VictorJuiz/thesis huggingface dataset:
Investigation of Modern Basketball Movement Demands by Film Analysis to Inform Training Interventions

The feasibility and utility of film-analysis for studying basketball movements completed by NBA guards in the context of performance training was examined.The action type, plane of movement and estimated joint actions of ten NBA guards in five 4th quarter performances were characterized using count data. Athletes made 0.74 + 0.15 movements of interest per minute of performance. Four movements; Change of Direction, Single Leg Bound, Single Leg Jump, and Forward Curvilinear Acceleration, comprised > 80% of observations. Movements were primarily in the sagittal plane. Ankle Plantar Flexion, Knee Flexion, Hip Flexion, and Hip External Rotation were frequently observed. Principal Component Analysis indicated Flexion actions at the hip, knee and ankle were highly linked, while external rotation of the hip was independently important. The film analysis techniques were successfully utilized. Variation in exercise selection for the features of movement plane and joint action may better prepare athletes to meet demands.

Keywords: Basketball
Demands
Film-Analysis
Movements
Performance
Training Interventions
Advisor: Thomas, Scott
Taha, Tim
Novel and Scalable Template Compression Methods for Neural Spike Sorting

This thesis aims to provide perspective on the challenges of neural spike sorting, or spike sorting for short. Spike sorting is a process responsible for attributing the electrical activity recorded by neural probes to individual neurons. Improvements in probe technology have drastic implications on spike sorting algorithms as the amount of data available grows exponentially. We provide an overview of spike sorting, describing the process for offline and online applications. The work has two contributions, the derivation of an analytical model and a novel template compression method. Our analytical model identifies templates as the primary bottleneck, as they take 90.4\% of the overall memory requirements. We evaluate our template compression, composed of indirect quantization, K-means clustering, segmented delta encoding, bit trimming and duplicate storage, on multiple scales, which reduces template memory usage by 8-11x, an overall reduction from 577M to 102M bits.

Advisor: Moshovos, Andreas
Characteristics of Child and Adolescents Hospitalized with Eating Disorder Diagnoses in Ontario Over Time

Methods: Population-based repeated cross-sectional design using linked health administrative and demographic datasets of individuals aged 5-17 years residing in Ontario between April 2002 and March 2020. Outcomes included rates, and relative changes in rates, of hospitalization overall and by patient sex, age and eating disorder diagnoses. Poisson regression models examined risk ratios of multiple hospitalizations.Results: The largest relative changes in rates per 10,000 population were observed for males (417%, 0.2 to 1.1), individuals aged 12-14 (196%, 2.8 to 8.1) and those with eating disorders other than anorexia or bulimia nervosa (254%, 0.6 to 2.2). Risk ratios of multiple hospitalizations decreased after 2011. Conclusion: Changes over time in the characteristics of hospitalized pediatric eating disorder patients have implications for health service planning, evaluation, clinical research and healthcare provider education.

Keywords: Eating Disorders
Advisor: Charach, Alice
Investigating Bacterial Fitness Determinants in a Humanized Mouse Model of Gonococcal Infection

Neisseria gonorrhoeae causes the sexually transmitted bacterial disease, gonorrhea, which can have devastating consequences on reproductive health. Climbing rates of gonococcal infection and the rise of antibiotic resistance has prompted the development of novel therapies. Our lab previously identified genetic adaptations consistently selected for in N. gonorrhoeae after passaging under in vivo and in vitro conditions, revealing a GCN5-related N-acetyltransferase (GNAT) whose role in N. gonorrhoeae had not yet been explored. Here, I generated a GNAT knockout in N. gonorrhoeae (DGNAT). DGNAT was outcompeted by its isogenic wild type strain during co-infection in a murine model. DGNAT also exhibited impaired invasion of human epithelial cells and an altered metabolic profile compared to the wild type strain. Proteomic analyses were conducted to highlight differences in global acetylation between the strains. This work explores the potential role of a GNAT and the effects of protein acetylation on bacterial fitness of N. gonorrhoeae.

