ground based measurements and manually delineated data were used as reference to evaluate results. Using multi-source data to delineate canopy gaps produced an average overall accuracy of 99.35%, whereas using the imagery and CHM individually resulted in average overall accuracies of 81.41% and 82.45%, respectively. For the delineation of ITCs, the watershed and region growing segmentations resulted in average overall accuracies of 67.5% and 65.5%, respectively.

Keywords: remote sensing
GIS
Advisor: He, Yuhong
Caspersen, John
Pain and Psychological Outcomes Following Traumatic Musculoskeletal Injury

Background: Traumatic musculoskeletal injury (TMsI) often leads to chronic pain and post-traumatic stress disorder (PTSD). This study examined factors of a modified diathesis-stress model in the development of PTSD symptoms following TMsI. Methods: 205 patients were recruited in this prospective, observational study. Within 14 days of injury, participants completed an in-hospital questionnaire investigating acute symptoms of anxiety, depression, pain, and PTSD. Results: Logistic regression identified multiple factors associated with symptoms of PSTD (p<.0001). Neuropathic pain (odds ratio[OR]=1.091, 95% confidence interval[CI] 1.020-1.168), general anxiety (OR=1.176, 95%CI 1.046-1.318), pain anxiety (OR=1.056, 95%CI 1.018-1.094), and pain catastrophizing (OR=1.168, 95%CI 1.016-1.348) were associated with acute symptoms of PTSD. Conclusions: The results support the modified diathesis-stress model indicating that neuropathic pain, general anxiety, pain anxiety, and pain catastrophizing are associated with symptoms of PTSD. Future studies should examine the influence of these acute factors on the development of chronic pain and PTSD following TMsI.

Keywords: Traumatic musculoskeletal injury
Pain
Anxiety
Depression
Posttraumatic Stress Disorder
Advisor: McCartney, Colin