VictorJuiz/thesis huggingface dataset:
Biocompatibility of Poly-3-amino-4-methoxybenzoic Acid-Gelatin Hydrogel as a Novel Therapy for Cardiac Arrhythmia

After myocardial infarction, the nonconductive nature of fibrotic tissue results in ventricular dysfunction by electrically uncoupling the remaining viable cardiomyocytes in the scar region. The uneven conductive properties between normal myocardium and scar tissue may result in arrhythmias leading to sudden cardiac death or heart failure. Our laboratory has synthesized a conductive biomaterial polymer, poly-3-amino-4-methoxybenzoic acid-gelatin (PAMB-G), that can re-synchronize myocardial contraction in vivo. To evaluate the potential of PAMB-G for clinical application, its toxicity must be assessed. I found that PAMB-G was non-cytotoxic to cardiomyocytes and stem cells. The therapeutic dose of PAMB-G was below biomaterial’s no-observed-adverse-effect-level. The infarct rat hearts injected with PAMB-G have similar toxicity parameters (body weight, organ-brain ratios, hematologic parameters, serum parameters, and histology) compared to those injected with saline up to 3 months. PAMB-G did not result in any reproductive toxicity. In conclusion, PAMB-G is a non-toxic conductive biomaterial that should proceed to clinical evaluation for patients with desynchronized contraction.

Keywords: arrhythmia
biomaterial
cardiology
conductive
polymer
toxicity
Advisor: Li, Ren-Ke
Investigating Analogues of Parathyroid Hormone (PTH) and PTH-related Peptide (PTHrP) using UMR106-01 Osteocytic Cells to Determine Anabolic and Catabolic Response Ratios and Predict in Vivo Responses

Decreased bone mineral density due to Osteoporosis stems from an imbalance of bone resorption and deposition. Anabolic agents, Teriparatide and Abaloparatide increase bone deposition via PTH1R activation. These are analogues of endogenous peptides parathyroid hormone (PTH) and parathyroid hormone-related-peptide (PTHrP), respectively. However, they also induce hypercalcemic side-effects. We compared various PTH/PTHrP analogues for abilities to regulate anabolic and catabolic effects and used this to predict in vivo responses. UMR106-01 cells were used to measure PTH1R stimulation (xCELLigence) and PTH induced anabolic (SOST, DKK1 and Osteocalcin) and catabolic (RANKL/OPG, M-CSF and IL-6) responses. Teriparatide, PTHrP1-34 and Abaloparatide were most potent for PTH1R stimulation and for the anabolic and catabolic regulation. Tyr1PTH1-34 and PTH2-34 exhibited significantly decreased potencies and β-Arr-biased-agonist, D-Trp12Tyr34PTH7-34 produced no response. These findings show N-terminal modifications alter peptide activity; however, all responsive peptides were predicted to act similarly in vivo except Abaloparatide, predicted to increase the catabolic response.

Advisor: Mitchell, Jane
Modelling Guided Attention using Learned Target-category Associations

In addition to saliency and goal-based factors, a scene’s semantic content has been shown to guide attention in visual search tasks. Here, we ask if this rapidly available guidance signal can be leveraged to learn new attentional strategies. In two variants of the scene preview paradigm (Castelhano Heaven, 2010), participants searched for targets embedded in real-world scenes with target locations linked to scene gist. In one experiment, we found that activating gist with scene previews significantly increased search efficiency in a manner consistent with formal theories of skill acquisition. In the second experiment, search efficiency significantly increased across the experiment; however, this learning effect did not differ between preview condition. Results from a computational model suggest that, when preview information is useful, stimulus features may amplify the similarities and differences between exemplars.