Advisor: Gray-Owen, Scott
Analyzing Stability and Protein Interaction of RNA Loaded “OnpattroTM” Lopid Nanoparticle

RNA medicines show potential to be viable treatments for multiple diseases, although treatments suffer from low bioavailability given the efficiency of the immune system at degrading RNA. This creates an urgent need for delivery systems, and lipid nanoparticles are the leading non-viral delivery systems. The stability and protein interactions of RNA loaded lipid nanoparticles made with the formulation used in OnpattroTM was analyzed. Size measurements were performed to analyze the nanoparticle characteristics as size is a sensitive attribute. Size is often measured initially for release of LNP drugs because it is a good reporter of undesirable traits in a nanoparticle formulation. Size measurements were performed using Nanoparticle tracking analysis, and Cryo-TEM was used to observe size and morphology. This project aims to understand the storage stability of the RNA loaded LNPs to establish better practices for handling and understanding protein interactions to better support future cell and animal studies.

Keywords: Drug carrier
LNP
NTA
Protein corona
RNA
TEM
Advisor: Walker, Gilbert
A Low-Cost Low-Power Wide-Area Network For Environmental Sensing

Sustainability and climate monitoring efforts create a need for long-term, in-situ sensing of large geographic areas. However, environmental monitoring in developing countries remains impeded by a lack of low-cost, scalable IoT solutions. Most existing IoT systems for in-situ sensing are either low-cost or suitable for large areas, but not both. This thesis presents CottonCandy, a LoRa-based mesh network solution with which nodes self-organize in a spanning-tree topology in a distributed fashion. Scalability is achieved by developing methods that mitigate packet collisions during data collection. Each CottonCandy node runs on a low-cost, custom-built circuit board and can operate for years on 2 AA batteries. Evaluations by simulation show that a CottonCandy network can be scaled to at least 100 nodes across hundreds of square kilometers and achieve a packet delivery ratio of >90%. Measurements of an outdoor deployment with 15 nodes corroborate the high packet delivery ratio in a real-life setting.

Keywords: Internet of Things
LoRa Mesh Network
LPWAN
Advisor: Liebeherr, Jorg
Pulmonary Microbial Composition and Density as Prognostic Markers in Lung Transplantation

Introduction: Allograft microbial community composition and density are associated with chronic lung allograft dysfunction (CLAD) in lung transplant recipients. Approach & Hypothesis: We assessed the performance of allograft microbiota for prediction of CLAD and hypothesized that quantitative (continuous) microbial predictors of CLAD would outperform categorical composition-only models of the lung allograft microbiota. Methods & Results: 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) from two cohorts of lung transplant recipients revealed three compositional ‘extremes’ of the lung allograft; community state types (CST). In a case-control study of lung transplant recipients who did or did not develop CLAD, clinical culture and density-normalized relative abundance of Gammaproteobacteria outperformed sequencing-based CSTs for prediction of CLAD. Conclusions: Clinical culture and absolute abundance of BALF microbes may predict CLAD in lung transplantation. The identification of these targets may allow the use of widely available, rapid, and sequencing-independent microbiome analysis for this application.

Keywords: Bronchoalveolar Lavage Fluid
Chronic Lung Allograft Dysfunction
Lung Transplantation
Pulmonary Microbiome
Advisor: Coburn, Bryan
Demonstration of a Plarization-frequency Hyperentangled Photon Pair Source based on Periodically Poled Silica Fiber

Hyperentangled photons are particles of light that exhibit quantum correlations in multiple degrees of freedom simultaneously. The simultaneous entanglement in these degrees of freedom allows hyperentanglement to provide a distinct advantage over entanglement by increasing the information capacity per particle. Therefore, there is much demand for a high quality hyperentangled source, especially in fiber-based applications such as long distance quantum communication. Periodically poled silica fiber is a strong candidate for directly generating photon pairs in fiber, producing broadband collinear polarization-frequency hyperentangled photon pairs. However, collinear photon pairs cannot be simply accessed for practical applications without reducing their available information capacity. In this thesis, I investigate a method for separating these photon pairs while maintaining their original information capacity. I demonstrate the separation of the photon pairs, measure the degradation of the entanglement quality, and discuss the sources of this degradation as well as possible improvements to avoid degradation.

