VictorJuiz/thesis huggingface dataset:
Examining the Role of Failure and Success Experiences on Task Persistence and Neurocognition in Schizophrenia

The mechanisms driving neurocognitive impairment in schizophrenia, as well as the effect of failure and success experiences on neurocognition, remain unknown. Many psychological mechanisms of neurocognitive functioning have been proposed that warrant investigation. This cross-over study examined whether the experience of failure or success affects persistence and neurocognition and whether motivation, defeatist performance beliefs, and mood mediate this relationship. Twenty-one participants with schizophrenia and 22 healthy controls aged 18-60 completed success and failure inductions, psychological questionnaires, an anagram persistence task, and neurocognitive testing at two time-points. Individuals with schizophrenia had poorer persistence and processing speed, but this was not affected by prior failure or success. Individuals with schizophrenia made worse decisions after failure, while healthy controls made better decisions after failure. There were no significant mechanisms of persistence or neurocognition. This study demonstrates that the experience of failure differentially affects the decision-making capabilities of healthy controls and individuals with schizophrenia.

Advisor: Best, Michael W
Preventing Infection-induced Myometrial Inflammation by a Broad-spectrum Chemokine Inhibitor

Prophylactic administration of a Broad-Spectrum Chemokine Inhibitor (BSCI) led to the suppression of uterine activity, a complete blockade of preterm birth (PTB) induced by Group B Streptococcus in a nonhuman primate, and inhibition of uterine cytokine/chemokine secretion and bacterial endotoxin (LPS)-induced PTB in pregnant mice. This thesis aims to determine the mechanism(s) of the BSCI (FX125L) action on uterine smooth muscle (myometrium). I hypothesize that a BSCI prevents infection-induced contraction of uterine myocytes by inhibiting the expression of pro-inflammatory cytokines and contraction-associated proteins (CAPs). Myometrial biopsies were collected from women at term (not in labour) undergoing elective caesarean section and primary myocytes were isolated. I have shown that the BSCI inhibited: 1) LPS-induced activation of transcription factor NF-kB in myocytes, 2) which caused decrease in chemokine secretion, CAP expression and myocyte collagen gel contraction. I suggest that the BSCI could represent a novel class of therapeutics for PTB prevention in women.

Keywords: Broad-Spectrum Chemokine Inhibitor
Chemokine
Infection
Inflammation
Myometrium
Preterm Birth
Advisor: Lye, Stephen
Shynlova, Oksana
The Role of Cdk1 in the Regulation of Cardiomyocyte Proliferation in the Early Postnatal and Adult Period

Adult mammalian cardiomyocytes (CM) are postmitotic cells that lose their proliferate capacity shortly after birth. This is problematic specially when the heart is subjected to an insult resulting in CM loss. Thus, understanding factors that regulate CM proliferation needed for repair is of great clinical importance. There is differential expression of Cdk1 gene, a cell cycle regulator that initiates cytokinesis throughout the early post-natal period. We hypothesized that the loss of Cdk1 would result in perturbation in cell cycle progression. The loss of Cdk1 in the murine heart, results in prolonged CM proliferation with concomitant alterations in the expression of cell cycle activators and inhibitors as determined by mRNA profiling and Western blot analysis. These results provide novel data on the molecular mechanisms that govern the switch of CM from a proliferative to quiescent state.

Keywords: Cardiomyocyte proliferation
Cardiomyocyte regeneration
Cdk1
Cell cycle
Cyclin
Advisor: Billia, Filio
Remote Monitoring RF Safety of MRI Guided Cardiac Interventions at 1.5T

Image guided cardiac interventions can benefit by implementing MRI for procedural guidance due to the availability of real-time soft tissue contrast. However, these procedures are not performed under MRI guidance due to the potential for dangerous heating near the interventional devices while imaging. A quick method to remotely monitor patient safety throughout a procedure would help ensure patient safety without greatly increasing procedure times. The proposed method uses the changes to the impedance of a single MRI transit coil due to the addition of an interventional device into the region being imaged as a measure of current induced on the interventional device. After an initial temperature calibration for a static device configuration, changes to the transmit coil impedance difference due to new device configurations is used to scale the initial temperature calibration to predict safety at the new device configuration.