Keywords: Attention
Attentional guidance
Computational modeling
Learning
Scene perception
Visual perception
Advisor: Mack, Michael L
Assessing the Impact of Curing on Chloride Penetration Resistance of the Concrete Cover Zone

There is a lack of rapid test methods for accurately assessing the impact of curing on the differential hydration through the depth of the concrete cover as well as the impact on chloride penetration resistance. In the absence of adequate performance assessment tools, prescriptive curing specifications have been adopted for concretes exposed to chlorides and other exposures, such as in CSA A23.1-19. There is a desire to switch to a performance specifications for curing, particularly by the precast concrete industry, that could be used to assess the impact of using of accelerated heat curing methods widely used to obtain high early-strength gain and maturity. Two methods are presented and evaluated in this thesis. The first involves proling the initial rate of absorption of a sodium chloride solution. The second makes use of embedded arrays of electrodes to map the formation factor with depth, enabling a multi-mechanistic approach to the problem.

Keywords: Chloride Penetration
Concrete Cover
Differential Hydration
Electrical Resistivity
Performance Test
Sorptivity
Advisor: Hooton, Robert D
Distinct CSF1 Microenvironments Maintain Monocytes within a Perivascular Bone Marrow Niche

Hematopoietic stem and progenitor cells reside within specialized niches. Colony stimulating factor 1 (CSF1) might serve as a monocyte niche factor given its critical role in regulating survival, proliferation, and differentiation of myeloid lineage cells. However, the role of CSF1 in adult monopoiesis and its functionally important cellular sources remain uncertain. Here, we show that conditional deletion of Csf1 in adulthood regulated monocyte abundance independent of its effects on bone development. Bone histology revealed monocytes reside near sinusoidal endothelial cells (ECs) and leptin receptor (Lepr)-expressing perivascular stromal cells. Concomitantly, targeted in vivo deletion of Csf1 from sinusoidal but not arteriolar ECs selectively reduced Ly6Cnegative monocytes in the bone marrow and blood. Combined depletion of Csf1 from both Lepr-expressing perivascular stromal cells and ECs had additive effects, further decreasing classical Ly6Chigh cells. Thus, different monocyte subsets are supported by distinct cellular sources of CSF1 within a perivascular bone marrow niche.

Keywords: bone-marrow
CSF1
microenvironment
monocyte
niche
Advisor: Robbins, Clinton S
A Control-theoretic Model of Sensorimotor Adaptation

This thesis presents a preliminary control theoretic model of sensorimotor adaptation driven by visual error feedback. We formalize qualitative experimentally observed dynamic properties of adaptation as transient response characteristics of stable linear systems, and we explore implications on the validity of classes of models. The adaptation process is formulated as a disturbance rejection problem. To solve this problem we utilize an adaptive internal model with error feedback. Stability and convergence of the proposed model are proved using averaging theory. The model is validated using simulations of a visuomotor rotation experiment with fast arm reaches, illustrating preservation of the dynamic properties of adaptation. Finally, an extension of the model is explored in order to recover more novel experimental results.

Advisor: Broucke, Mireille E
Relationships between 12,13 Metabolites of Linoleic Acid and Cognitive Performance in Patients with Type 2 Diabetes Mellitus

Background: Type 2 diabetes mellitus (T2DM) is linked with diabetes-related cognitive decline. Oxylipins are bioactive molecules derived from polyunsaturated free fatty acids. Hydrolysis of cytochrome p450-derived epoxides into diols by soluble epoxide hydrolase (sEH) are of relevant interest due to their involvement in diabetic microvascular disease. Methods: This thesis examines peripheral concentrations of 12,13-species of linoleic acid (LA)-derived oxylipins and associations with cognitive performance in patients with T2DM or prediabetes. Cognition was assessed through multiple cognitive tests evaluating domains including executive function and memory. Serum oxylipin concentrations were measured via ultra-high-performance liquid chromatography tandem mass-spectrometry. Results: Serum concentrations of 12(13)-EpOME and 12,13-DiHOME were negatively associated with executive function. Serum concentrations of 12(13)-EpOME were also negatively associated with verbal memory. Conclusions: In T2DM, concentrations of 12,13-species of LA-derived oxylipins were negatively associated with cognitive performance, suggesting a possible role in the pathogenesis of diabetes-related cognitive decline.