Keywords: Hyperentanglement
Photon pairs
Quantum entanglement
Advisor: Qian, Li
Mental Health Outcomes in Childhood Survivors of Physical Assault: A Population-Based Study

Objectives: Compare the risk of adverse mental health outcomes and describe patterns of mental illness among children who experienced physical assault vs. non-assaulted children.Methods: Population-based matched cohort study comparing physically assaulted children 0–13 years old (n=5487) and age-matched non-assaulted children (n=27,435). Hazard ratios (HR) were generated for the primary outcome, incident mental illness. Results: Incident mental illness was highest in assaulted children (exposed: 53.3/1000 person-years, unexposed: 32.2/1000 person-years; adjusted HR (aHR) 1.96; 95%CI 1.85-2.08). The greatest risk of mental illness was observed in the first year following assault (aHR 3.08; 95%CI 2.68-3.54). Non-psychotic disorders were the most common mental health disorder in both groups and exposed children more frequently sought acute care compared to unexposed children (14.0% vs. 2.8%). Conclusions: Children who experience physical assault were at high risk of mental illness. Findings suggest there is an opportunity to support children in the first year following assault.

Keywords: Childhood
Mental health
Physical assault
Advisor: Saunders, Natasha R.
Vigod, Simone
A Reconfigurable Sequential Wave Imprinting Machine for Visualizing Radio Waves and Phenomena

The Lock-In Amplifiers are a type of scientific equipment used to isolate, lock onto, and amplify a specific signal from its background noise. The output of traditional lock-in amplifiers are either a meter or a scope to display the amplified signal. The Sequential Wave Imprinting Machine (S.W.I.M) was originally invented around the 1970s to visualize the electromagnetic phenomena in the environment to expand, enhance the sensory capabilities of humans and allow such phenomena to be recorded onto photographic materials. Many endeavors had been done to combine the two to study, analyze, and visualize various types of physical phenomena, which endows the lock-in amplifier roles within phenomenological augmented reality, a special type of augmented reality. We propose that a new re-configurable SWIM system that has lock-in capabilities can be designed, which has the capabilities to visualize electromagnetic phenomena across a wide range of frequencies as a prototype for similar scientific equipment in the future.

Advisor: Mann, Steve S
Advances in Mine Pit Wall Geological Mapping using Unmanned Aerial Vehicle Technology and Deep Learning

With rising costs and decreasing high-grade reserves, there has been an increased focus in mining operations to improve and to optimize current practices, including pit wall geological mapping. Proper mapping is critical for open pit mining operations since accurately and efficiently identifying the location, spatial variation, and type of geological features on mine faces will greatly decrease dilution and increase geological certainty. Conventional techniques rely on physically examining the pit walls in close proximity and laboratory testing of collected field samples, which are labour-intensive and can expose personnel to hazards such as falling rocks and machineries. Unmanned Aerial Vehicle (UAV) and deep learning (DL) techniques can improve and complement existing practices by efficiently acquiring high-resolution pit wall images and automatically predicting geological units. This thesis investigates the application of geological mapping using UAV-acquired RGB image data with DL models, and also demonstrates the advantages and limitations using these methods.

Keywords: Deep Learning
Drone
UAV
Advisor: Esmaeili, Kamran
FCRC: A Fully Connected Recurrent Convolutional Network for Recommendation

In pursuit of superior recommendation performance, it is compulsory to leverage information that goes beyond simple user-item interaction histories. Traditional supervised learning recommenders, like factorization machines (FM), collect both userand item attributes to enhance their recommendation while treating each interaction as an independent data instance. Later research showed that interaction histories can be effectively organized into a knowledge graph (KG), thereby exploiting the data’s spatial information and interconnectedness. Although these KG-equipped methods are capable of superior performance, the advent of KGs, caused prevalent literature to bifurcate into item or user attribute models. By exploiting only a single knowledge domain, such models forego additional performance. This work combines both knowledge domains into a single Fully Connected Recurrent Convolutional Neural Network (FCRC). Specifically, a method for concurrently leveraging both knowledge domains into a single graph is presented, alongside a novel recurrent pooling approach for improved message passing throughout the graph.