Keywords: device safety
interventional MRI
RF heating
RF safety
Advisor: Wright, Graham
Molecular Dynamics Study of the Structural and Mechanical Properties of Elastin-like Peptides

Elastin is a disordered protein that imparts elasticity to vertebrate tissues, and its mechanical properties include elastic recoil, resilience, and stress relaxation. Elastin is formed from tropoelastin monomers, which are composed of cross-linking and hydrophobic domains. Studies using elastin-like peptides (ELPs) have shown that the hydrophobic effect and peptide’s conformational disorder maintain the equilibrium structural ensemble of ELPs, suggesting that these properties also govern protein elasticity. To investigate the effects of sequence changes on structural and mechanical properties, we use all-atom molecular dynamics simulations of different ELP3 variants. Compared to WT ELP3, stiffer peptides arise from glycine to serine mutations in the hydrophobic domains and KA-rich cross-linking domains with a longer poly-alanine region. Stress relaxation studies further show differential changes in structural properties over time depending on the extension at which peptides are held. Ultimately, this knowledge will help in the rational design of biomaterials for use in tissue engineering.

Keywords: biomechanics
computational biology
elastin
intrinsically disordered proteins
molecular dynamics simulations
protein elasticity
Advisor: Pomès, Régis
Evaluating the Use of Twitter in Gauging the Effects of a Transit Service Intervention on Customer Satisfaction

Due to the prominence of customer satisfaction in decision making, transit agencies are shifting focus from using operational-based measures only to incorporating customer-oriented metrics. This study expanded on utilizing Twitter as a new source to gauge the opinions of riders by developing a novel transit-specific sentiment lexicon to enhance the accuracy of the sentiment analyses. This study also manually investigated the applicability of Twitter by assessing the impact of an intervention - the introduction of Calgary Transit's MAX routes- on customer satisfaction for several service quality attributes. Additionally, the study analyzed the relationship between the perception of users and the performance of vehicles for a commonly used reliability measure, on-time performance. The developed sentiment lexicon improved the accuracy and F-1 score compared to generic sentiment lexicons. Furthermore, the analysis showed a similar trend between customer-oriented measures obtained from Twitter and operational measures related to on-time performance.

Keywords: Customer satisfaction
Intervention
Sentiment lexicon
Transit
Twitter
Advisor: Shalaby, Amer AS
El–Diraby, Tamer TE
The Role of Family Factors in Substance Use Treatment for Youth With Without Learning Disabilities: A Case Study

Youth substance use is a pervasive phenomenon. Research suggests family-based treatments provide healthy mechanisms to combat problems experienced by youth due to substance abuse. The relationship between learning disabilities (LDs) and substance use treatment is not well understood. This study investigated differences in externalizing behavior and family functioning between youth with and without LDs in a residential treatment centre, and if differences were explained by family functioning. Multi-level modelling analyses revealed no significant difference between youth with an unclear diagnosis (β = 11.60, p > .05), a LD diagnosis (β =. 23, p > .05), or ADHD, (β = -6.92, p > .05) on externalizing behavior from pre-treatment to two years post-treatment. Family functioning predicted differences in externalizing behavior individually (β = 14.82, p

Keywords: Family Functioning
Learning Disabilities
Residential Treatment Centres
Substance Use Treatment
Youth Substance Use
Advisor: Cunningham, Todd
Aerodynamic Shape Optimization of a Boundary-layer Ingesting S-duct Intake

An aerodynamic shape optimization framework based on the Reynolds-averaged Navier-Stokes equations is applied to the optimization of a boundary-layer ingesting S-duct designed for an embedded engine on a high-subsonic, unmanned flight vehicle. Two composite objective functions are considered. The first combines distortion and swirl at the fan interface plane as well as total pressure recovery, with user-defined weights for each objective, while the second involves pressure recovery, fan blade load variation, and fan blade incidence variation. Pareto fronts are generated that demonstrate the trade-offs between objectives. Single-point and multipoint optimizations are conducted at cruise, descent, and climb conditions to evaluate the robustness of the design. Results indicate that compared to the baseline geometry, a simultaneous improvement in all objectives can be obtained, depending on the priorities pre-assigned by the user. Lastly, multipoint optimization results show that a single S-duct geometry can perform well during cruise, climb, and descent conditions.