Keywords: cognitive decline
executive function
linoleic acid
oxylipins
type 2 diabetes mellitus
verbal memory
Advisor: Swardfager, Walter
Towards End-to-end Learning of Monocular Visual-inertial Odometry with an Extended Kalman Filter

Classical visual-inertial fusion relies heavily on manually crafted image processing pipelines, which are prone to failure in situations with rapid motion and texture-less scenes. While end-to-end learning methods show promising results in addressing these limitations, embedding domain knowledge in the form of classical estimation processes within the end-to-end learning architecture has the potential of combining the best of both worlds. In this thesis, we propose the first end-to-end trainable visual-inertial odometry (VIO) algorithm that leverages a robo-centric Extended Kalman Filter (EKF). The EKF propagates states through a known inertial measurement unit (IMU) kinematics model and accepts relative pose measurements and uncertainties from a deep network as updates. The system is fully differentiable and can be trained end-to-end through backpropagation. Our method achieves competitive results among state of the art classical and learning based VIO methods on the KITTI dataset.

Keywords: deep learning
localization
robo-centric EKF
supervised deep learning
visual inertial odometry
Advisor: Waslander, Steven L
Identifying Clinical Subtypes of Patients with Post-Concussion Syndrome: Evaluating Brain-Behaviour Relationship with a Computational Approach

To better capture the heterogeneity of the symptoms of patients with Post-Concussion Syndrome (PCS), we hypothesized that brain changes could be used to separate the patients into clinical subtypes. Subject specific structural and functional connectomes were created based on Diffusion Weighted Imaging (DWI) and Resting State Functional Magnetic Resonance Imaging (rs-fMRI), respectively. We identified the structural and functional connectivity differences between the PCS patients (N=83) and the healthy controls (HC, N=13) with a random forest algorithm; then identified subtypes of PCS, using a gaussian mixture model. Based on structural and functional connectivity, we observed 2 subtypes; a sub-group that had similar connectivity and behavioural profiles (i.e. neuropsychiatry, symptoms) as the HCs and a subgroup that showed great deviation from the first subgroup and HCs. Defining PCS subtypes will allow us to move towards precision medicine in PCS patients and a better understanding of the heterogeneity in presentation and recovery.

Keywords: Concussion
Diffusion Imaging
Machine Learning
Neuropsychiatry
Post-Concussion Syndrome
Resting State fMRI
Advisor: Tartaglia, Carmela
Metabolism Regulates Phenotype of Inner Annulus Fibrosus Cells Within Tissue Engineered Constructs

Previous work has suggested a link between metabolism and inner annulus fibrosus (iAF) cell phenotype; however, tissue engineering approaches rarely consider the impact of cellular metabolism on matrix accumulation. It was hypothesized that growing iAF cells on multi-lamellar scaffolds in a low-glucose medium would activate a signalling pathway that would allow the cells to maintain their phenotype, thereby contributing to a more functionally appropriate ECM. iAF tissues grown in low-glucose maintained their native phenotype and showed activation of the AMPK-PGC-1α-Sox9 signalling axis. Inhibition of PGC-1α led to a loss of the iAF cell phenotype demonstrating a link between phenotype and metabolism. Exogenous ATP and salicylate treatment led to increased tissue accumulation but loss of the iAF phenotype. These studies have provided novel insights into the pathways that regulate the iAF phenotype within tissue engineered constructs, and whose findings may facilitate the identification of the conditions needed for IVD tissue regeneration.

Keywords: Biomaterials
Metabolism
Tissue engineering
Advisor: Kandel, Rita A
Santerre, J P
The Role of Career Self-determination Theory in the Retraining Experiences of Professional Immigrants in Canada

Professional immigrants come to Canada with valuable skills, education, and hopes for future career success. However, they are often met with barriers to desired employment which impact vocational, physical, and psychological well-being. During the adjustment process, immigrants strive to fulfill basic needs, both physical and psychological in nature. This study explored the role of a recent psychology theory titled career self-determination theory (CSDT) in the retraining experiences of professional immigrants in Canada. Specifically, this study examined how professional immigrants negotiated, fulfilled, and were influenced by, three key determinants in CSDT: career autonomy, career competence, and career relatedness. Using a constructivist grounded theory approach, qualitative interviews were analyzed. Results indicated evidence for the key themes posited by CSDT, as well as relevant subthemes, and suggest the importance of need fulfillment within vocational contexts and a consideration of self-determination in career development. Findings provide preliminary theoretical contributions to the CSDT framework and practical implications for supporting professional immigrants.

