title: Patronage of Collectives: The Relations Between Patrons and Local Communities in Northern Italy

contributor:
Eilers, Claude
George, Michele
Beckmann, Martin
Classics

subject: Civic Patronage; Northern Italy; Epigraphy; Roman History.

abstract: The role of Roman patrons and their relations with local communities is investigated. Northern Italy has been chosen as the region where this investigation will be carried out. It will be shown that the institution of patronage in northern Italy underwent a process of decline as the rest of the empire. This point will be displayed by taking into consideration the legal, literary, and epigraphic body of evidence related to the institution of patronage in northern Italy. A careful reading of the sources will show that the title of patronus was granted by local communities as a reward for the patronus’s generosity. Such title did not obligate these patroni to benefit their communities, although many did. This gradual process of decline ultimately reached its peak under the 2nd century AD when patronage transformed into a symbolic institution.

abstract: Thesis

abstract: Master of Arts (MA)


title: Identifying Biologically Active Compounds to Provide T Cell Costimulation for Cancer Immunotherapy

contributor:
Bramson, Jonathan
Biochemistry and Biomedical Sciences

abstract:
Adoptive cell therapy (ACT) is a powerful cancer immunotherapy platform, where T lymphocytes are collected from cancer patients, expanded ex vivo, and infused back into the patient as a cellular drug. Genetic modification with chimeric receptors redirects T cell tumour-specificity. While ACT is a clinical success in many cancers, it is dependent on T cell proliferation following infusion, where robust expansion is a predictor of a positive outcome.
Costimulation is the activation of a class of receptors which provide maximal stimulatory signals to T cells, resulting in an enhancement of proliferation, survival, and memory. Costimulatory receptor signaling occurs in cooperation with the T cell receptor, and is provided by several receptor families that converge on costimulatory signaling pathways.
Chimeric receptors can be modified with costimulatory domains however, the non-canonical signaling can lead to overstimulation and serious toxicity in the clinic. We hypothesize that pharmacological costimulation can be used to boost T cell proliferation, where drug administration and dosage is controlled and the drug can cease to be administered should toxicities manifest. Small molecule costimulation may prove to be a useful approach to boost the efficacy of ACT as a cancer therapy.
The objective of my research project is to screen and characterize for small molecules that enhance T cell proliferation.  Specifically, I will investigate the ability small molecule drugs to enhance T cell expansion following antigen-specific stimulation of T cells engineered with T cell antigen coupler (TAC) receptors.
Methods:  I identified candidate small molecules with costimulatory effects on TAC T cells using two strategies.  First, I generated a database of small molecules that were predicted to interact with costimulation pathways based on connectivity mapping, provided by the Broad Institute, using the transcriptomes of TAC T cells activated in the presence or absence of costimulation.  As a second screening strategy, I developed a bioluminescent reporter system that was used for high throughput screening of small molecules libraries available at the Centre for Microbial and Chemical Biology. Following the identification of several hits, these compounds were tested in vitro for their modification to TAC T cell proliferation and function.
Results: We have identified several chemical classes of compounds which contributed to a robust increase in TAC T cell proliferation in the absence of costimulation, and have evaluated the top three drugs in vitro by proliferation and RNA sequencing assays. Ferutinin, and protein kinase C activating compounds mezerein and phorbol 12,13-dibutyrate, were found to robustly increase TAC T cell proliferation.
The significance of this project is to identify costimulatory small molecules to enhance the efficacy of T cell cancer therapy, and yield novel insight into the chemical space that modulates costimulation.

abstract: Thesis

abstract: Master of Science (MSc)


title: Experiences and Trajectories of Former Youth in Care

contributor:
Pawluch, Dorothy
Sociology

subject:
youth in care
trajectories
child welfare
foster care
symbolic interactionism

abstract: This dissertation draws on semi-structured interviews with 20 former youth in care to examine their experiences in Ontario’s child welfare system and the long-term impacts of those experiences. Using a symbolic interactionist approach, the study analyzes the biographical disruption that experiences in the care system represented for participants and how this affected their life trajectories. The findings are organized and discussed around three themes: a) participants’ involvement with the system – how they experienced entering, being in, and exiting the system; b) the stigma participants experienced while in care, and their efforts to neutralize or manage the stigma; and c) the impact that their care experiences had on participants as adults. The data reveal a range of challenges that participants encountered while they were in care, including loneliness, isolation, neglect, general mistreatment and in some cases, abuse. Particularly damaging were the stigma and assaults on “self” that participants experienced as a result of their care status. The data also reveal that in one way or another, these early experiences followed participants into their adult lives, leaving them with a myriad of issues and concerns. The dissertation ends with a discussion of the substantive and theoretical contributions of the findings, as well as a section that addresses the policy implications of the research.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation draws on semi-structured interviews with 20 former youth in care to examine their experiences in the care system and the long-term impacts of those experiences. Participants described their time in care, including the stereotyping, stigma, abuse, and general mistreatment they encountered, as well as the loneliness and isolation they experienced. Leaving the care system also came with a distinct set of challenges that often persisted into their adult lives. The analysis focuses on impacts relating to identity, self-perception, and material circumstances for those who pass through Ontario’s child welfare system.


contributor:
Chen, Jun
Electrical and Computer Engineering

subject: Video Enhancement

abstract:
Recent years, we have witnessed significant progress in the quality enhancement of compressed video by deep learning methods. In this paper, we propose an effective method for Video Quality Enhancement(VQE) task. Our method  is realized via \textbf{A Parallel Network for Compressed Video Enhancement(PEN)}. To tackle optical flow estimates and complicated motion, PEN has two branches which are \textbf{Offset Deformable Fusion Network(ODFN)} and \textbf{Complex Motion Solution Network(CMSN)}.
During the alignment stage, existing methods typically estimate optical flow for temporal motion compensation. However, because the compressed video may be severely distorted as a result of various compression artifacts, the estimated optical flow is typically inaccurate and unreliable. Therefore in ODFN we use deformable convolution to align frames in a fast and efficient way.
At the same time, we adopt pyramidal processing and cascading refinement in CMSN which can address complex motions and large parallax problems in alignment. Furthermore, we use the target frame's neighbor Peak Quality frames(PQFs) as reference frames, which adjusts for video quality variations.
Extensive experiments show that our method has improved the average video quality by 0.7 decibel.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
The quality of video is improving as cameras improve, but the size of the video is also increasing. As a result, we will need to compress the video. Video compression, on the other hand, is always accompanied with a loss of video quality.
Deep learning approaches have made tremendous progress in improving the quality of compressed video in recent years.
In this paper, we propose an effective method PEN for Video Quality Enhancement(VQE) task by parallel processing of multiple frames.


title: Pathways of Adaptive Immune Activation During Sensitization and Recall in Food Allergy

title: Adaptive Type 2 Immunity in Food Allergy

contributor:
Jordana, Manel
Medical Sciences

subject: Immunology Allergy

abstract:
Approximately 10% of North Americans have at least one food allergy. Allergic reactions to foods are mediated by IgE antibodies which, upon allergen exposure, are crosslinked on the surface of mast cells and basophils, resulting in degranulation. The granule contents of mast cells and basophils are responsible for the diverse signs and symptoms of food allergy, including hives, itchiness, edema, vomiting, diarrhea, and a potentially lethal form of systemic shock called anaphylaxis. The clinical recommendation for food allergic Canadians is strict allergen avoidance, and emergency epinephrine use upon an accidental exposure. There are presently no disease modifying therapeutic options for allergic Canadians.
The work in this PhD thesis focuses on the pathways which result in the production and memory of allergen-specific IgE. Using murine models of food allergy and anaphylaxis, we have delineated pathways of early allergic sensitization which may occur prior to allergic patients presenting in the clinic during the first allergic reaction. We have demonstrated that CD4+ T cell activation can occur in the absence of B cell activation, but can hold the memory of IgE responses persistently, potentially for a lifetime. Upon re-exposure to the allergen, CD4+ T cells can activate naïve B cells, which pursue either direct or sequential isotype switching to IgE, both resulting in clinical reactivity against food allergens. Our findings will inform future diagnostic and prognostic tests in pre-allergic patients, and to design novel therapeutics with disease modifying capacity in humans.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Enabling Trimap-Free Image Matting via Multitask Learning

subject:
Natural Image Matting
Deep Learning
Trimap-Free

abstract:
Trimap-free natural image matting problem is an important computer vision task in which we extract foreground objects from given images without extra trimap input.
Compared with trimap-based matting algorithms, trimap-free algorithms are easier to make false detection when the foreground object is not well defined. To solve the problem, we design a novel structure (SegMatting) to handle foreground segmentation and alpha matte prediction simultaneously, which is able to produce high-quality mattes based on RGB inputs alone. This entangled structure enables information exchange between the binary segmentation task and the alpha matte prediction task interactively, and we further design a hybrid loss to adaptively balance two tasks during the multitask learning process.
Additionally, we adopt a salient object detection dataset to pretrain our network so that we could obtain a more accurate foreground segment before our training process.
Experiments indicate that the proposed SegMatting qualitatively and quantitatively outperforms most previous trimap-free models with a significant margin, while remains competitive among trimap-based methods.

