VictorJuiz/thesis huggingface dataset:
Investigating the Molecular Basis for Cooperative Behaviour in a Mutualistic Plant-Ant

This thesis investigates the molecular basis for cooperative behaviours by the plant-ant Allomerus octoarticulatus toward its host myrmecophyte, Cordia nodosa. In exchange for the food and shelter its host plant provides, A. octoarticulatus performs a ‘bodyguarding’ service for the plant, attacking herbivores that attempt to feed on plant leaves and other tissues. I measured bodyguard effectiveness across 60 naturally occurring colonies of A. octoarticulatus in the Peruvian Amazon, collected bodyguards and broodcare workers, and used RNA-Seq to perform a differential gene expression analysis on samples from 14 colonies, comparing high- and low-quality bodyguards, and bodyguards and broodcare workers. The analysis found 32 genes that were differentially expressed between high- and low-quality bodyguards, and 632 genes that were differentially expressed between bodyguards and broodcare workers, indicating that gene expression plays a significant role in ant bodyguard behaviour.

Keywords: ant
behaviour
genomics
mutualism
myrmecophyte
Advisor: Frederickson, Megan E
Precompression: A Prelude to Cache Compression

Processors face steep penalties when accessing on-chip memory in the form of high latency. On-chip caches help mitigate this latency by storing the most used data close to the processor. Despite this, cache space limitations limit their effectiveness. Compressing data in caches can improve performance by increasing effective cache capacity, but can incur additional access latency. Current cache compression schemes focus on just one granularity | either a single cache line or a small number of contiguous lines. In this thesis, we propose Precompression a novel technique that transforms cache data, making it more amenable to compression. In contrast to prior compression techniques, our work takes advantage of the redundancy existing across multiple cache lines, stored anywhere in the cache. Precompression works by exploiting the similarity between cache lines to improve compression. For applications within the SPEC2006 and Polybench suites, we observe improvements to the effective compression ratio of up to 13.33%.

Keywords: Cache
Compression
Computer Architecture
Advisor: Enright Jerger, Natalie
Regulation of Claudin-3 Expression in Kidney Tubular Epithelial Cells

The overall objective of my studies was to gain insight into the regulation of the tight junction protein, claudin-3, upon inflammatory stimuli in kidney tubular epithelial cells. Claudins mediate paracellular transport and modulate key cellular events like proliferation, migration and differentiation. The inflammatory cytokine Tumor Necrosis Factor-α (TNFα) is a pathogenic factor in kidney disease and alters epithelial permeability. However, the effect of TNFα on claudin-3 expression in the tubules and the mechanisms are not defined. My studies showed that TNFα elevated claudin-3 expression in kidney tubular cells. This effect was due to increased claudin-3 synthesis and mediated by two signaling pathways: extracellular signal regulated kinase-dependent activation of NFκB and protein kinase A-induced CREB1 activation. Claudin-3 overexpression elevated transepithelial resistance in tubular cells and it may play a role in regulating tubular epithelial permeability. Claudin-3 downregulation also affected cell cycle proteins; thus, claudin-3 may also affect cell proliferation.

Keywords: Claudin 3
Inflammation
Kidney
Signal transduction
TNF-alpha
Advisor: Szaszi, Katalin
Implicit Feedback Deep Collaborative Filtering Product Recommendation System

In this thesis, several Collaborative Filtering (CF) approaches with latent variable methods were studied using user-item interactions to capture important hidden varia- tions of the sparse customer purchasing behaviours. The hidden latent factors are used to generalize the purchasing pattern of the customers and provide product recommenda- tions. CF with Neural Collaborative Filtering (NCF) was shown to produce the highest NDCG performance on the proprietary dataset provided by the Company. Different hy- perparameters were tested for applicability in the CF framework. External data sources like click-data and metrics like Clickthrough Rate (CTR) were reviewed for potential extensions to the work presented. The work presented in this thesis provides techniques, the Company can use to provide product recommendations to enhance revenues, attract new customers, and gain advantages over competitors.