Keywords: Aerodynamic Shape Optimization
Boundary-Layer Ingestion
Computational Fluid Dynamics
S-Duct
Advisor: Zingg, David W
Applying Videogame Narrative and Level Design To Museum Exhibit Design

This thesis examines how practices of narrative and level design used in the videogame industry can be applied to the museum sector, and from this research, propose a set of design lessons that can be used for the creation of exhibits. To that end, this thesis hypothesizes that these practices from gaming will serve the purpose of elevating the visitor experience—specifically in the way museum spaces, artifacts and their stories are presented, navigated, and experienced by the visitor. In order to produce this set of design lessons for exhibit creation, a qualitative study of five videogames was conducted for the purpose of identifying methods of narrative delivery, and level design practices. In regard to narrative design, I establish three methods of narrative embedding, partly inspired by Huaxin Wei’s work, in addition to summarizing Ahmed Khalifa et al.’s findings, which contributed to this studies understanding of level design. The combined knowledge of these works where foundational in developing a unit of analysis, which was used to identify narrative and level design practices within my sample. The findings from this research was then translated into applicable design practices for museum exhibit creation, called design lessons. Moreover, the design lessons developed from this study were used in the creation of a prototype exhibit for the purpose of demonstrating its effectiveness. Thus, this study advocates that there are indeed lessons to be learned from videogames which offer new perspectives in design to the museum sector. That in doing so, this study’s interest in providing museum professionals with new views on narrative and level design, will have a positive affect on the visitor experience.

Keywords: Exhibit Design
Level Design
Museum Studies
Narrative Design
Videogame
Visitor Experience
Advisor: Tang, Anthony
A Semi-supervised Pipeline for Detection of Anomalies in Medical Images

With the breakthroughs in the field of deep learning and computer vision problems, manyworkflows have been revolutionized, including diagnostic medical imaging. In this work we developed a Generative Adversarial Network - based pipeline for augmentation of data and detection of anomalies in the form of Viral Pneumonia and COVID-19 in chest X-ray images. By eliminating the need for more labelled data for training our model, we offered a pipeline that reduced the strain on radiologists when curating data for deep learning models. We demonstrated that our pipeline improves results compared to the previous state-of-the-art generative model for detection of anomalies in the images.

Keywords: Anomaly detection
Machine learning
Medical Imaging
Advisor: Khalvati, Farzad
An Accelerated Aging Protocol Based on Thermomechanical and Biochemical Challenges for Dental Bonding Agent Development

Current in vitro aging protocols for the testing of dental adhesive resins often require long periods of incubation. Protocols that could accelerate aging while maintaining relevance to oral conditions would provide a novel platform to study the degradation of resin materials used to reconstruct dental caries. The aim of this thesis was to develop and test a combined biochemicalthermocycling (BC-TC) protocol to study the chemical and mechanical degradation of total-etch adhesive resins formulations and compare the rates of degradation with the established biochemical (BC) protocol. The BC-TC protocol was found to accelerate the chemical aging of the adhesive resins, significantly increasing the rate of 2,2-Bis[4(2,3-hydroxypropoxy)phenyl] propane (BisHPPP) and drug release in comparison to samples aged by the BC protocol. Interfacial stiffness also differed significantly between protocols. This novel BC-TC protocol canaccelerate certain aspects of aging, however further study is needed to refine the parameters ofthe protocol.