abstract: Thesis

abstract: Master of Science in Electrical and Computer Engineering (MSECE)


title: Deciphering The Heterogeneity in Transit Service Quality: The Role of Utilitarian, Psychological, Behavioural, and Built Environment Aspects

contributor:
Mohamed, Moataz
Civil Engineering

subject:
Transit Service Quality
Preference Heterogeneity
Discrete Choice Models
Spatial Analysis
Public Transit

abstract: A thorough understanding of transit customers’ preferences and travel behaviour is fundamental to offering a high-quality urban transportation system. The dominant approach in transit quality literature is rooted in understanding current transit users’ preferences. However, disregarding the heterogeneity in transit customers’ desired quality yields suboptimal conclusions regarding their preferences. Therefore, an effective transit system should strive to understand the broad spectrum of transit and non-transit users’ preferences to increase transit ridership. Towards that end, this research aims at deciphering the heterogeneity associated with transit customers’ service desired quality. The research utilized a primary dataset elicited from an online survey that was part of Hamilton Street Railway (HSR) Public Engagement efforts in Hamilton, Ontario, Canada. The research employed state-of-the-art discrete choice models (e.g., error components logit models, latent class choice models, nested logit models) along with multivariate statistical and spatial analysis. In this respect, this dissertation quantified and unveiled latent heterogeneity in transit customers’ preferences and its implications on their willingness to pay for service improvements through various techniques and specifications. Unlike the conventional classifications for transit customers, our research classifies transit customers into three latent segments: Direct Trip Enthusiastic (DTE), Cost-Sensitive (CS), and Real-time Information Supporter (RIS). The dissertation also investigated and further quantified the influence of subjective psychological factors in shaping transit customers’ preferences towards service attributes. For instance, environmental consciousness is found to be associated with less sensitivity to walking time while higher appreciation to at-stop real-time information provision. Furthermore, the research highlighted how the built environment and its contextual effects influence customers’ travel behaviour while accounting for variations in socioeconomic characteristics. The spatial analysis concluded that the built environment's influence is not equally efficacious over geography. Overall, this research presents a unique contribution to the knowledge of public transit research for practitioners, policymakers, and academia.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Core Design Optimization and Steady State Criticality Analysis of the Canadian Nuclear Battery™

contributor:
Buijs, Adriaan
Luxat, John
Engineering Physics

abstract:
The nuclear microreactor, although not a novel concept, is a fast-emerging technology.
Microreactors are small modular reactors that have a thermal power level between
1 and 20 MW. They take the smallness and modularity to a whole new level in the
sense that they are entirely factory-built and shipped to the intended location, rather
than constructed onsite. One such design is the 2400 kWth Canadian Nuclear Battery™
(CNB) design being developed by Dunedin Energy System Ltd. for use in remote northern
territories as a potential alternative to diesel electric power plants. Key technical
features of the reactor include a heat pipe cooled core, graphite neutron moderator, high
assay low enriched uranium (HALEU), TRISO coated fuel particle and use of burnable
poison particles for long term reactivity control. This thesis reports the methodology
used for 3D neutronics modeling and core design of the CNB using the Monte Carlo
particle transport code SERPENT 2.1. Optimization of the fuel enrichment, amount
of burnable poison, lattice pitch, and poison particle size is carried out by performing
burnup calculations to achieve a reasonable reactivity swing over 20 years of full power
operation without refueling. The worth of the reactivity control system, shutdown margin, fuel
and graphite temperature reactivity coefficients, coolant void coefficients, neutron flux
, and power distribution over the reactor lifetime are evaluated. Additionally, a preliminary
single lattice cell thermal-hydraulic and neutronic coupling is performed along with
a viability study of the control drum system as an alternative form of reactivity control.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Modeling Cardiac Pacemakers With Timed Coloured Petri Nets And Related Tools

contributor:
Janicki, Ryszard
Computing and Software

abstract:
Verification Grand Challenge is one of the Grand Challenges for Computing Research. Verification, which is the strict proof of the correctness of software according to its specifications, results in reliable software and potential cost reductions. In addition, the capabilities of other software engineering techniques, such as requirements analysis and testing, can be complemented and extended by verification. Medical devices are well-known examples of safety-critical systems which require significant advances in verification (among other areas). The failure of safety-critical systems not only damages property or the environment but could also lead to human fatality. Therefore, software verification is one approach to prevent such negative consequences.
The cardiac pacemaker is an electronic device that monitors and controls the heart rhythm via sensing and pacing operations. The pacemaker treats cardiac arrhythmia, defined as abnormal patterns of the heartbeat. The Software Quality Research Laboratory at McMaster University proposed the pacemaker system specification as a pilot problem for the Verified Software Initiative.
This research utilizes formal methods to model and verify the interdisciplinary requirements of pacemaker systems. It additionally provides customizable data to assess and optimize various algorithms and parameters.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Pricing, Returns, and Donations in Single- and Dual-Channel Retailing

contributor:
Hassini, Elkafi
Parlar, Mahmut
Business Administration

abstract: In this dissertation, we study the operational planning problem of a retailer under single- and dual-channel settings with product returns and donations considerations. It is composed of 6 chapters. Having provided the overview and motivation of this work in Chapter 1, we present a structured literature review of the bricks-and-clicks dual-channels in Chapter 2. Next, we propose a quality-dependent newsvendor problem, which models a socially responsible food-retailer's operational planning problem for a continuously deteriorating inventory over two periods with the consideration of donation and quality-sensitive customers in Chapter 3. The retailer's operational planning comprises of inventory and pricing decisions, where she plans not only for the purchase of the goods but also for donating them. We assume each unit of donation generates a constant reward derived from a blend of government incentives and the improved public image of the company due to its corporate social responsibility effort. Our results reveal that charitable donations can enhance the profit while at the same time mitigate the waste and the retailer's optimal donation volume is increasing (decreasing) in the donation reward (quality of the goods). We extend this model in Chapter 4 to incorporate a tax deduction policy into the retailer's problem and examine the impacts of quality and tax subsidy parameters on the retailer's optimal decisions. Although the retailer is still better off engaging in donations, we observe that a larger tax subsidy (higher quality) does not always bring in more (less) donations. In Chapter 5, we develop an analytical model to help a bricks-and-clicks dual channel retailer determine the optimal price in each channel and whether to welcome the cross-channel returns to her physical facility. We find that the cross-channel returns are likely to cannibalize the physical channel sales and may hurt the retailer's profit when customer returns are highly sensitive to refund. Finally, Chapter 6 summarizes our main contributions and proposes future research directions.

abstract: Thesis

abstract: Candidate in Philosophy


title: THE ROLE OF TRANSCRIPTION FACTOR AP-2β IN THE DEVELOPMENT OF OCULAR ANTERIOR SEGMENT STRUCTURES INVOLVED IN INTRAOCULAR PRESSURE HOMEOSTASIS

subject:
Tfap2b
Trabecular meshwork
Development
Intraocular pressure

abstract: Previously, we showed that transcription factor activating protein 2-beta (AP-2β) deletion from the periocular mesenchyme (POM)-derived neural crest cells (NCCs) using Wnt1Cre (AP-2β NCC knockouts/AP-2β NCC KOs) resulted in anterior segment abnormalities and increased intraocular pressure (IOP). The present study investigated the role of AP-2β in development of structures of the conventional pathway including the trabecular meshwork and Schlemm’s canal, and the unconventional pathway including the ciliary muscle. Studies using NCC KOs revealed that the embryonic POM migrated appropriately, but a significant reduction in postnatal POM cell proliferation in the angle was observed, accompanied by reduced expression of trabecular meshwork and Schlemm's canal markers when compared to controls, which likely contributed to the elevated IOP in NCC KOs. However, since Wnt1Cre was expressed in multiple NCC derivatives, AP-2β was deleted specifically from the developing trabecular meshwork region (TMR) using Mgp-Cre knock-in (Mgp-Cre.KI) mice. Although migration of the POM giving rise to the trabecular meshwork was not affected, peripheral anterior synechia (PAS), a decrease in expression of trabecular meshwork and Schlemm’s canal markers, and significantly increased IOP was observed in TMR KOs compared to controls, paired with loss of retinal ganglion cells (RGCs), and reduced retinal thickness and function. However, treatment with latanoprost, a prostaglandin analog that increases outflow through the unconventional pathway, significantly reduced elevated IOP in TMR KOs. Overall, the results suggest that AP-2β plays a cell-autonomous role in trabecular meshwork development and a non-cell-autonomous role in Schlemm’s canal development, while also playing an indirect role in unconventional pathway function, and thus, is important for IOP homeostasis. Moreover, the AP-2β NCC KO and AP-2β TMR KO may serve as models of primary angle closure glaucoma that can be used to test IOP-lowering drugs, molecular targets and neuroprotective strategies to develop treatments for human glaucoma.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Glaucoma is the leading cause of irreversible blindness worldwide. Primary angle closure glaucoma is one type of glaucoma resulting from abnormalities in structures that allow aqueous humour found in the front of the eye from exiting the eye through two major routes, including the conventional and unconventional pathways. Defects in these structures lead to increased intraocular pressure (IOP) that damages specialized cells important for vision. This project examines the role of transcription factor activating protein 2-beta (AP-2β) in development of structures responsible for IOP balance. Data from the current study showed that AP-2β is required for formation of the structures of the conventional pathway, but does not directly affect development of unconventional pathway structures. The two AP-2β deletion mutants used here can model human primary angle closure glaucoma to test the effect of various drugs and cell protection strategies aimed at treating glaucoma.