Keywords: Collaborative Filtering
Deep Learning
Implicit Feedback
Machine Learning
Matrix Factorization
Recommendation System
Advisor: Lawryshyn, Yuri
Kundur, Deepa
A Modular Bi-directional Current-controlled Inverter with Masterless Interleaving and Active Power Decoupling

Single-phase inverters are critical for many applications, including solar energy harvesting, residential energy storage, and electric vehicle charging. This thesis presents two main innovations in the context of a bi-directional, power-dense, silicon carbide inverter that is modular and fault-tolerant. 1) Masterless interleaving between sub-inverters operating with variable frequency current control, and 2) a versatile Active Power Decoupling (APD) module using a unique topology variation that re-purposes a sub-inverter, and allows current-mode operation using the same hardware. Masterless control allows for system operation to continue in the presence of sub-module failure. The Interleaving of three sub-inverters decreases the peak current into the system EMI filter by 29\%. Reusing the sub-inverter full-bridge, inductors, and current sensing for APD improves the system modularity and allows for a symmetrical mechanical and thermal design. The proposed topology uses two half-bridges with a modified capacitor connection to enable hysteretic current control with a single current sensor.

Keywords: electric current control
Inverters
masterless interleaving
parallel sub-inverters
Advisor: Trescases, Olivier
Affective Responses to High-Intensity Interval Exercise and Moderate-Intensity Continuous Exercise in Female Cancer Survivors

High-intensity interval exercise (HIIE) is associated with positive health outcomes for female cancer survivors. However, little is known regarding how female cancer survivors feel while performing this exercise. The purpose of this study was to compare in-task and post-task affective response to a single bout of HIIE and moderate-intensity continuous exercise (MICE) in female cancer survivors. Participants (N=10) attended three laboratory sessions: baseline assessments, HIIE and MICE. Affective valence and arousal were measured before, during and after exercise. Results indicated negligible differences in in-task affective valence (dz=-0.02), but a large effect between conditions for affective arousal (dz=-0.92). Post-task affective response displayed a small effect for all domains (dz=-0.23, dz=-0.17, dz=-0.32) except Calmness, which exhibited a small effect (dz=0.38) of the difference between HIIE and MICE conditions. Preliminary results suggest HIIE and MICE result in similar psychological responses and may be equally likely to be performed by female cancer survivors.

Keywords: Affect
Cancer
Exercise Behaviour
High-intensity Interval Exercise
Advisor: Trinh, Linda
All-digital Calibration Algorithms for the Correction of Static Non-linearities in ADCs

This thesis presents all-digital calibration algorithms for correcting static non-linearities in an ADC. A bit-by-bit (BB) calibration is proposed as an alternative to the existing radix calibration. The proposed calibration algorithm is initially demonstrated using a non-uniform ADC model generated in Matlab. A hybrid radix/bit-by-bit calibration is also developed to reduce the computational complexity of the BB calibration. The calibration algorithms are then applied to measurement data from two different ADCs: first, a previously designed 6-bit folding-flash; and subsequently, a custom designed 10-bit dual-split capacitor (DSC)-DAC SAR ADC. In both ADC architectures, the BB and hybrid calibrations outperform the radix calibration. The BB calibration improved the SNDR and SFDR of the folding-flash ADC from 29.5 dB to 31.9 dB and 33.3 dB to 43.6 dB, respectively, when compared with the uncalibrated raw data. Likewise, after applying the hybrid calibration on the DSC-DAC SAR ADC, the SNDR and SFDR improved from 31.8 dB to 47 dB and 33.6 dB to 58.9 dB, respectively, also when compared to the uncalibrated raw data. The hybrid calibration achieves performance similar to that of the BB calibration while demonstrating a significant reduction in computational complexity.

Keywords: ADC
Data converter
Digital calibration
Error correction
LMS algorithm
Split-capacitor SAR ADC
Advisor: Chan Carusone, Anthony
Freshwater Mussel Adhesion: Interfacial Structures Antifouling Surfaces

Despite biofouling by the invasive mussel species Dreissena polymorpha (zebra mussel) and Dreissena bugensis (quagga mussel) causing millions of dollars in damage each year, a targeted antifouling strategy has yet to be developed, in part due to the freshwater mussel adhesion mechanism largely remaining unknown. The strong underwater adhesion of these mussels is established by forming an adhesive interface between the substrate and the mussels’ adhesive plaques. In this thesis, the role of the plaque- substrate interface in freshwater mussel adhesion has been investigated through 1) evaluating the antifouling capacity of silicone-oil-infused polydimethylsiloxane (iPDMS) against zebra mussels and 2) characterizing the ultrastructure of the quagga and zebra mussel adhesion interface on different substrates. We report here that the surface oil layer of iPDMS acts to minimize the strength of plaque- substrate adhesion and reveal new structures and patterns in the adhesion interface, advancing our understanding of mussel adhesion.

