VictorJuiz/thesis huggingface dataset:
Real-time Video Analytics at Scale: Design, Deployment and Evaluation
Keywords: big data
cloud computing
data analytics
deep neural networks
video analytics

A key determinant of a video analytics application success lies in its ability to operate in a real-time fashion and must do so, regardless of the number of video streams the system needs to process. Hence, there is a need for a scalable and distributed video analytics system that can leverage the power of the cloud and thus successfully deliver on its promise. This work addresses this challenge by taking a bottom-up approach in defining the required system architecture and design for enabling large-scale execution of video analytics jobs in the cloud in a distributed and scalable fashion. The proposed system is designed by leveraging the existing open-source big data technologies and is deployed and evaluated to shed light on several intrinsic aspects of modern real-time video analytics applications.
Umbilical Cord Derivatives Abrogate Carrageenan-induced Inflammation
Keywords: carrageenan
inflammation
mesenchymal stromal cell

Mesenchymal stromal cells (MSCs) behave as sensors of inflammation, and can adopt an anti-inflammatory phenotype that is, in part, caused by MSC derivatives. In this study we created derivatives from whole human umbilical cord tissue (WC), the perivascular tissue of the cord (PJ), and a cell lysate (CL) produced from cultured MSCs from the PJ, and tested their ability to abrogate a carrageenan-induced inflammatory response in the mouse hind paw. Edema and levels of inflammatory cytokines were reduced after treatment with the derivative, even when diluted up to 100x of their original concentration, and they performed similarly to living MSCs and MSCs engineered to overexpress IL-10. Characterization with mass spectrometry revealed ~200 proteins in the PJ with a known immune response, and an in-vitro scratch assay displayed potential wound healing effects of the PJ through enhanced cell migration. Thus, the derivatives elicited an anti-inflammatory therapeutic benefit.
Investigating the Role of BRCA1 in the Regulation of Osteoprotegerin
Keywords: BRCA1
breast cancer
osteoprotgerin

Recent evidence has implicated receptor activator of nuclear factor-κB (RANK)-associated signaling in the pathogenesis of BRCA1-associated breast cancer. BRCA1 mutation carriers at high risk of developing breast cancer have lower circulating levels osteoprotegerin (OPG), the endogenous inhibitor of RANK signaling, compared to non-carriers. A preliminary study by our group found a significant inverse association between circulating blood OPG levels and BRCA-associated breast cancer risk. My thesis project aimed to investigate the molecular mechanisms underlying the systemic reductions in OPG levels in BRCA1 mutation carriers using cell models of BRCA1 knockdown. My data showed that in U2OS, a bone-derived cell line, BRCA1 knockdown did not alter OPG protein nor mRNA expression. Conversely, in an immortalized human mammary epithelial cell line, suppression of BRCA1 expression decreased OPG secretion and OPG transcript levels. In sum, my findings suggest that BRCA1 may have a mammary-specific role in modulating OPG secretion through a transcriptional mechanism.
AquaFly: A Tilt-rotor Vertical Take-off and Landing Aquatic Unmanned Aerial Vehicle
Keywords: AquaUAV
Control
Tiltrotor
Transition
UAV
VTOL

This thesis presents the development of a novel tilt-rotor aquatic unmanned aerial vehicle that can land and take-off from water surfaces with an innovative box tail design, named AquaFly. The box tail provides buoyancy and flotation stability for the vehicle on water surfaces while improving its flight stability in forward flight. Flight tests demonstrated successful autonomous and piloted water take-off and landing in the presence of wave and wind disturbances. A nonlinear hierarchical adaptive control framework is proposed. It is designed to cover all flight modes of AquaFly which include hovering, transition, and forward flight. The adaptive nature of the control framework allows compensation for modeling errors, uncertainties, and disturbances. Stability analyses are presented to show asymptotic tracking performance as well as the boundedness of all signals for the proposed control framework. Finally, simulation analyses are conducted and show control effectiveness for all flight modes.
Quantifying the Physiological Demands and Kinematic Activity in Elite Wheelchair Basketball
Keywords: Applied Sport Physiology
Metabolic demands of Wheelchair Basketball
Paralympic Sport Physiology
Sport Science