title: Proportional Miniaturization of Microscale Features into the Nanoscale Using Pre-stressed Polymer Films and Formation of Plasmonic Nanostructures

contributor:
Selvaganapathy, Ravi Ponnambalam
Mechanical Engineering

abstract: Fabrication of nano structures and patterns is the basis of diverse technologies and applications in our life ranging from microelectronics and semiconductors to nanofludics, biosensors and lab-on-chip devices. However, creation of nano patterns by means of conventional nanofabrication techniques such as electron beam lithography is expensive and time consuming. Pre-stressed polymer films have been used as a miniaturization technique to fabricate features with smaller size than the initial patterned features. Microscale patterns can be miniaturized by shrinking induced due to thermal stress release of the pre-stressed films. However, there are several challenges such as lack to achieve sub-micron resolution, lack of proportional miniaturization and limited shrinkage ratio that prevent the use of current technology for effective and scalable approach to fabricate nanoscale patterns. This thesis presents development of new miniaturization approaches using shrinkable films that can proportionally miniaturize microscale patterns into nanoscale down to sub 100 nm. Low-cost, rapid and scalable method to fabricate high resolution nano patterns was demonstrated by developing a constrained shrinking process. This process was able to overcome the loss of resolution after thermal shrinking of imprinted polymer films. Moreover, the process design allowed to perform iterative miniaturization which significantly reduced the size of the initial patterns by more than 99% reduction in area. These new capabilities were applied to fabricate tunable plasmonic structures in order to demonstrate the potential of the developed miniaturization approaches that can be used in various applications including microelectronics, sensors and functional surfaces.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Reconsidering the Role of Synchronous Feedback in Learning Diagnostic Skills: Identifying the Impact of the Instructor

contributor:
Monteiro, Sandra
Health Science Education

subject:
Feedback
Diagnostic Skills
Cue Identification
Error Detection

abstract:
Introduction: This thesis hypothesized that synchronous feedback which is supportive in nature would have a positive impact on the learning and transfer of the skills of visual and auditory cue identification in osteopathic diagnostic procedures. It was believed that the positive impact of supportive feedback would be evident through accurate identification of both visual and auditory cues. The categories of cues were visually identifiable asymmetrical motion, visual or auditory expressions of pain, and visually identifiable cues of a possible soft tissue tear or motor nerve issue.
Methods: All participants received the same video-based learning resource which was optimized for content (what/how) and cognition (why) followed by the same instructions for the practice phase. During the practice phase all participants were shown a video of a previously learned diagnostic procedure which contained visual and auditory cues. Between videos, participants were all asked the same questions in the same order. In the Supportive Feedback with Specific Content (SC) group participants would receive supportive comments regardless of accuracy of answers and, if they had identified an appropriate physical phenomenon but ascribed it to an incorrect category, they would receive feedback to correct the categorization error. The Supportive Feedback (S) group would receive supportive comments regardless of accuracy of answers but no feedback in relation to categorization errors. The No Feedback (NF) group would receive no supportive comments or feedback in relation to categorization errors. Responses were coded as accurate detection of cues, or categorization errors (detection of cues that were not there, or incorrect categorization of cues).
Results: All groups performed similarly with respect to accurate identification of auditory and visual cues such that there was no identifiable impact in relation to group condition during both the practice and transfer phases. The SC group did commit less categorization errors (11.43%) when compared to the S (28.21%) and NF (31.43%) groups.
Conclusion: The experimental findings supported the hypothesis that supportive feedback enhanced learning outcomes. While not demonstrated through accuracy of cue identification, this was demonstrated through a reduction in cue categorization errors. An additional hypothesis generated from the results of this thesis is that educational designs that allow for the commission of errors by learners followed by correction in the form of direct feedback or group lecture may predict faster attainment of expertise as noted in the reduction of errors.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Synchronous feedback has the ability to aid learning. It was hypothesized in this thesis that
synchronous feedback that was supportive in nature would improve learning and transfer for
learning the skill of visual and auditory cue identification in osteopathic diagnostic procedures.
All participants received the same initial learning material, the same instructions for the practice  phase of the experiment, and the same videos of a previously learned diagnostic procedure that  they identified visual and diagnostic cues from. During the practice phase the three groups were  the Supportive Feedback with Specific Content (SC), Supportive Feedback (S), and No Feedback (NF). The differences between groups were evident between diagnostic videos subsequent to the collection of answers for identified cues. The material differences were the delivery of supportive comments regardless of accuracy of answers (SC and S groups), the delivery of specific feedback when accurate cues were identified but placed in the wrong category (SC group only), or the absence of any commentary (NF group). All groups identified cues at similar levels such that the supportiveness of feedback showed no impact on performance. There was a notable difference between groups in relation to the commission of categorization errors where the SC group made less categorization errors with the S group and NF group committing errors at similar rates. The primary benefit of synchronous feedback in this experiment is that the instructor is able to identify errors and provide insight for correction.


title: A Comparison of Numerical Methods for Solving Backward Stochastic Differential Equations

contributor:
Pirvu, Traian
Mathematics and Statistics

abstract:
We study several different numerical methods for solving Backwards Stochastic Differential Equations and Partial Differential Equations. The main methods reviewed are a least-squares Monte-Carlo method, and a method utilizing Artificial Neural Networks: the Deep BSDE method. We implement both algorithms and compare their performance solving a BSDE to find the fair price of a financial option in an incomplete market. We find that the Deep BSDE method can provide similar approximation efficiency to the Monte-Carlo algorithm with a limited number of partition points, but outperforms it as the number of partition points increases.

In addition, we examine another technique that utilizes artificial neural networks to solve Partial Differential Equations directly, the Deep PDE Method. This method provides solution dynamics across the entire domain of the problem, as opposed to the Deep BSDE method which provides solution dynamics only for a small subset of points in the domain. This method is computationally intensive to train, and also requires bounded domains and boundary conditions and bounded domains, unlike the Deep BSDE algorithm where the domain is unbounded.  It remains a future research question to see whether the Deep BSDE method could be modified to work with bounded domains or if the Deep PDE Method could somehow be expanded to work on unbounded domains.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Regulation and Dynamics of Type IV Pili

title: THE REGULATION AND DYNAMICS OF TYPE IV PILI IN PSEUDOMONAS AERUGINOSA

contributor:
Burrows, Lori
Biochemistry and Biomedical Sciences

subject:
type IV pili
Pseudomonas aeruginosa

abstract: Type IV pili (T4P) are hair-like adhesins involved in many processes, including surface attachment, twitching, DNA uptake, electron transfer, and pathogenesis. These flexible filaments are expressed in various pathogens, including the opportunistic pathogen Pseudomonas aeruginosa. The pilus fibre is primarily composed of the major pilin structural subunit, PilA, which is rapidly polymerized or depolymerized during pilus extension or retraction, respectively. The transcription of pilA is tightly controlled by the PilS-PilR two-component system, which responds to fluctuating levels of PilA in the inner membrane. In addition to pilA, the response regulator, PilR, also regulates a subset of other non-T4P related genes. Here, we used hyperactivating point mutants in the PilS-PilR two-component system, which induce hyperpiliation without loss of pilus function, to assess the effects of increased surface pili expression on virulence against Caenorhabditis elegans, and to identify additional non-T4P genes regulated by the PilS-PilR two-component system. We hypothesized that dysregulation of the PilS-PilR two-component system impacts the expression of pilA and other genes, which impacts both surface piliation and T4P dynamics, resulting in altered P. aeruginosa virulence. C. elegans slow killing assays revealed that hyperpiliation, independently of T4P function, reduces virulence of model P. aeruginosa strains PAK and PA14. We propose a model whereby a surfeit of pili reduces virulence, potentially through impeding effective engagement of contact-dependent antagonism systems, such as the type III secretion system. Transcriptomic analysis of the hyperactive PilR point mutant also identified a subset of 26 genes, including those related to phenazine biosynthesis, quorum sensing, and ethanol oxidation, regulated by the PilS-PilR two-component system. Last, a T4P cysteine-labelling system was implemented for P. aeruginosa, allowing for the visualization of real-time pilus dynamics. Together, this work provides new insights into the consequences of hyperpiliation and the scope of the PilS-PilR signalling network, as well as novel tools for investigating P. aeruginosa T4P dynamics in vivo.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Pseudomonas aeruginosa is a major contributor to hospital-acquired infections and is of particular concern due to its intrinsic resistance to many frontline antibiotics. To aid in infection, Pseudomonas encodes an arsenal of virulence factors, including type IV pili (T4P), hair-like adhesins involved in many processes, such as twitching motility and surface attachment. T4P are primarily composed of the major pilin, PilA, whose expression is tightly regulated by the PilS-PilR two-component system. The sensor kinase, PilS, monitors the inner membrane PilA inventory and modifies activity of the response regulator, PilR, to regulate pilA transcription. Here, we demonstrate that P. aeruginosa virulence in a roundworm infection model is reduced when the amount of T4P expressed at the cell surface increases, regardless of the ability of the bacteria to twitch. We propose that inappropriate increases in surface T4P expression may impair pathogenicity-associated systems which require intimate host-cell contact. New genes in the regulon of the PilS-PilR two-component system were also identified. A tool to fluorescently label and image T4P in real-time using microscopy was established in the lab. This work highlights the consequences of increased surface T4P expression, providing potential new targets for antipseudomonal therapeutics which act on components involved in T4P expression and function.