Keywords: adhesion interface
antifouling
biofouling
quagga mussels
zebra mussels
Advisor: Sone, Eli D
Hatton, Benjamin D
Multi-tracer Experiment in a Bioretention Cell to Study the Transport of Trace Organic Stormwater Contaminants

Bioretention cells are constructed in urban areas for infiltration and treatment of stormwater runoff. This thesis reports the results of a field tracer experiment to track the fate of nitrate, phosphate, rhodamine WT, and benzotriazole. With a short hydraulic retention time and a poor use of the bioretention cell volume, moderate mass reductions were observed for nitrate (38%), phosphate (48%), rhodamine WT (36%), and benzotriazole (29%). Two benzotriazole biotransformation products, 1-methyl-1H-benzotriazole and methoxy-benzotriazole and two phytotransformation products, benzotriazole alanine and benzotriazole acetyl-alanine were detected in the first natural runoff event that occurred 26 days after the tracer test. These data showed that between-event transformation of benzotriazole can occur in bioretention cells. These results demonstrate the need to use new design strategies to effectively adsorb or transform these contaminants, such as increasing the retention time, incorporating soil amendments, and selecting specific plant species for better treatment performance.

Keywords: benzotriazole
bioretention cell
stormwater runoff
Advisor: Passeport, Elodie
Development of a Test Rig and Testing Method for Shimmy Damper Characterization

The research detailed in this thesis was focused on developing an experimental testing system to characterize the nose landing gear shimmy damper. The testing rig was designed to simulate the ground operation of an aircraft nose landing gear of a small business jet. The proposed solution uses a drum to simulate landing and takeoff speeds, forcing shimmy vibration through tire slip with the use of an impact moment mechanism. Vertical force is added with the use of weights to mimic the effects of aircraft fuselage weight which tends to amplify the vibration. This shimmy vibration measuring process was developed by integrating mechanisms to capture rotational acceleration and methods to process the acquired data was outlined. Newly developed shimmy damper was tested for verification by comparing the response with systems without shimmy damper and the original shimmy damper.

Advisor: Behdinan, Kamran
An Investigation of Display Shapes and Projections for Supporting Spatial Visualization Using a Virtual Overhead Map

A novel map display paradigm named "SkyMap" has been introduced to reduce the cognitive effort associated with using map displays for wayfinding and navigation activities. Proposed benefits include its overhead position, large scale, and alignment with the mapped environment below. This thesis investigates the substantiation of these benefits by comparing a conventional heads-down display to flat and domed SkyMap implementations through a spatial visualization task. A within-subjects study was conducted in a virtual reality simulation of an urban environment, in which participants indicated on a map display the perceived location of a landmark seen in their environment. The results showed that accuracy at this task was greater with a flat SkyMap, and domes with stereographic and equidistant projections, than with a heads-down map. These findings confirm the proposed benefits of SkyMap, yield important design implications, and inform future research.

Keywords: distance estimation
human factors
human-computer interaction
navigation
virtual reality
Advisor: Milgram, Paul
The Business of being Comfortably Uncomfortable: A Qualitative Study of the Conceptualization and use of Mindfulness Meditation by Psychotherapists

Stemming from traditional Buddhist thought and practice, mindfulness meditation has shown an exponential increase in the West. However, there has been some criticism that the way in which mindfulness is applied in the West departs somewhat from its original form and meaning, thereby reducing the efficacy with which this practice could be used to enhance wellbeing. The aim of this current study is to initiate a shift in the understanding and application of mindfulness meditation back to its origins by assimilating a more comprehensive understanding of the current state of conceptualization and utilization of mindfulness in real-world clinical settings. Grounded theory was used to analyze semi-structured interview data from eight psychotherapists who practiced mindfulness meditation. The study identified two core themes, each containing a number of subthemes that are discussed in relation to each other and within the context of relevant Eastern philosophy and Western empirical research.