Keywords: Career Psychology
Career Self-Determination Theory
Immigrant Professionals
Immigration
Vocational Wellbeing
Advisor: Chen, Charles
Assessing the Performance of Stormwater Management Facilities in Oshawa, Ontario

Stormwater management facilities can protect against urbanization-induced downstream channel erosion, but detention-based approaches commonly used in Ontario tend to exacerbate the underlying issue. This thesis presents two case studies evaluating the performance of stormwater management alternatives in urban and suburban settings to protect against downstream channel erosion while maintaining flood protection requirements using a high-level modelling and estimation method intended to act as a screening tool. Performance results indicate that reducing runoff volume tends to reduce the potential for erosion. When performing assessments in practice, engineers are inevitably limited in resources, which may deter study approaches and simulation techniques best suited to address the objective. Maintaining the stability and ecological integrity of the downstream watercourse is the overarching purpose of stormwater management and facilities implemented on upstream sites should be designed and tested using a comprehensive set of metrics with an explicit link to this objective.

Advisor: Karney, Bryan
Mapping Partition: The Cartographic Construction of Pakistan

In the summer of 1947, a British barrister who had never before set foot in India used paper maps to sketch out the lines that would lead to its partition. Today, the border he designed is one of the most militarized and surveilled spaces on earth. Thousands of floodlights installed along its perimeter render it visible from space in a bright orange hue, underscoring the power of pencil lines drawn decades ago. In this thesis, I investigate how British and Muslim political interests used cartography to construct, reinforce, and contest ideas of nationhood and statehood during India’s partition; and show how maps can at once be used as tools of colonial intervention and decolonial struggle.

Keywords: Cartography
Imagined Geographies
Imperialism
Nationalism
Pakistan
Partition
Advisor: Gilbert, Emily
Does Pronoun Resolution Incorporate Antecedent Semantics?

Pronouns (she, they, ...) are semantically underspecified and convey minimal information about their intended referents. Their interpretation is often described in relation to mental models that encode possible referents. On classic memory reinstatement accounts, this process involves "reactivating" a pronoun’s antecedent. Contemporary work adopts an indexical approach, combining referential interpretation with attentional binding. Here, the pronoun acts as a cue to directly refer to an attentionally restricted candidate. The current study explored a key element of the indexical account, namely whether there is any processing relationship between an antecedent expression’s semantics and a subsequent coreferential pronoun. To assess this, the task involved novel situations where unfolding actions entailed that a previous description for an object was or was not viable at the point when a subsequent pronoun was encountered. The results demonstrate that pronouns have indexical meaning and are not mediated by activating antecedent semantics in memory representations.

Keywords: eye tracking
philosophy of language
pronoun resolution
psycholinguistics
psychology of language
reference
Advisor: Chambers, Craig G
A Computer Vision Approach to Analyse Sleep in Infrared Video

Sleep apnea is a respiratory disorder characterized by repetitive interruptions of breathing during sleep. About 10% of the population have sleep apnea. Depending on the presence of breathing effort, respiratory events during sleep are divided into obstructive and central events. The severity of sleep apnea is often associated with sleeping position. Choosing the appropriate treatment relies on identifying types of apneas and detecting sleep positions during apneas. Available diagnosis methods are expensive, need a trained technician to set up, and require attachment of sensors to the user, rendering them inconvenient during sleep. To address these problems, this thesis proposes non-contact computer vision-based algorithms that automatically analyze and track movement on infrared videos to detect sleep position and to differentiate obstructive from central apneas. These algorithms can be used to develop an affordable and easy-to-use home assessment technology that could help physicians choose suitable treatments.