title: Development of BCMA-specific engineered T cells targeting multiple myeloma

title: Engineered T cells for multiple myeloma

contributor:
Bramson, Jonathan
Medical Sciences

subject:
Engineered T cells
BCMA
Multiple Myeloma
Immunotherapy

abstract:
Multiple myeloma is a plasma cell cancer that progressively evolves to an aggressive, multi-drug resistant disease, which presents an unmet clinical need. In clinical trials, myeloma shows susceptibility to novel immunotherapeutic agents, particularly those targeting B-cell maturation antigen (BCMA). Among different classes of immunotherapies, T cell-based approaches have progressed the most due to their ability to induce durable responses in patients with advanced drug-resistant blood cancers. Most T cell engineering strategies rely on the use of chimeric antigen receptors (CARs), which although effective, can cause serious life-threatening toxicities. We created a new synthetic receptor, T cell antigen coupler (TAC), which recruits the endogenous T cell receptor and allows T cells to autoregulate their activity. Our experience in solid tumor models has shown that TAC-T cells are similarly efficacious and significantly less toxic than CAR-T cells. This thesis describes our optimization of BCMA-specific TAC-T cells and analysis of different anti-BCMA antigen-binding domains.
TAC receptor functions by engaging endogenous TCR-CD3 complex and redirecting it to the target of interest. In Chapter 3, we characterize optimization and humanization of the CD3-recruitment domain in the TAC scaffold and provide evidence that TAC-T cells are effective against multiple myeloma, irrespective of receptor surface levels. In Chapter 4, we describe selection of the human BCMA-binding domain and the creation of a fully humanized TAC receptor against BCMA. Chapters 5 and 6 describe how a BCMA-targeting antigen-binding domain that cross-reacts with an unknown antigen in mice augments in vivo efficacy of TAC- and CAR-T cells, respectively.
The work described in Chapters 3 and 4 presents an optimized, fully human BCMA-TAC that is being moved into clinical testing. The work in Chapters 5 and 6 improves our understanding of how antigen-targeting domains in synthetic receptors influence the functionality of engineered T cells.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: Multiple myeloma is an incurable blood cancer that has a remarkable ability to develop resistance to different types of chemotherapy. In recent years, treatments redirecting immune cells against tumors have shown impressive clinical responses against different types of chemotherapy-resistant blood cancers, including multiple myeloma. Our lab has developed a new technology for redirecting T cells against tumors, called T cell antigen coupler (TAC) receptor. This thesis describes optimization of a fully human TAC receptor specific for a target on the surface of myeloma cells, known as BCMA. Durable remissions induced by TAC-engineered T cells in a preclinical mouse model of myeloma in the absence of toxicity warrant further testing of this therapeutic in a clinical trial.


title: PASSIVITY-BASED CONTROL OF MULTIPLE QUAD-COPTERS WITH A CABLE-SUSPENDED PAYLOAD

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

abstract:
This thesis proposes several motion controllers to allow multiple quad-copters cooperatively
carry a cable-suspended payload. The problem is motivated by a desire for
developing a resilient scalable delivery vehicle that can be easily customized to its
payload. The control problem poses a number of challenges that complicate its design.
These include the quad-copter under-actuation, non-rigidity of the cables that
connect the payload to the copters, external disturbances, potential for inter-drone
collisions, and communication time-delay among the quad-copters. Simple robust
controllers with guaranteed stability are highly desirable in such safety critical applications. In this thesis, the energetic passivity property of the multi-body system combining
the quad-copters, cables and payload is employed to design novel motion controllers
for the system. These controllers make no assumption about the tension status of
the cables since this property holds whether the cables are in tension or not. The
design and stability analysis of the controllers rely on storage functions inspired by
the physical energy of the system. Quad-copters are able to produce thrust force
only along their propellers' axis. This under-actuation prevents direct application of
passivity-based controllers to the system under study. A cascade control structure
with an outer-loop position control and an inner-loop attitude control is employed to deal with the under-actuation. The first proposed controller assumes that the cables are attached to the quadcopters center of masses (COMs). This helps decouple the angular dynamics of the
quad-copters from the rest of the dynamics. As a result, the inner-loop attitude controllers
can be designed independently. First, angular controllers with exponentially
stable tracking errors are considered. While this produces nice theoretical results,
it requires measurements of linear acceleration and jerk, limiting its practical use.
Then, a modified cascade control structure is proposed that takes into account the
under-actuation and only needs measurements that are typically available in such
systems. Semi-global stability of the closed-loop system is shown, where the region
of attraction can be made arbitrary large by proper choice of control gains. An energy
observer/compensator is proposed to estimate perturbation-induced energy and
dissipate it through time-varying dampers. This helps suppress disturbance-induced
oscillations in the system response. The proposed controller is further revised to allow the cables be attached to the quad-copters and the payload at arbitrary points. This controller is augmented with an inter-drone collision avoidance term to prevent potential collisions among the drones. Another variation of the controller is developed by introducing inter-drone
coupling terms meant to improve the controller ability to preserve the formation shape
of the quad-copters. These coupling terms could potentially introduce time delay into
some of the feedback signal paths. An analysis is carried out to establish conditions
that the controller gains must satisfy in order to ensure closed-loop stability in the
presence of these time delays. The final contribution of this thesis focuses on the design of the reference positions for the quad-copters for the use in the controllers introduced earlier. In the proposed approach, the user specifies the desired position and orientation for the
payload. Given this desired pose, an optimization problem is formulated to find a
set of reference positions for the quad-copters that would minimize the total power
consumed under quasi-static conditions. The proposed controllers have been successfully evaluated in an indoor laboratory setting using measurements from a motion capture system and on-board IMUs. Results of the experiments are provided throughout the thesis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: INVESTIGATING THE EFFECT OF CLUSTER-BASED PREPROCESSING ON SOURCE-TO-SOURCE CODE TRANSLATION

contributor:
Paige, Richard
Computing and Software

abstract:
Numerous programming languages have been proposed over the last 60 years. Programming languages, like other software systems, can become obsolete: their compilers, virtual machines, interpreters and libraries are no longer fit for purpose. As such, programs written using obsolete programming languages may need to be modernized, relying instead on modern languages, libraries and tools. Modernization is both a technical and social process; in this thesis, we focus on the technical aspects of modernization, particularly software migration, wherein a program written in one programming language is transformed into an equivalent or similar program written in a different language. Migration happens because many software systems that were developed decades ago can no longer be maintained and need to be overhauled to make it possible to implement new processes that can take advantage of new technologies recently developed.
Migrating an existing codebase to a more efficient and modern programming language is often expensive, and there are different types of risks involved; for example, many functionalities may not be implemented properly after migration, i.e., the migration is inaccurate; or concerns for code quality may not be considered until the end of the migration; and for large code bases, the migration process may be slow, and may demand substantial resources to implement. Recent advancements in Artificial Intelligence in natural language translation have been widely accepted but their application to programming language translation have been limited due to the scarcity of parallel data (i.e., the collection of equivalent phrases in source language and their translations in a target language). This thesis explores a preliminary investigation into the use of unsupervisedlearning methods – specifically, a newly proposed K-Means clustering approach for preprocessing and analyzing the source code – prior to rule-based code translation. The thesis investigates such a process both generally and abstractly, and specifically, in the context of a concrete migration from C++ to Java. The thesis also presents a test set for evaluating such an approach, based on open source, which can be used as a general resource for both validating migration approaches and assessing their performance. The test results and our experiments show that our proposed translation approach based on unsupervised machine learning for preprocessing has a very good translation accuracy score of 77.89% and 81.34% when compared against an alternative approach with accuracy score of 33.24% and 59.96%, and also when compared with rule-based translation that excludes the preprocessing step with accuracy score 37.39% and 41.26%.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating the protective effects of physical activity on acute stress reactivity in IBS patients

contributor:
Heisz, Jennifer
Kinesiology

subject:
Gut-brain axis
Irritable bowel syndrome
Physical activity
Stress reactivity

abstract:
Introduction: Irritable bowel syndrome (IBS) is characterized by gastrointestinal (GI) symptoms, and as a consequence of dysregulated communication via the gut-brain axis, is highly comorbid with mental illnesses such as anxiety and depression. With no known cure, IBS patients must manage their symptoms through lifestyle factors. Physical activity is one such lifestyle factor that reduces GI symptoms and improves mental health; however, it remains unclear whether physical activity buffers against the acute worsening of IBS symptoms following a stressor.
Method: To investigate this, we evaluated the stress reactivity and recovery of 9 IBS patients and 13 healthy controls following exposure to acute stress. We exposed participants to an electronic Trier Social Stress Test (e-TSST) and measured changes in psychological stress (state anxiety), physiological stress (sympathovagal balance, where higher LF/HF ratio indicates greater stress system activation), and GI symptom severity before, during and every 20 minutes for one hour after. Physical activity was measured using the Stanford Seven-Day Physical Activity Recall questionnaire and quantified as weekly energy expenditure.
Results: IBS patients had higher state anxiety (p = .05), LF/HF ratio (p = .01) and GI symptom severity (p = .01) than healthy controls. Although the e-TSST did not exacerbate these group differences, higher state anxiety at baseline (p = .03) and higher LF/HF ratio in response to an acute stressor (p < .001) were associated with more severe GI symptoms within the first 20 minutes following the e-TSST. Importantly, IBS patients who were more physically active experienced less severe GI symptoms during that same timeframe (p = .03).
Conclusion: Physical activity may be a promising lifestyle factor for lessening GI symptom severity in response to an acute stressor.