Keywords: components
conceptualization
meditation
mindfulness
psychotherapists
Advisor: Moodley, Roy
In Support of Pedagogical Salutogenesis: Exploring Holistic, Traditional and Indigenous Health Methodologies Toward an Ethic of (Self/School) Care

21st Century health literacy and health promotion in Ontario public schools reflect international shifts towards considerations of mental health, student wellbeing, whole-child education and comprehensive school health practices. This thesis situates these contemporary trends in the history of pedagogical salutogenesis in Ontario, drawing attention to the emerging integration of holistic, traditional and Indigenous health methodologies in elementary health education curricula. Drawing upon critical ontology, health identity and salutogenic theory, themes of holism, embodiment and environmental interdependence are explored through an empirical qualitative literature review, comparing the lenses of Ontario elementary curricula with select holistic, traditional and Indigenous health methodologies. Adapting Foucault’s (1997c) care of the self for the context of health construction, an Ethic of (Self/School) Care is proposed as both a foundational component of individual health literacy and promising avenue for collective organizational school culture, arguing for authentically holistic, culturally safe and ethical spaces to facilitate salutogenic school praxis.

Keywords: health promotion
holistic health
Indigenous methodologies
Ontario elementary education
pedagogical salutogenesis
student wellbeing
Advisor: Heller, Monica
Regional Cerebral Blood Flow and Blood-oxygen-level-dependent Smoking-cue Reactivity Responses to Abstinence, Satiety, and Nicotine Replacement Therapy in Treatment-seeking Smokers: A Functional Magnetic Resonance Imaging Study

Tobacco dependence alters regional cerebral blood flow (rCBF) and blood-oxygen-level dependent (BOLD) smoking-cue responses, but the influence of smoking cessation treatment on these biomarkers is unclear. Treatment-seeking smokers (N=20) receiving nicotine replacement therapy and behavioural counselling completed magnetic resonance imaging at baseline, end-of-treatment (12 weeks), and 6-month follow-up. Per-protocol abstinence rates at 12 weeks ranged from 42.9% to 75% depending on nicotine replacement regimen. Intent-to-treat abstinence was 42.9% at weeks 12 and 26, and 28.6% at week 52. At baseline, smoking satiety increased rCBF compared to overnight abstinence in the left anterior cingulate and right orbitofrontal cortices and decreased BOLD responses to smoking versus neutral cues in right anterior cingulate, inferior frontal, and precentral gyri; temporal and frontal poles; and insular cortex. Treatment modulated anterior cingulate, posterior cingulate, and occipital cortex BOLD responses but not cerebral perfusion. Smoking cessation treatment may modulate salience and internal processing during cue-induced craving.

Keywords: Arterial Spin Labelling
Cue Reactivity
Magnetic Resonance Imaging
Nicotine Replacement Therapy
Regional Cerebral Blood Flow
Smoking Cessation
Advisor: Zawertailo, Laurie
Selby, Peter
Cellular-based Localization for Mobile Devices with Structured Motion

Global Navigation Satellite System (GNSS) has been the main mechanism for positioning, navigation, and timing purposes. In spite of its popularity, it suffers from several disadvantages such as poor accuracy or unavailability in some conditions. This thesis is considered cellular-based localization as a supplement or substitute to satellite navigation. The focus of the work is on positioning of mobile devices which move on a structured route, such as streetcars. Various localization methods and two most famous cellular signals, i.e., Wide-band Code Division Multiple Access (WCDMA) and Long Term Evolution (LTE) are studied. Two different positioning methods are proposed, and their performance is evaluated through running simulations. Using the first approach, we show that with specialized receivers, we can reach the distance error of less than 2 m. Additionally, the latter method estimates the location of the vehicle with receiving signal powers and using Machine Learning algorithms.

Advisor: Sousa, Elvino S
From Clients to Service Providers: The Workplace Learning Experience of Young Adult Peer-support Workers

Despite the known and documented benefits of peer-support work in young adult mental health services, there is a limited understanding of the learning and development processes that young adults in these roles experience. This study explores the workplace learning experience of young adult peer-support workers in community-based mental health organizations in Toronto, Canada. Self-Determination and Situated Learning Theories guided the research design and analysis. Five semi-structured interviews with young adult peer-support workers were conducted and the data was thematically analyzed. The findings illustrate that young adults who work as peer-support workers are autonomously motivated to take on the role, learning is common through participation in communities of practice, and they develop a unique professional identity through the work. Recommendations for practice and future research are made based on these findings.