Keywords: Computer Vision
Deep Learning
Machine Learning
Obstructive and Central Apnea
Position Detection
Sleep Apnea
Advisor: Taati, Babak
Yadollahi, Azadeh
Try Smarter, not Harder: The Role of Exploration in Infant Persistence

The ability to persist through difficulty is central to learning. However, effort is costly and limited, requiring humans to be scrupulous in their deployment of effort. While repetitive engagement in unsuccessful behaviours may lead to disengagement, exploration may present the promise of success and information gain as previously untried behaviours are tested. Using post-hoc behavioural coding, we explore how infants distribute their effort across imitative and exploratory behaviours, examining whether infants rationally disengage from unsuccessful behaviours and increase novel behaviours to buffer this disengagement. Indeed, infants spent more time engaged in exploratory behaviours overall, and those individuals who prioritized exploration relative to imitation early in trials stayed engaged for longer overall. Thus, infants do not randomly persist, but rather calibrate to evidence of the utility of their efforts. Further, exploration may play a unique role in persistence by providing new avenues for engagement without utility loss.

Keywords: Cognitive Development
Exploration
Imitation
Infancy
Persistence
Utility Maximization
Advisor: Sommerville, Jessica A
Buchsbaum, Daphna
High-frequency Oscillations in Children with Epilepsy and Neural Oscillations that Support Attention

Epilepsy is a brain disorder characterized by frequent and recurrent seizures and interictal discharges. Children with epilepsy are known to manifest significant behavioural and psychosocial comorbidities, most commonly attention deficits. The causes of these impairments are poorly understood. Brain regions that generate seizures are known to express high-frequency oscillations (HFOs), but challenges in automated detection of these events hinder efforts to understand how they relate to neurocognitive deficits in children with epilepsy. In this thesis, I first present an HFO detection framework that I validate on multiple published datasets and intracranial recordings from SickKids. Second, the HFO detector is applied to intracranial recordings from children with epilepsy undergoing an attention-demanding task. My findings demonstrate that HFOs are associated with the disruption of attentive behaviour in children. I further show that this may be mediated by impairment of neural oscillations within the anterior cingulate cortex that support attention.

Keywords: Attention
Epilepsy
High frequency oscillations
Phase resetting
Advisor: Ibrahim, George M
Through the Looking Glass: Distinguishing Neural Correlates of Relational and Non-relational Self-reference and Person-representation

Neuroimaging research finds a substantial overlap between self-related and social cognitive processes. This study examines this overlap by comparing participant brain activity across three different judgments about the self and a friend that varied based on their degree of social embeddedness - traits, roles, and groups. Contrasting trait and role judgments, there was preferential activation for roles in canonical mentalizing regions, whereas traits activated areas associated with semantic processing. Additionally, activations associated with roles overlapped substantially with those associated with reflecting on the friend (rather than the self), as well as with the degree to which participants believed that the stimulus reflected a social specialization. Our findings provide evidence for a dissociation between two modes of self-reference - one associated with more social relational processing (roles) and the other associated with semantic memory processes (traits). This suggests that socially-embedded aspects of identity may form a significant component of the self-concept.

Advisor: Cunningham, William A
The Quest for Autonomy: Transformations of South Asian Women Immigrants in Canada

This study explores how South Asian immigrant women in Canada perceive autonomy and the transition of their decision making process after experiencing Canadian post-secondary education. Through using feminist standpoint as a theoretical framework and narrative inquiry as a research approach, the study found out: The prevalence of patriarchy was stronger before immigration. A greater sense of autonomy has been achieved through Canadian educational and professional experience and financial independence. Awareness regarding patriarchy exists among the participants, with evidence of acceptance of patriarchy and resistance towards patriarchy. Greater happiness and confidence are achieved after immigration through sacrifice, struggle, and conformation with evidence of a subdued presence of patriarchy. This study has shown a nuanced way of understanding autonomy. The participants try to find subtle ways of showing their confidence which contributes to the current feminist literature concerning the autonomy of educated South Asian immigrant women.

Keywords: Autonomy
Feminist standpoint
Immigrant Women
Narrative inquiry
Patriarchy
South Asia
Advisor: Vieta, Marcelo
Ryan, Sherida