abstract: Thesis

abstract: Master of Science in Kinesiology


title: Fall-related behavioural risk factors in community-dwelling older adults

title: Fall-related behavioural risk factors

contributor:
Wojkowski, Sarah
Rehabilitation Science

subject:
Falls
Community-dwelling older adults
Risk Factors
Fear of falling
Risk-taking

abstract:
This thesis includes three manuscripts with an overarching objective to improve understanding of behavioural risk factors for falling in community-dwelling older adults.
The first manuscript presented in Chapter two, presents a protocol for a scoping review. The objective of this scoping review was to highlight the current methods used to identify fall-related risk-taking behaviours in community-dwelling older adults, and to identify factors that might contribute to these behaviours.
The second manuscript (Chapter three) presents the results of the scoping review written in the format for publication. The review identified older adults are generally aware of their own falls risk and engage in protective behaviours to reduce their risk of falling. Older adults engaged in risk-taking behaviours based on the potential benefits outweighing perceived risk of the behaviours. An individual’s abilities, self-perception, personal values, and the environment likely influence the perception of risk which contributes to risk-taking behaviours.
The third manuscript (Chapter four) includes the analysis of clinical data from a community-based multi-component fall prevention program – the Building Balance Program. Individuals who participated in this six-week fall prevention program improved in balance ability, lower extremity muscle strength, mobility, and reduced fear of falling from baseline. Fear of falling (FoF) was the highest amongst the youngest participants despite having better physical function at the outset of the Program. This suggests that in addition to physical function, other factors, like psychological and social factors may be involved with FoF.

abstract: Thesis

abstract: Master of Health Sciences (MSc)

abstract: Falling is very common for older adults. Falling can lead to injuries and long-term side effects like fear of falling. Community-based exercise programs are a cost-effective way to help large groups of older adults reduce their risk of falling. Exercise programs can reduce older adults’ risk of falling by improving their balance and muscle strength. But exercise might not be enough to prevent falling in older adults. Falls can happen for various reasons, such as the activities or behaviours in which the individual participates. This thesis includes two studies presented in three papers aimed to better understand behavioural components which may be associated with falls. The results of this research suggest there is a psychological and social component involved with falling. The findings from this thesis highlight the importance of a holistic approach to and may help to inform the development of comprehensive interventions for fall prevention.


title: Examining Other Diplomacies of Sri Lankan Migrant Workers in South Korea: A Human-Centric Approach to Diplomatic Studies

contributor: Political Science - International Relations

subject:
International Relations
Diplomatic Studies
Other Diplomacies
Diplomacy
Non-State Actors
Societal-non-state-actors
Sri Lanka
Consular Affairs

abstract: This dissertation examines the concept of Other Diplomacies and argues for a human-centric approach to studying diplomacies.

abstract:
The academic field of Diplomatic Studies has long been insulated from critical interventions in the broader discipline of International Relations. While critical discussions surrounding gender, race, and class have been in ascendance in International Relations, Diplomatic Studies has managed to police its traditional disciplinary boundaries by centring scholarship around states and their accredited agents. The state-centric focus of the field has resulted in scholarship privileging the interests of states, which are abstract entities, over those of actual living communities; therefore, engage with issues primarily important to masculine, Eurocentric, and elite actors.
This dissertation intervenes in the academic field of Diplomatic Studies to decentre the state and reorient the field’s focus towards human-centric issues. It argues that societal non-state actors engage in Other Diplomacies as they interact with each other across boundaries of perceived differences. Thereby the dissertation contributes to the literature on Other Diplomacies by showing how Sri Lankan migrant workers engage in Other Diplomacies as they interact with their interlocutors in South Korea. It shows how Sri Lankan migrant workers utilise diplomatic skills to understand and navigate their gendered, racialised, and classist identities. This dissertation also contributes to the literature on consular affairs by arguing that it constitutes a part of Diplomatic Studies rather than a separate field of study. I sustain the human-centric focus of Other Diplomacies and shows that societal non-state actors provide and receive consular assistance from each other due to inadequate levels of assistance from their state. I propose that Other Diplomacies scholarship sustain a human-centric focus to uncover the gendered, racialised, and classist power hierarchies that societal actors must negotiate across as they interact with other actors, both state and non-state. Thereby this dissertation contributes to the critically inclined scholarship of Diplomatic Studies in particular and International Relations in general.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The academic study of diplomacy has focused on states and their accredited agents. This has resulted in scholarly work that mostly limits itself to issues, interests, and solutions relevant to states and their leaders. While these concerns are important and relevant, the scholarship has neglected to take the concerns of ordinary people and communities into account. The implications of this have been the excluding of issues related to race, class, and gender, among other distinctions from the scholarship. This dissertation argues that scholars studying diplomacy should also place humans at the centre of concern, rather than only states. It does so by examining how Sri Lankan migrant workers in South Korea engage in diplomacy through the functions of representation, communication, and negotiation. Therefore, the dissertation contributes by centring ordinary people and communities in the study of diplomacy and international relations and showing how they matter.


title: Foundations for a Contractualist Theory of Global Justice

contributor:
Waluchow, Wil
Humanities

subject:
Global Justice
Environment
Race, Gender, and Disabilities
Philosophy
Colonialism
Moral Philosophy
Political Philosophy
Ethics

abstract: This dissertation is the first step in a larger research project aimed at bridging the gap between Western philosophy and Indigenous thought. Here, I identify a methodological approach to the social contract by analyzing the tradition under an historical lens. I highlight that, along with the justificatory capacities of the social contract, comes a great deal of modelling involved in different versions of the social contract. This modelling comes in the form of four pre-contractual elements that different authors model in different ways. I show how different authors choose different structural problems or injustices that such theories want to address, as well as normative commitments that their theories are committed to, a standard of considerability of interests that identifies whose interests matter for those deliberating the terms of the contract, and a contractual device. I then go on to develop a framework for the development of a theory of global justice. I focus on the first three pre-contractual elements. For the sake of a global theory of justice, I identify four circumstances that need to be the focus of our concerns about global justice: Serious existential uncertainty due to climate change and massive animal extinction; the existence of a shared global institutional framework that forces us to think in terms beyond the state; the disproportionate distribution of the planet’s scarce resources; and the pervasive racial, gender and disabled-bodied-targeted inequalities that are characteristic of today’s world. I then move on to identify the “dignity of being” as a non-anthropocentric, core normative commitment that can be used as the basis for a theory of global justice. I conclude by developing a standard of considerability of interests that can adequately incorporate the interests of diverse beings into the social contract deliberations.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation is the first step in a larger research project aimed at bridging the gap between Western philosophy and Indigenous thought. Here, I identify a useful methodological approach to the social contract by analyzing the tradition under an historical lens. I highlight that, along with the justificatory capacities of the social contract, comes a great deal of modelling involved in different versions of the social contract. This modelling comes in the form of four pre-contractual elements that different authors model in different ways. I show how different authors choose different structural problems or injustices that such theories want to address, as well as normative commitments that their theories are committed to, a standard of considerability of interests that identifies whose interests matter for those deliberating the terms of the contract, and a contractual device. Once that has been established, I am able to provide some foundational elements for establishing a framework for the development of a theory of global justice. I focus on the first three pre-contractual elements.


title: Examining Face Template Representation and Adaptation Across Social and Emotional Categories in Adults and Children

contributor:
Rutherford, M.D.
Psychology

abstract: The ability for humans to quickly and accurately extract information from faces is a highly relevant social-cognitive skill. Much of the expertise adults have with faces has been attributed to norm-based coding (Valentine, 1991), referring to cognitive representations of face templates. Our face templates are generated based on our experience with faces and are consistently updating. Several separate face templates for different social categories have been observed. These mental representations can be manipulated within the lab to examine more about adults and children’s organization and reliance on face templates. This dissertation explored how children’s reliance on norm-based coding develops, new circumstances in which separate face representations are formed, and how long in-lab manipulations of multiple face representations persist. Chapter 2 revealed novel information about children’s reliance on norm-based coding for facial expression perception, demonstrating a long developmental trajectory to adult-like perception from 6-15 years of age. Chapter 3 discovered a new social categorical mental representation, religion. This chapter demonstrated that adults are capable of having separate cognitive representations for Christian and Muslim faces if the religion is made relevant to them; however, this was not observed in 8-year-olds. Chapter 4 found the first ability to manipulate mental representations of faces that are diverse, and that diversity itself can be a cue to face category membership. Chapter 5 examined how long manipulating multiple face representations persists through an opposing aftereffects paradigm, revealing a slower decay from other forms of manipulations. These studies demonstrated the complex nature of our cognitive face representations. This dissertation contributes new discoveries on norm-based coding, uncovering children’s developing reliance on norm-based coding, new circumstances in which separate face templates evolve in adults and children, and how long manipulating our face space may persist under opposing aftereffects paradigms. Recognizing differences in faces is an essential human skill; examining face template representations allows for discovering how our mind develops this face perception expertise.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Humans are quick at noticing social aspects of faces and rely on mental representations of how faces appear. Our mental representation of a face is based on faces we encounter and can be influenced within the laboratory. Across four studies we examined and manipulated adults and children’s mental face representations. Chapter 2 revealed that children’s reference to facial expression mental representations develops from 6-15 years of age. Chapter 3 discovered that if religious membership is made significant to adults, they have separate representations for Christian and Muslim faces, but 8-year-olds do not. Chapter 4 found that our mental representations may incorporate the diversity of social groups as a separate social category of faces. Chapter 5 revealed that manipulating multiple face representations persists for several days. This body of work demonstrates the complexity of our face representations, and how this beneficial skill for face perception adapts based on our experience.