Keywords: Community
learning
Mental Health
Peer Support
young adults
youth
Advisor: Vieta, Marcelo A
Ryan, Sherida
Therapeutic Efficacy of Mesenchymal Stromal Cell Derived Microparticles to Protect Against Pulmonary Capillary Barrier Permeability in Acute Respiratory Distress Syndrome

Acute respiratory distress syndrome (ARDS) is a highly fatal condition, characterized by an excessive immune response leading to pulmonary microvascular permeability and lung edema. With no effective cure thus far, mesenchymal stem/stromal cells (MSCs) have emerged as potential treatment, proposed to function through released microparticles (MPs). This study demonstrated MPs produced constitutively by MSCs enhanced barrier function after thrombin-induced permeability in human pulmonary microvascular endothelial cells, by promoting re-distribution of VE-cadherin to cell junctions. Barrier enhancement depended on surface CD44 on MPs, while CD73 had a less crucial role in therapeutic function of MPs. Modulating ceramide content in MPs demonstrated ceramides were damaging to the endothelium, and MSC MPs containing less ceramide were more therapeutic. Sphingosine-1-phosphate (S1P) signaling was crucial for endothelial barrier enhancement as MPs lacking S1P were non-therapeutic. These mechanistic factors in therapeutic function of MSC MPs will ultimately guide development of new therapies for ARDS.

Keywords: ARDS
Endothelium
Lung injury
Mesenchymal stromal cells
Microparticles
Advisor: Kuebler, Wolfgang M
Neuropeptide Mimetics: The Physiological Effects of Kinin and CAPA Analogs in Rhodnius prolixus

In the Chagas disease vector Rhodnius prolixus, the kinin and CAPA neuropeptides modulate a host of feeding and diuresis-related behaviours that are implicated in disease transmission. CAPA and kinin neuropeptide analogs have been developed to elicit potent changes in physiology, to be later incorporated in novel pest-control strategies. Here, the effects of kinin and CAPA analogs were investigated on feeding and diuresis-related tissues, with the kinin and CAPA analogs inducing physiological changes in vivo and in vitro. Within the hindgut, novel intracellular interactions were uncovered between RhoprCAPA, Rhopr-kinin, and serotonin [5- hydroxytryptamine (5-HT)]. Following identification and sequencing of the Rhopr-kinin receptor, the receptor transcript was observed throughout the gut, with RNA interference (RNAi)-mediated knockdown of the receptor causing reductions in hindgut contractions and increasing the size of blood meal consumed. Overall, these findings highlight the role of kinin and CAPA within R. prolixus, and the promise of their neuropeptide analogs to be used as lead compounds in pest- control strategies.

Keywords: Diuresis
GPCRs
Insect
Kissing bug
Muscle contraction
Neuropeptide analogs
Advisor: Lange, Angela B
Can the QuickDASH Score at the Time of Initial Assessment Predict Recommendation for Surgery in Patients with Shoulder Pain

The causes and consequences of shoulder pain are diverse, resulting in inappropriate referral for surgical assessment and long surgical wait times. This work assessed whether the QuickDASH questionnaire could predict surgeons’ recommendation for surgery at consultation, and thus inform patient triage. Data were collected from an historical cohort of shoulder pain patients referred to an upper extremity surgical clinic. Guided by the Andersen model of healthcare utilization, the predictive validity of the QuickDASH score was assessed alone and in combination with additional predisposing, enabling and need variables. In 507 patients, surgeon recommendation could not be predicted by QuickDASH score alone, but QuickDASH scores significantly predicted the likelihood of receiving a recommendation for surgery after controlling for age, sex, symptom duration and pathology on imaging (OR 1.02, 1.004-1.03). This work shows the QuickDASH score in combination with additional patient factors may be useful to aid patient triage. Additional research is warranted.

Keywords: Orthopaedics
QuickDASH
Shoulder
Advisor: Hawker, Gillian