Keywords: AI
Graph Convolutional Network
Knowledge Graph
Machine Learning
Recommendation
Recommender
Advisor: Lawryshyn, Yuri A
Plataniotis, Konstantinos N
Reuse-Aware Temporal Partitioning of Data-Flow Graphs on a Coarse-Grained Reconfigurable Array

We design, implement and evaluate an Integer Linear Programming (ILP) model to partition dataflow graphs (DFGs) that exceed the resource capacity of a Coarse-Grained Reconfigurable Array (CGRA) based system, called T-CGRA. T-CGRA tightly couples the CGRA to system memory, which gives rise to partitioning concerns not addressed in prior work. First, it leverages the opportunity to reuse a cache line to multiple load nodes in a DFG partition. This results in an increase in throughput by up to 56% compared to when reuse is ignored. Second, T-CGRA has a limit on concurrent memory transactions that can be issued, which the model enforces. This leads to a reduction of up to 33% in throughput. Third, the inter-partition reads/writes are modeled for correctly measuring communication traffic, as opposed to inter-partition edges, which a bulk of the prior work has done. This leads to an increase in throughput of up to 48%.

Keywords: CGRA
Data-Flow Graphs
Temporal Partitioning
Tight coupling
Advisor: Abdelrahman, Tarek
Development of a Cell-mediated Passive Immunization System for Protection against SARS-CoV-2 Infection

Immunologically impaired individuals respond poorly to vaccination, underscoring the need for alternative strategies to protect these vulnerable populations from COVID-19. The work contained in this thesis combines cell and monoclonal antibody engineering in an attempt to overcome the transient protective immunity afforded by passive monoclonal antibodies. Here, both mouse and human pluripotent stem cells engineered for safety and allogeneic acceptance were genetically modified to secrete potent SARS-CoV-2 neutralizing biologics (nBios). When transplanted subcutaneously, transgenic mouse embryonic stem cells and their differentiated derivatives deliver a supply of protective nBio titers for long periods of time in vivo, resulting in high and persistent plasma SARS-CoV-2 neutralizing activity. Altogether, this work establishes the foundation for a novel approach to passive immunization by demonstrating the potential for long-lived ‘off-the-shelf’ cell products that secrete neutralizing antibodies to confer sustained passive prophylaxis against current and future viral pathogens.

Keywords: Cell therapy
COVID-19
Monoclonal antibody
Neutralizing antibody
Passive immunization
SARS-CoV-2
Advisor: Nagy, Andras
Performance of Pillar Wrapping Cable Slings in Block Cave Mines

Pillar wrapping refers to a ground support system that uses rope or cable slings. It is commonly used to support the drawpoint pillars in the extraction level of block cave mines. An instrumentation study was conducted at the New Afton Mine to quantitatively assess the field performance of pillar wrapping used in the B3 Extraction Level. Instrumented cable slings were installed at two drawpoints to capture the behavior of the support system through cave initiation and propagation. Key factors that influence the performance of cable slings during early stages of the caving process were determined through the analysis and interpretation of the field data. A series of practical recommendations have been provided for designing and implementing cable slings and a comprehensive monitoring system to be used in the extraction level of block cave mines.

Keywords: block cave extraction level support
ground support
instrumented cable slings
pillar wrapping
Advisor: Hadjigeorgiou, John
Automated Real-time 3D Visual Servocontrol of Single Cell Surgery

Automating the cell surgery processes is a potential solution to eliminate human involvement and promote the development of cell surgery. Here, we propose a real-time 3D visual servocontrol system for single cell surgery with the experimental results of single cell microinjection of an embryo and analysis of experimental data. Real time 3D image processes are a necessary requirement, since during cell surgery, when a micropipette contacts the embryo, the embryo is deformed, repositioning the internal components of the cell to be injected. An innovative 3D edge extraction algorithm is demonstrated for the real time 3Ds image processes. Visual servocontrol of the cell surgery process acquires the real-time target cell blastomere 3-dimensional position which is used to maneuver the micropipette under real-time closed-loop feedback control. The automated embryo microinjection process is conducted using the proposed real-time 3D visual servocontrol system, which is proven to be a potential solution for microinjection automation.