title: DEGRADATION MECHANISM OF PEROVSKITE SOLAR CELLS

contributor:
Xu, Gu
Metallurgy and Materials Science

subject:
degradation
phase transition

abstract: The perovskite solar cells have attracted much attention recently due to their low fabrication cost and high power conversion efficiency. However, the instability of such devices remained a serious challenge, which is yet to be resolved despite many attempts. In this thesis, the moisture degradation mechanism has been uncovered. It was found that the perovskite structure can be reconstructed when annealed at around 90℃, which leads to a reversible device of a much higher device lifetime. Following the experimental explorations, modelling work has also been conducted to simulate the water diffusion during the degradation and recovery. It was found that the moisture diffusion was initiated at the surface imperfection, where the activation energy for diffusion can be reduced. Based on these discoveries, a fresh structural negotiation method has been proposed to obtain a stable FAPbI3 phase of a suitable bandgap for photovoltaics, which showed a reduced Gibbs free energy of 0.12eV compared with the δ phase. In addition, the activation energy for such phase transition was calculated to be 0.45eV, meaning that the discovered phase is protected by both thermodynamics and kinetics. All this opens an unprecedented avenue in perovskite research, which will hopefully be of intrinsic interest to the broad materials research community as well.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Study of Hunting Scenes and Virtus in Roman Art, Third to Sixth Centuries A.D.

contributor:
George, Michele
Classics

subject:
Classics
Roman Art
Late Antiquity
Sarcophagi
Virtus
Mosaics
Silverware

abstract: In Rome, the activity of hunting was a pastime traditionally associated with the emperor and aristocracy. As such, hunting imagery in Roman art became symbolic of masculinity and power, expressions of which were important for the self-representation of status-conscious citizens. More specifically, virtus, often translated as “manliness” or “courage,” is the principal quality that is expressed through hunting scenes, although other ideas such as wealth and erudition were alluded to in these scenes as well. This thesis examines hunting scenes in the media of sarcophagi, mosaics, and silverware from the third to the sixth centuries AD. It focusses on the kinds of hunting imagery found on different media in order to discern the values that were important to patrons in the later Roman period, and the ways in which these values were expressed in the visual arts. In the funerary context, mythological hunting scenes on sarcophagi most often present the deceased as a man of virtus. However, owing to the Entmythologisierung of Roman sarcophagi during the third century, the ways in which virtus was expressed through these scenes underwent significant change during this period. On domestic floor mosaics, virtus was also a principal virtue that was expressed, but other ideas such as wealth and generosity were also displayed on hunting scenes in this medium, both mythological and non-mythological. Moreover, hunting scenes on silverware often highlight the wealth of the vessel’s owner. Additionally, allusions to a patron’s paideia, his formal educational background in Greek and Latin literature, as well as expressions of one’s Christian faith, also served as claims of membership in exclusive groups.

abstract: Thesis

abstract: Master of Arts (MA)


title: Knowledge translation: The Development, Evaluation, and Follow-up of Online  and In-person Do-Live-Well Workshops for Occupational Therapists

contributor:
Letts, Lori
Rehabilitation Science

subject:
Occupational therapy
Continuing education
Health promotion
Online learning

abstract:
This dissertation presents knowledge translation processes regarding the Do-Live-Well (DLW) framework for Canadian occupational therapists (OTs) and consists of five chapters. The first chapter explains why this DLW educational research was needed and provides a description of the theoretical frameworks used in the DLW educational project, including knowledge translation, program evaluation, and adult education frameworks.
	In chapter 2, I described the process of developing the equivalent online and in-person educational workshops that were evidence- and theory-based. Three phases were undertaken to develop the DLW workshops: (1) understand DLW training needs, (2) develop educational content and apply the problem-based learning approach, and (3) conduct a usability test of the online workshop website. The findings from each phase were used in DLW online and in-person workshops.
	In chapter 3, findings of a mixed-methods study are presented. The study was designed to (1) compare the effectiveness of online education with in-person learning regarding the DLW framework for Canadian OTs and (2) further explore workshop participants’ experience in both learning formats. While there were no statistically significant differences in knowledge gained, the in-person group was more satisfied with their learning. Participants in both groups valued the importance of personal interactions in learning; the online learners said online learning did not provide the same quality of in-person interactions that in-person education provided.
	In chapter 4, I explored workshop participants’ experiences of using the DLW framework in practice three months after DLW workshops by asking about benefits, facilitators, and barriers of using the DLW framework in practice. Participants valued the importance of the DLW framework, but there were challenges of using the DLW framework, associated with structural, organizational, provider, innovation, and patient factors.

	In chapter 5, the contributions of the DLW educational project are discussed by providing insights related to knowledge translation using Knowledge-To-Action cycle.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The purpose of this dissertation is to present the processes of how knowledge about the Do Live Well (DLW) framework, a Canadian health promotion approach, has been disseminated and applied in Canadian occupational therapy practice. This dissertation presented three major contributions: (a) It describes the detailed processes of developing theory- and evidence-based educational workshops regarding the DLW framework for Canadian occupational therapists (OTs) that could be replicable in continuing education for health care professionals. (b) It compares the effectiveness of an online DLW workshop compared to a traditional in-person DLW workshop for Canadian OTs and explores learners’ experiences in participating in the two different educational workshops. (c) It offers an understanding of workshop participants’ experiences and perspectives on the use of the DLW framework in practice after they completed the workshops.


title: Nuclear Vision: Canada, Modernity, and the Nuclear Age, 1942-1979

contributor:
McKay, Ian
History

subject:
Canadian History
Nuclear Energy
The Nuclear Age
Modernity
Atomic Energy

abstract:
This thesis proposes that the nuclear age offered high modernity and technological nationalism a central position in the making of modern Canada. The nuclear age influenced modern Canada’s social, economic, and political history and it did so by telling Canadians they were, essentially, a modern people governed by a modern state. From the 1940s to the end of the 1970s, Canada’s development of the nuclear industry reflected the pursuit of science and technology to create modern forms of energy production. Canadians were urged to see in nuclear power a way of remaining competitive in a changing global order. It offered them new industries at many stages of the nuclear cycle. The post-war era reflected a changing direction in the country’s central ideological direction – one defined since the 1840s by liberalism and a subordinate role in the British Empire. The creation of the Canadian nuclear cycle signified a transition to a new stage in which Canada, now imagined by some to be a nation, actively sought out modern forms of social and economic progress. Nuclear energy systems came to fruition at a moment when Canada was establishing new directions as a sovereign state vying for greater global political and economic influence on the global stage. This thesis argues that this pattern was no mere coincidence: this technological nationalism was the logical outcome of deep-seated tendencies.
	Yet, many citizens remained skeptical of the nuclear age’s possibilities. Although the federal government had established its nuclear cycle to develop the peaceful uses of atomic energy, its birth in the shadows of the Second World War and the Manhattan Project also provoked a widespread sense of discomfort. The dropping of the atomic bomb in 1945 solidified fears of nuclear energy long before the AECL built its first reactor on the shores of Lake Huron. Canadians en masse rejected the country’s participation in the development of nuclear weapons and, as Lester Pearson learned to his cost in 1963, were adamant that Canada should remain a nuclear-weapons-free nation. Successive governments in the 1950s and 1960s faced public backlash regarding Canada’s complicity in the stockpiling of nuclear arms, the production of uranium for American weapons, and its involvement in weapons tests. Born out of the peace movements and ecological movements of the 1960s, anti-nuclear groups emerged in the 1970s to oppose the nuclear industry. These groups shared members, ideas, and momentum, and the chasm between anti-war and environmental activism was progressively bridged as the 1970s proceeded. Both the anti-nuclear and anti-bomb activists were essential to challenging the path and direction of the Canadian nuclear system and its role in creating political and environmental uncertainty. Such fears remained a constant social reminder throughout the post-war era of the mutually assured destruction associated with atomic energy and the Cold War arms race. Indeed, Canada’s peaceful nuclear program did not always seem so peaceable, as activists in both camps argued more and more empathetically.
Canada’s nationalistic pursuit of a nuclear modernity also entailed the quest of a narrow form of utopianism – one in which a future-oriented Canada provided greater social and economic freedoms under the aegis of liberal democracy. At the community level, nuclear energy symbolized the changing senses and sensibilities of living through modernity – the perception that the core structures of society were giving way to new social realities and that the relations of time and space were shifting. While nuclear energy symbolized the social and economic benefits of the cultural revolution of the nuclear age, it also aroused the concerns and fears about modernity. The conflicts between the pro- and anti-nuclear movements of the 1970s and 1980s were in many respects an extension of debates over high modernity and techno-nationalism.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: This thesis explores the history of Canada’s nuclear age between 1942 and 1979 and examines how both Canadians and the state perceived the development of the country’s nuclear industry. It examines how Canada gained entrance into the nuclear club – joining the ranks of the Manhattan Project – its post-war developments in nuclear power, and the ways in which nuclear energy bolstered a form of nationalism predicated on technological prowess. The need to develop Canada’s nuclear industry reflected the larger social, political, and economic changes occurring in the post-war era. In many ways, the history of Canada’s nuclear age is the history of how societies act and react to modernity – the radical transformation of perceptions of space and time. This thesis examines that process of change and its influence on Canadians’ responses to the modern world around them.