Advisor: Finer, Yoav
Our Needs Will Not Diminish: Perspectives of Ontario Non-profit Organizations on Experiential Learning Partnerships with Post-secondary Institutions

This study investigates the perspectives of staff within non-profit organizations that host post-secondary students in experiential learning (EL) placements. Post-secondary institutions within Ontario and across North America have experienced increasing pressure to ensure that students have opportunities to learn by doing through experiential learning placements. Community-based non-profit organizations host many of these placements. Interviews with ten Canadian non-profit staff members who supervise placement students revealed both tensions and possibilities inherent in campus-community EL partnerships. The findings make clear that non-profit organizations vary in their needs and available resources and these affect their interactions with post-secondary institutions. The study has important implications, for those at the provincial and administrative levels as they develop expectations and policies around campus-community engagements, and for the staff and faculty within universities and colleges who send students to non-profit organizations.

Keywords: Campus-community Partnerships
Canada
Education Policy
Experiential Learning
Neoliberalism
Service Learning
Advisor: Childs, Ruth
Vieta, Marvelo
Using Machine Learning Algorithms for Clinical Decision Support for Breast Cancer Screening at Sunnybrook Health Sciences Center

Clinical decision-making has been a major challenge for healthcare providers in recent years. We apply a number of machine learning algorithms to two clinical breast imaging problems at Sunnybrook Health Sciences Center. In Phase 1, we predict missed magnetic resonance imaging (MRI) exams during 2017-2019 and 2020. We indicate that the 2020 model’s performance is highly dependent on the features related to exam essentiality, and the best f1-score increases from 53% in the 2017-2019 model to 76% in the 2020 model due to the growth in the no-show rate mitigating the target class imbalance. In Phase 2, we predict whether high-risk breast cancer patients require to undergo a biopsy after a series of follow-up MRI exams to detect the source of an abnormality and show that the important features for this problem include radiologist measure and patient age. We deal with target class imbalance using data balancing and hyper-parameter tuning.

Keywords: biopsy
follow-up
healthcare
machine learning
MRI
Advisor: Carter, Michael
Reducing the Cost of Ensemble-based Data Assimilation in Multiple-query Scenarios through Covariance Augmentation

We present and assess a method to reduce the computational cost of performing data assimilation (DA) for reacting flow in multiple-query scenarios, where we consider several scenarios with similar underlying dynamics. We focus on ensemble-based DA, in particular the ensemble Kalman filter (EnKF). The accuracy of the EnKF, which depends on the quality of the sample covariance, improves with the ensemble size, but so does its computational cost. To reduce the ensemble size while maintaining accurate covariance, we propose a data-driven approach to augment the covariance based on the statistical behavior learned from model evaluations. We assess our augmentation method using one-dimensional model problems and synthetic reacting flow cases. We show in all cases that ensemble size, and thus computational cost, may be reduced by a factor of three to four while maintaining accuracy.

Keywords: Augmentation
Data assimilation
EnKF
Ensemble Kalman filter
Multiple-query scenario
Reacting flow
Advisor: Yano, Masayuki
Steinberg, Adam M
Understanding Cortical Astrocyte Distribution through Perinatal Birth Dating

Cortical astrocytes are highly heterogeneous cells with distinct gene expression profiles, phenotypes, and functions. Peak astrogenesis occurs between E15-P7; whether astrocytes occupy distinct cortical layers depending on their time of birth is not known. To determine whether time of birth influences astrocyte distribution in the upper (UL) vs. lower (LL) cortical layers, we permanently labelled ventricular subventricular zone (V-SVZ) NSPCs and their progeny throughout embryonic and postnatal astrogenesis periods using in utero electroporation and 5-ethynyl-2’deoxyuridine (EdU) labelling. Immunohistochemistry (IHC) for the astrocyte lineage marker SOX9 was performed and SOX9+ astrocytes were quantified and compared between UL and LL cortical layers within each timepoint. SOX9+ astrocytes born in the late embryonic period showed an UL bias, whereas SOX9+ astrocytes born in the postnatal period were primarily restricted to the LL. Altogether, these results suggest that the distribution of SOX9+ cortical astrocytes is influenced by time of birth.