Keywords: 3D computer vision
image processing
object detection
single cell surgery
visual servoing
Advisor: Mills, James
In-Vitro Characterization of the Effects of a Developing Oral Probiotic Against Dental Caries in Orthodontic Patients (Streptococcus Salivarius LAB813, a Probiotic Against Dental Caries)

Dental caries is the most common worldwide chronic disease with an increased incidence in patients undergoing orthodontic treatment. Streptococcus salivarius, LAB813, has shown inhibitory activity against Streptococcus mutans (MS), the major cariogenic bacterial species. This study investigated the antimicrobial activity of S. salivarius, LAB813, against S. mutans biofilms using mono-, dual-, and multi-species cariogenic biofilms formed on three types of orthodontic appliances. Our results demonstrated that LAB813 significantly inhibited S. mutans biofilms with cell killing of approximating 99% in a mono-species biofilms and 90% in a complex multi-species biofilm on all tested orthodontic materials. Furthermore, precoating the appliances with LAB813 strongly inhibited the formation of S. mutans biofilm. Finally, the addition of xylitol potentiated the inhibitory effects of LAB813 against S. mutans embedded in a more complex biofilm. In conclusion, LAB813 possesses strong antimicrobial activity against S. mutans, potent anti-biofilm properties, and enhanced antimicrobial activity in the presence of xylitol.

Advisor: Gong, Siew-Ging SGG
Beyond Landscape: Self-Expression in Xie Lingyun’s (385–433) Music Bureau Poetry and Imitation Poems Series

The Southern Dynasties poet Xie Lingyun 謝靈運 (385–433) is known as the pioneer of Chinese landscape poetry (shanshui shi 山水詩). Scholarly attention has been focusing on the accomplishments of Xie Lingyun’s landscape poetry and his philosophical thoughts; meanwhile, studies of his other poetic works are relatively few. While scholars argue that the writing of imitation poems was from the perspective of literary criticism, and the motivation was to express the inheritance and respect of Jian’an建安 (196–220) literature and Music Bureau (yuefu 樂府), they neglect the poet’s self-expression of writing styles and emotions. The thesis will concentrate on Xie Lingyun’s lesser-studied imitation poetry. It argues that the poems demonstrate the poet’s distinctive writing styles, personality traits and sentiments. This thesis aims to interpret Xie Lingyun’s imitative poem series and music bureau poetry as a form of self-expression that will reveal individual and diverse values and meanings.

Keywords: Imitation
Medieval China
Music Bureau
Self-expression
Xie Lingyun
Advisor: Sanders, Graham
Role of the Complement System and Vascular Endothelium in COVID-19 Pathogenesis

While COVID-19's pathophysiology remains poorly understood, evidence links complement system and endothelial injury to organ damage that increases mortality of this disease. In this study, sera from SARS-CoV-2-positive patients with mild (n=7) and severe COVID-19 (n=7) were used to investigate complement activation and endothelial injury. Complement products C3b and C5b-9 on endothelial cells (ECs) exposed to patient sera were measured using immunofluorescence assays, and endothelial monolayer exposed to patient sera was tested for permeability using a transwell model. C3b and C5b-9 deposition was significantly higher on ECs treated with SARS-CoV-2-positive sera than with normal human serum. ECs treated with mild COVID-19 sera had greater C3b deposition, whereas ECs treated with severe COVID-19 sera had higher C5b-9 deposition. Regardless of severity, SARS-CoV-2-positive patient sera increased monolayer permeability over time. Thus, we show that complement is overactivated in SARS- CoV-2-positive patients, and anti-complement treatments may be beneficial in treating COVID- 19-associated vascular injury damage.

Advisor: Licht, Christoph
GATA6: A Molecular Regulator of Pancreatic Tumour Growth and Phenotype

Pancreatic ductal adenocarcinoma (PDAC) has been classified into two main transcriptional subtypes, Basal-like and Classical. The Classical subtype correlates with GATA6 expression, and ~16% of tumors show amplification in GATA6. The goal of this project is to understand the role of GATA6 as a molecular regulator of the Classical subtype. Competition assays show loss of GATA6 reduced cell fitness. Gene expression analysis showed GATA6 was integral in maintaining Classical gene expression and loss led to shifts towards more Basal-like expression and pathways. Despite a transcriptional shift towards Basal-like expression, phenotypic characteristics of the Basal-like subtype were notably absent (i.e., no EMT, MYC expression, or aggressive growth). This data suggests that loss of GATA6 is not sufficient to cause a full Basal-like phenotype and may lead to a transitional state that does not offer the same growth advantages as being in a full Basal-like state.

Keywords: Basal-like
Classical
CRISPR
GATA6
Pancreatic Cancer
Pancreatic Subtypes
Advisor: Notta, Faiyaz