title: A triboelectric-based method for rapid characterization of powders

contributor:
Rajabzadeh, Amin
Srinivasan, Seshasai
Mechanical Engineering

subject:
Tribocharging
Powder characterization
Particle-laden flows
Particle-wall collision number

abstract: In this research, a tribocharging model based on the prominent condenser model was used in combination with an Eulerian-Lagrangian CFD model to simulate particle tribocharging in particle-laden flows. The influence of different parameters on particle-wall interactions during particle transport in a particle-laden pipe flow was elucidated. An artificial neural network was developed for predicting particle-wall collision numbers based on a database obtained through CFD simulations. The particle-wall collision number from the CFD model was validated against experimental data in the literature.  The tribocharging and CFD models were coupled with the experimental tribocharging data to estimate the contact potential difference of powders, which is a function of contact surfaces' work functions and depends on the physicochemical properties of materials. While the contact potential difference between the particles and wall is an essential parameter in the tribocharging models, the accurate measurement of the property is a complex process requiring a highly controlled environment and special equipment. The results from this research also confirm that particle tribocharging is very much dependant on the particle-wall collision number influenced by various parameters, such as particle size and density, air velocity, and pipe dimensions. Plotting the experimentally measured charge-to-mass ratios against the calculated contact potential differences for samples with different protein contents uncovered a linear trend, which opens a novel approach for protein quantification of powders for a given particle size. Therefore, an algorithm is proposed for rapid quantification of protein content and particle size determination of samples during transport in particle-laden flows based on the triboelectric charge measurement. The algorithm requires a CFD-based artificial neural network to estimate the particle-wall interactions based on the hydrodynamic characteristics of the particles and flow systems.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: ὉI ΠΟΛΎΤΡΟΠΟΙ ἭΡΩΕΣ: A STUDY OF HOMERIC HEROISM

contributor:
Mattison, Kathryn
Classics

subject:
Greek Epic
Greek Literature
Heroism

abstract: This thesis investigates how the foundational value of connection underlies all forms of heroism within the Homeric epics. It argues that the traditional values of honour and shame that inform heroic choices require the framework of connection to operate upon. Homer takes the foundational value of connection, and the secondary values of honour and shame and presents many forms of both complicated and uncomplicated heroism across two distinct mediums. The Iliad presents the reader with a variety of Iliadic heroes who operate within the medium of the battlefield, including Ajax as the uncomplicated form of Iliadic heroism and Achilles and Hektor as complicated forms of this heroism. The Odyssey showcases the evolution of Homeric heroism from the medium of the battlefield to the medium of the nostos, with Odysseus’ evolution across the poem paralleling the evolution of Homeric heroism. The foundational value of connection is what allows the values of honour/shame to have significance in Homeric society, and therefore by engaging with connection and then the honor/shame matrix, a hero was able to gain time which upon his death was converted into kleos by his connections. Odysseus serves as the focal point for multiple types of heroism as his characterization in the Iliad, while he operates within the parameters of the Iliadic hero, is proleptic of his evolution into the Odyssean hero in the Odyssey.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: This thesis investigates how the foundational value of connection underlies all forms of heroism within the Homeric epics. It argues that the traditional values of honour and shame that inform heroic choices require the framework of connection to operate upon. Homer takes the foundational value of connection, and the secondary values of honour and shame and presents many forms of both complicated and uncomplicated heroism across two distinct mediums. I lay out the many varying forms of heroism through an examination of the various characters that embody them. There is a specific focus on the character of Odysseus as he operates within Iliadic heroism in the Iliad as well as he redefines heroism through his journey in the Odyssey, creating the form of Odyssean heroism.


title: CYB5D2 IN BREAST CANCER

contributor:
Tang, Damu
Medical Sciences

abstract: Breast cancer (BC) the second leading cause of cancer death in Canadian women.1 The disease is affected by numerous genes with more to be discovered. Our lab has recently published cytochrome b5 domain containing 2 (CYB5D2) as a candidate tumor suppressor in BC.2 My research further supports this concept. In a tetracycline inducible CYB5D2 lines previously constructed in HER2+ HCC1954 BC cells, induction of CYB5D2 inhibited cell proliferation. The inhibition can be partially recovered once induction pressure was removed; recovery level was associated with the length of CYB5D2 expression with longer CYB5D2 induction accompanied with reduced recovery ability. This in vitro inhibition is supported by in vivo evidence; in xenografts formed by HCC1954 Tet-CYB5D2 cells, induction of CYB5D2 via administration of doxycycline in drinking water significantly inhibited tumor growth. To examine the potential mechanisms underpinning CYB5D2-derived inhibition, I was able to co-immunoprecipitate (Co-Ip) CYB5D2 and PTEN (phosphatase and tensin homolog) following ectopic expression of both in 293T cells, indicating the formation of the CYB5D2-PTEN complex. This possibility is further supported by co-localization of both ectopic proteins in 293T cells detected by immunofluorescence analysis. Furthermore, in HCC1954 Tet-CYB5D2 cells, a complex containing CYB5D2 and endogenous PTEN was co-immunoprecipitated following induction of CYB5D2 expression. Collectively, evidence supports an association of CYB5D2 with PTEN. I further characterized this association. Binding of PTEN with CYB5D2 was determined in 293T cells using a set of CYB5D2 mutants, including ΔCYB5, ΔTM, D86G, R7P, R7G, and Q167K. Complexes containing PTEN and individual CYB5D2 mutants could be precipitated via either CYB5D2 or PTEN, but not both. While the situation was not ideal, evidence nonetheless indicates that these structural elements of CYB52 were not essential for its association with PTEN.

abstract: Thesis

abstract: Master of Science in Medical Sciences (MSMS)


title: Examining the associations of physical activity, resiliency, mental health, and heart rate variability in graduate students during a pandemic

title: Physical activity, resiliency, mental health, and heart rate variability in graduate students during a pandemic

subject: Physical activity, Mental health, Resiliency, COVID-19

abstract:
Introduction: The COVID-19 pandemic has resulted in higher-than-normal levels of anxiety and depression, especially among graduate students whose academic trajectory was disrupted. Physical activity and trait resiliency have both been shown to protect against stress-induced anxiety and depression during the pandemic. However, it remains unknown whether the same was true for graduate students and what biological mechanism, such as heart rate variability (HRV) might underpin these relationships.
Method: We examined change in stress, current physical activity, and trait resiliency to identify key factors associated with better mental health outcomes in a national sample of graduate students (N = 61) who were recruited during the COVID-19 pandemic. We evaluated the unique contributions of change in graduate-school-related stress, physical activity (moderate, vigorous, and fitness), and trait resiliency to both anxiety and depression. We conducted moderation analyses to explore the processes through which these variables interact and mediation analyses to examine whether HRV was part of the underlying mechanism. Questionnaire were used to assess graduate-school-related stress, physical activity (moderate, vigorous), and trait resiliency. We estimated physical fitness using the six-minute walk test and captured resting HRV using a validated mobile application.
Results: Graduate students reporting greater change in school-related stress were more anxious and depressed; however, those who engaged in more moderate physical activity were less anxious and those with higher trait resiliency were less anxious and depressed. Moderation analyses revealed a “stress threshold” for moderate physical activity whereby students who were more physically active were more protected from anxiety symptoms than their lower active peers; but this was only true for people whose stress levels increased a little or moderately but not for people whose stress levels increased a lot. In contrast, trait resiliency was shown to buffer against depression regardless of change in stress level. HRV did not mediate these relationships.
Conclusion: Graduate students experienced significant mental strain during the COVID-19 pandemic, but physical activity and trait resiliency may be promising protective factors.

abstract: Thesis

abstract: Master of Science in Kinesiology


title: Exploring Online and Offline Social Hierarchies and their Influence on the Motor Resonance System

contributor:
Obhi, Sukhvinder
Psychology

subject: Motor Resonance

abstract: Previous physiological work has established that factors such as power and status modulate the motor resonance system. Motor resonance is classified as motor activity that occurs during action observation in the absence of action execution. However, no previous work has explored whether these factors have downstream behavioural effects on automatic imitation using a community sample (as opposed to a university student sample). In addition, no prior work has examined whether online social hierarchies (as opposed to real-world social hierarchies) also modulate this system. As such, this dissertation aims to corroborate and extend on previous physiological work in the field and explore whether online status has similar downstream effects on motor resonance compared to previously documented effects of offline (real-world) status using behavioural and physiological methods. In chapters 2-3, I provide evidence from community-based behavioural studies that suggest high socioeconomic status (SES) and high power individuals are less susceptible to automatically imitating “other-oriented” social stimuli compared to their low SES and low power counterparts. In chapters 4-5, I show that Instagram followers exhibit significantly greater motor cortical output (via transcranial magnetic stimulation induced motor-evoked potentials) during action observation compared to Instagram leaders. I also show that this effect can be extended behaviourally using the automatic imitation task, whereby Instagram leaders are less susceptible to automatically imitating “other-oriented” social stimuli compared to Instagram followers. In chapter 6, I begin to explore the effect of online status on behavioural mimicry. I show that Instagram leaders exhibit reduced behavioural mimicry during an online interaction compared to Instagram followers. In the final chapter of this dissertation, I summarize the contributions and limitations of each chapter and recommend future avenues of research. Overall, this dissertation furthers our understanding on how online and offline social hierarchies modulate the motor resonance system using behavioural and physiological methods.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Droplets as model systems for investigating 2D crystals, glasses and the growth dynamics of granular aggregates

contributor:
Dalnoki-Veress, Kari
Physics and Astronomy

subject:
Soft-Matter
Emulsion
Crystal-to-glass
Micropipette deflection
Crystal
Glass

abstract:
The research presented in this thesis focusses on the experimental study of two fundamental questions: the crystal-to-glass transition and how aggregates of adhesive droplets spread on a surface. Aggregates made of lightly adhesive oil droplets are used as models for crystals or amorphous glasses. The force applied on the aggregates can be directly measured as they are compressed.