Keywords: Astrocyte
Astrogenesis
Cortical development
Gliogenesis
Advisor: Faiz, Maryam
Absurding the Absurd: Use and Transformation as Resistance in Performance

Sara Ahmed’s What’s the Use? On the Uses of Use (2019) offers a critical framework as I question the use of my art form, contemporary dance, and follow an artistic inquiry into the potentially useful idea of the absurd. I problematize the absurd’s white and male-dominated past and move beyond theatre-centric canons to focus on works of dance where the absurd generates ways of being against the dominant sense as forms of resistance capable of transformative action and meaning-making. I apply Ahmed’s notion of queer use to the absurd itself in examining Miguel Gutierrez’s This Bridge Called My Ass (2019), Maya Deren’s Meshes of the Afternoon (1943), Alyssa Martin’s fantasylover (2018), Dimitris Papaioannou’s Sisyphus / Trans / Form (2019), and Pina Bausch’s Café Müller (1978). Through a feminist lens, I explore how these works use the absurd as a feeling and a verb to subvert expectations and transform perceptions.

Advisor: Cesare Schotzko, T. Nikki
Biplanar Ultrasound Investigation of Tongue Shape during Mastication: A Tale of Two Textures

Tongue movement in chewing is complex and three-dimensional. The present study explored quantitative features of tongue movement during mastication of two solid textures (almond vs beef jerky). Temporally linked sagittal and coronal real-time ultrasound tongue videos from nine typical participants were analyzed using outcome measures of chew duration, cumulative displacement, and surface concavity. There was greater posterior tongue travel for the almond texture, and a longer chew duration for beef. Cumulative tongue displacement was significantly greater for the posterior tongue. The concavity distributions showed mostly flatness in the coronal view, and mainly convexity in the sagittal view. A principal component analysis demonstrated that the front and back of the tongue moved independently, with lateral free margins clustering with the center and back. The new measures served to describe global aspects of tongue movement. Future research should test these global measures in clinical populations with typical and disordered chewing.

Keywords: Biplanar
Mastication
Shape
Texture
Tongue
Ultrasound
Advisor: Bressmann, Tim
Fructose Metabolism in the Ruby-throated Hummingbird (Archilochus colubris)

Ruby-throated hummingbirds drink nectar that is 50% fructose and 50% glucose, as monosaccharides and the disaccharide sucrose. Remarkably, hummingbirds can use either ingested glucose or fructose to fuel metabolically demanding hovering flight. Currently, the metabolic pathways that could support flight with fructose carbon remain unclear as traditional vertebrate models cannot use this sugar directly as a muscular fuel. I use metabolomics to identify possible metabolic pathways in the pectoralis muscle, heart, and liver that process fructose at relatively rapid rates. I hypothesize that the hummingbirds can use exogenous fructose directly in their muscles to power flight but also convert the fructose to other energy metabolites, including glucose, in their liver. I found support for both of these hypotheses. Surprisingly, I also found evidence suggesting that the heart plays an important role in fructose metabolism.

Keywords: Fructose
Glucose
Hummingbirds
Metabolism
Metabolomics
Advisor: Welch, Kenneth C.
Detailed Morphology of the Skull and Dentition in a New, Exceptionally Preserved Microraptorine Specimen (Theropoda: Dromaeosauridae) from the Early Cretaceous of China

The evolution of non-avian dinosaurs to birds is one of the most significant evolutionary events in the history of life. Microraptorinae, a clade of small, four-winged dromaeosaurs that exhibit both avian and non-avian dinosaurian features, is a fossil group important to this transition. Microraptorine specimens are known from the Early and Late Cretaceous deposits of Asia and North America and are represented by several specimens in the literature; however, well-preserved craniodental material is lacking. Here I describe an exceptionally preserved microraptorine specimen from China, JLUM Y-MR160501, which includes a near-complete skull and dentition in both jaws. The delicate cranial bones retain their shape and are only slightly disarticulated, allowing for the first detailed description of cranial anatomy in microraptorines. This exceptional specimen brings critical new information on microraptorine cranial anatomy and morphology that fills in the current gaps in our knowledge of Microraptorinae and the evolutionary relationships within the clade.

Keywords: cranial anatomy
dentition
Dromaeosauridae
Microraptorinae
microraptorine
Theropoda
Advisor: Reisz, Robert R
Evans, David C