This study described the physiological and locomotor demands of elite wheelchair basketball. Players (n=12) had two data collection periods; (1) laboratory and field-based testing to determine peak physiological and locomotor responses, (2) in-game collection of oxygen consumption (VO2), heart rate (HR), and locomotor activity (Speed). Players averaged 31.3 ± 6.9 minutes of playing time, a VO2 of 32.4 ± 5.8 ml·kg-1·min-1 and spent the game at 85.8 ± 10.7 %VO2peak. Further, HRmean was 159.4 ± 14.6 bpm and they spent the game at 87.3% ± 8.1-1 -1 %HRpeak. Speedmean was 1.29 ± 0.15 m·s and players averaged a Speedpeak of 3.23 ± 0.35 m·s . There were no significant differences in VO2, %VO2peak, HRmean, %HRpeak, Velmean, or Velpeak (t- test, p > 0.05) between low and high classification players. The results from the present study demonstrate that wheelchair basketball requires intermittent efforts of high physiological demands for both low and high classification players.
A Novel Platform for Hyperpolarized Carbon-13 MRI of the Heart
Keywords: Carbon-13
Cardiac imaging
Heart failure
Hyperpolarization
Magnetic resonance imaging
MRI

Heart failure, one of the leading causes of death in North America, has several metabolic alterations associated with its progression. However, the majority of these alterations are known only from preclinical studies or in vitro assessment. Hyperpolarized carbon-13 MRI is an emerging modality for metabolic imaging in vivo that can supplement the current body of knowledge. This thesis addresses areas of improvement in the hyperpolarized carbon-13 MRI cardiac methodology to optimize it for clinical translation. First, technological advancements such as a flexible quadrature transmit-receive coil and real-time accessory imaging platform were implemented, modernizing the protocol. Then, a method for rapid transmit field calibration during clinical scans was developed. This was required due to the flexible nature of the transmit-receive coil. This thesis ends with a presentation of the applications made possible by these developments, including a clinical trial that is currently actively recruiting heart failure patients.
The Physiological and Molecular Characterization of SIFamide and the SIFamide receptor in Rhodnius prolixus
Keywords: bloodmeal
immunohistochemistry
insect
neurohormone
SIFamide

SIFamides are a family of highly conserved arthropod neuropeptides. Largely studied in holometabolous insects, this peptide is mainly expressed in four medial neurons in the pars intercerebralis of the brain. Little is known about SIFamide’s role in hemimetabolous insects. Rhodnius prolixus is a blood-gorging hemimetabolous insect and a vector for human Chagas disease. In this study, the R.prolixus SIFamide (Rhopr-SIFa) transcript and receptor (RhorprSIFR) has been cloned and sequenced, and the distribution and function of Rhopr-SIFa, in relation to feeding, explored. Immunohistochemistry shows the characteristic four medial SIFamidergic cells. Projections from these cell bodies extend into the corpus cardiacum, suggesting for the first time in insects, that SIFamide may be a neurohormone. We also observed enhanced feeding behavior in insects injected with Rhopr-SIFa and decrease with RNAi mediated knockdown. This work suggests SIFamide may play an important function in controlling R. prolixus feeding behavior, as a central and peripheral neuromodulator/neurohormone.
Associations between Serum Osteocalcin and Subjective Stress in People with Depression and Type II Diabetes
Keywords: Depression
Osteocalcin
Perceived Stress
Type 2 Diabetes

Low serum osteocalcin is a risk factor for type 2 diabetes mellitus (T2DM), and osteocalcin (OCN) release from bone is associated with an acute stress response. Both T2DM and stress are associated with depression. Here, a depressive episode was not associated with OCN concentrations among people with T2DM; however, higher concentrations of carboxylated OCN (cOCN) were associated with higher perceived stress among participants with depression (r=0.546, p=0.013) and T2DM. Controlling for age, sex, body mass index, glycemic control (HbA1c), insulin resistance (homeostatic model), depression, and antidepressant use, carboxylated OCN was associated with perceived stress (F=9.602, p=0.003), and this relationship was stronger in those with depression (depression × cOCN interaction F=4.702, p=0.033). The results identify circulating OCN as a neuroendocrine marker associated with chronic stress among people with T2DM experiencing a depressive episode.
TeamCare: An Interprofessional Team-based Primary Health Care Program for Patients with Complex Health and Social Needs
Keywords: Health Care Utilization
Interprofessional
Primary Care
Program Evaluation
Team-Based Care