A large portion of the work focusses on the crystal-to-glass transition and tries to answer the following question: how many defects are needed in a crystal for its mechanical response to be like a glass? To answer this question, the mechanical response of a perfect mono-crystal is measured. It is found that crystals deform elastically until they fail catastrophically in a single event once the force exceeds a critical value: the yield stress. The force measured during the compression of a crystal shows a well defined number of peaks which only depends on the initial geometry of the aggregate. As defects are added (the amount of disorder increased) the number of peaks in the force measurement increases rapidly before it saturates at a value obtained for model glasses. The magnitude of the force peaks also decreases as disorder is introduced. This work concludes that even a small amount of disorder in a crystal has a significant impact on its mechanical properties.

In the second project, the spreading of a monodisperse aggregate of oil droplets is studied. Droplets are added one-by-one to a growing aggregate and the area covered on the interface is measured. It is found that after an initial 3D growth, the height of the aggregate saturates and the growth only happens in 2D along the horizontal direction. The growth is analogous to a puddle of liquid. In analogy with the capillary length in liquids, the ``granular capillary length" is introduced to characterize the balance between buoyancy acting on the droplets and the adhesion strength. The height of the aggregates, in the later stage of the growth, is set by this length scale. A method was developed to characterize the adhesion between two droplets, a key parameter in this experiment, as a function of the relevant experimental parameters.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Low-loss tellurium oxide devices integrated on silicon and silicon nitride photonic circuit platforms

contributor:
Bradley, Jonathan D. B.
Engineering Physics

subject:
Photonics
Silicon photonics
Optical amplifier
Tellurium oxide
Integrated optics
Erbium
Resonators

abstract: Silicon (Si) and silicon nitride (Si3N4) have become the dominant photonic integrated circuit (PIC) material platforms, due to their low-cost, wafer-scale production of high-performance circuits. However, novel materials can offer additional functionalities that cannot be easily accessed in Si and Si3N4, such as light emission. Tellurium oxide (TeO2) is a novel material of interest because of its large linear and non-linear refractive indices, low material losses and large rare-earth dopant solubility, with applications including compact low-loss waveguides and on-chip light sources and amplifiers. This thesis investigates the post-processing integration of TeO2 devices onto standardized Si and Si3N4 chips to incorporate TeO2 material advantages into high-performance PICs. Chapter 1 introduces the state-of-the-art functionality for various integrated photonic materials as well as methods for integrating multiple materials onto single chips. Chapter 2 presents the development of a high-quality TeO2 thin film fabrication process by reactive RF sputtering, with material refractive indices of 2.07 and optical propagation losses of <0.1 dB/cm at 1550 nm. Chapter 3 investigates a conformally coated TeO2-Si3N4 waveguide platform capable of large TeO2 optical confinement and tight bending radii, characterizing fiber-chip edge couplers down to ~5 dB/facet, waveguide propagation losses of <0.5 dB/cm, directional couplers with 100% cross-over ratio, and microresonators with internal Q factors of 7.3 × 105. In Chapter 4 a spectroscopic study of TeO2:Er3+-coated Si3N4 waveguide amplifiers was undertaken, with internal net gains of up to 1.4 dB/cm in a 2.2-cm-long waveguide and 5 dB total in a 6.7-cm-long sample demonstrated, predicted to reach >10 dB could 150 mW of pump power be launched based on a developed rate-equation model. Chapter 5 demonstrates TeO2-coated microtrench resonators coupled to silicon waveguides, with internal Q factors of up to 2.1×105 and investigates environmental sensing metrics of devices. Chapter 6 summarizes the thesis and provides avenues for future work.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Claim Reserving: Classical versus Machine Learning Methods

contributor:
Abdallah, Anas
Pirvu, Traian
Statistics

abstract: In this thesis, we investigate loss reserving with classical methods and deep learning approach. Claim reserving is a crucial task in non-life insurance. Insurance companies have historical data on claim amounts. These data are usually aggregated to loss triangles, which can be analyzed to predict the claim reserve. The reserves for different business lines are related and a copula regression model can link the claims of different business lines. We apply the models on real data and obtain both reserve estimates and risk capitals. Product copula, Gaussian copula, Frank copula and Student’s t copula are used to model the dependence of the two business lines. The AIC of Student’s t copula model is 1.3 percent smaller than the AIC of the Gaussian copula model. The AIC of Frank copula model and Product copula model is within 0.9 percent of the Gaussian copula model’s AIC. The Gaussian copula model generates the largest risk capital gain among all the copula models. Neural networks are popular machine learning methods and have been applied to the loss reserving problem. The DeepTriangle model is a deep learning framework for forecasting paid losses. At each accident year and development year for which we have data, we predict future losses based on observed history. Each training and testing sample is associated with an accident year - development year pair. The input for the training and testing sample is the observed incremental paid loss and claims outstanding as of the accident - development year pair. To capture the dependency between two lines of business, we use the incremental paid loss from two business lines as input to the deep triangle model. The incremental paid loss from the personal auto line and the incremental paid loss from the commercial auto line correspond to the first and the second component of the sample. The predicted reserve from the deep triangle model is within two percent, three percent and nine percent of the predictions from the Gaussian copula, Frank copula and Student’s t copula models, respectively.

abstract: Thesis

abstract: Master of Science (MSc)


title: Analogue Hawking radiation as a logarithmic quantum catastrophe

contributor:
O'Dell, Duncan
Physics and Astronomy

subject:
Black holes
Hawking radiation
Catastrophe theory
Logarithmic catastrophe theory
Caustics
Quantum mechanics
Bose-Einstein condensate
Analogue black holes
Higher-energy theory
Saddle-point method
Airy function
Pearcey function
Bifurcation

abstract: Masters thesis of Liam Farrell, under the supervision of Dr. Duncan O'Dell. Successfully defended on August 26, 2021.

abstract: Caustics are regions created by the natural focusing of waves. Some examples include rainbows, spherical aberration, and sonic booms. The intensity of a caustic is singular in the classical ray theory, but can be smoothed out by taking into account the interference of waves. Caustics are generic in nature and are universally described by the mathematical theory known as catastrophe theory, which has successfully been applied to physically describe a wide variety of phenomena. Interestingly, caustics can exist in quantum mechanical systems in the form of phase singularities. Since phase is such a central concept in wave theory, this heralds the breakdown of the wave description of quantum mechanics and is in fact an example of a quantum catastrophe. Similarly to classical catastrophes, quantum catastrophes require some previously ignored property or degree of freedom to be taken into account in order to smooth the phase divergence. Different forms of spontaneous pair-production appear to suffer logarithmic phase singularities, specifically Hawking radiation from gravitational black holes. This is known as the trans-Planckian problem. We will investigate Hawking radiation formed in an analogue black hole consisting of a flowing ultra-cold Bose-Einstein condensate. By moving from an approximate hydrodynamical continuum description to a quantum mechanical discrete theory, the phase singularity is cured. We describe this process, and make connections to a new theory of logarithmic catastrophes. We show that our analogue Hawking radiation is mathematically described by a logarithmic Airy catastrophe, which further establishes the plausibility of pair-production being a quantum catastrophe

abstract: Thesis

abstract: Master of Science (MSc)


title: MAMMOTHS, MASTODONS, AND CHRONOSPATIAL WARMING: EVOLUTIONARY ANALYSES OF PLEISTOCENE PROBOSCIDEANS FROM TEMPERATE AND TROPICAL LOCALES

contributor:
Poinar, Hendrik N.
Golding, G. Brian
Evans, Ben J.
Biology

subject:
Ancient DNA
Palaeogenetics
Mammoths
Mastodons
Pleistocene

abstract: The Quaternary (the approximately the last 2.6 million years) of North America is a tremendously exciting time period to study with respect to ecology. It saw periods of immense climatic turbidity - the expansion and retreat of continental ice-sheets and large swings in temperature, resulting in the wide scale restructuring of terrestrial ecosystem. It also saw widespread migrations of many species and out of Eurasia, mostly notably of modern humans. Ancient DNA offers powerful tools to examine the relationships and responses of megafunal species to these events, but has largely focused on cold-adapted species, and within radiocarbon-time (i.e. the last 50 thousand years). In this thesis I work to expand our understanding of the genetic landscape of Pleistocene megafuna in three ways. First, I describe the analysis of coprolites from Bechan Cave, Utah and characterize the mammoth inhabitants in the broader context of North American mammoths. Second, I characterize the diversity of American mastodons across the continent and through time, showing that their range likely repeatedly expanded and contracted in response to Pleistocene glaciations. Lastly, I begin to fill in some of the gaps in the American mastodon dataset from chapter 3, and begin to address some of the taxonomic and biogeographic questions about American and Pacific mastodons in Idaho. Understanding how North American megafauna responded to these climatic and anthropogenic stresses may help to explain why so many species went extinct at the end of the last glaciation, and how species may respond to present day warming. However, it is important to include taxa from warmer locales and environments to ensure our models and hypotheses are comprehensive.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: Pleistocene North America was a time period of immense climatic turbidity, with temperature swings greater than 15°C in response to the expansion and contraction of continental ice-sheets. Despite these massive swings in temperature, many species managed to thrive on the continent and adapt to glacial-associated ecosystem restructuring. Ancient DNA from Pleistocene megafauna can serve as a very useful tool to answer many questions about the distribution of megafaunal species, and how they may have responded to these climatic events. However, most studies have largely focused on species adapted to cold environments and from the last fifty thousand years. In this thesis I extend our knowledge of the genetic landscape of Pleistocene proboscideans, characterizing the mammoth inhabitants of Bechan Cave, Utah, and producing the first look at American mastodon diversity through space and time. This work increases our representation of warm-adapted specimens and characterizes the effects of glacial cycles on megafauna populations.