TeamCare encompasses several programs designed to improve access to team-based care for complex patients that have been implemented through Community Health Centres (CHCs) in Ontario. Two studies were conducted to determine whether TeamCare has reached its intended population of patients with complex health and social needs and evaluate its impact on patient health care utilization. The studies used electronic health record data from CHCs linked with administrative data for fiscal years 2013-2016. A modified Difference-in-differences approach was employed to analyze the impact of participation in TeamCare on emergency department, primary, and secondary care utilization. The results of the studies indicate that TeamCare reached its intended population but did not have a meaningful impact on the utilization of formal healthcare services for patients enrolled in 2015. The results of this study and continued research will inform efforts to expand access to interprofessional team-based primary care in Ontario.
The Relationship Between Physical Activity and Mental Health in Adults with Chronic Disabilities
Keywords: disability
ill-being
mental health
physical activity
well-being

Compromised mental health (MH) is a common secondary outcome for adults with disabilities. While physical activity (PA) has psychological benefits, PA levels remain low in adults with disabilities. Guided by self-determination theory and Lubans and colleagues’ PA-MH model, this thesis examined the PA-MH relationship in adults with disabilities (N = 100, Mage = 36.61). Three moderate-to-vigorous PA (MVPA) modes [combined (p = .34, p = .01), strength (p = .36, p = .01), aerobic (p = .38, p = .01)] were positively correlated with MH. Autonomy, competence, and relatedness were positively correlated with MVPA and MH. Athletes reported significantly greater MVPA (t(98) = 6.31, p
Cascade Health Service use in Families of Children with Cardiomyopathy: Implications for Health Technology Assessment
Keywords: Cardiomyopathy
Cascade Effects
Child Health
Cost Analysis
Health Technology Assessment
Methodology

Background: Cardiomyopathy (CMP) is a genetically heterogeneous disease of the myocardium. Clinical practice guidelines recommend cascade genetic testing and clinical screening to relatives of affected individuals, however health technology assessment (HTA) does not account for these cascade effects. Purpose: To report the pattern and costs of cascade health service use in relatives of children with CMP. Methods: A retrospective cohort study was conducted among children with CMP who underwent genetic testing. A cost analysis of services offered to probands’ relatives was undertaken from the health care payer perspective. Results: Data were available for relatives of 53 probands. The mean cost of offered cascade health services was $1,173 per family. Multiple one-way sensitivity and scenario analyses were undertaken to address uncertainty. Conclusions: Quantifying cascade health services is essential to economic evaluation of emerging genetic technologies. Optimizing HTA methods for incorporating cascade effects will enhance economic evaluation of genomics for funding decisions.
Improving Decision Making in Empiric Antibiotic Selection (IDEAS)
Keywords: antibiotic resistance
antimicrobial stewardship
antimicrobials
clinical decision making

Timely initiation of adequate antibiotics has been associated improved patient. However, selecting adequate empiric antibiotics is difficult due to increasing resistance rates and the competing desire to apply antimicrobial stewardship principles. We developed, implemented and evaluated two interventions to optimize empiric antibiotics using prospective audit and feedback. The interventions included providing suggestions to prescribers at two points in the empiric period: (1) prior to availability of any culture results, empiric therapy was altered to ensure concordance with prior cultures that have predictive relevance for future infection (2) when Gram-negative bacteremia was identified, previously derived and validated multivariable models were used to recommend the most narrow-spectrum adequate antibiotic. The first intervention improved time to concordant therapy, increased the proportion of patients receiving concordant empiric antibiotics, and reduced vancomycin use. The second intervention facilitated de-escalation of antibiotics and increased the proportion of patients receiving the narrowest adequate antibiotic at blood culture finalization.
A Method for the Directed Evolution and Protein Engineering of Synthetic CRISPR-Cas9 Inhibitors
Keywords: anti-CRISPR
CRISPR-Cas9
directed evolution
protein engineering

CRISPR-Cas9 is a powerful genome-editing tool in biotechnology and biomedical research. However, one concern around the use of this technology in clinical applications is the potential for off-target activity of Cas9 that could have deleterious effects. The discovery of anti-CRISPR (Acr) proteins, natural protein inhibitors of CRISPR-Cas systems, could provide a solution. The presence of Acrs in the context of CRISPR-Cas applications could provide temporal and spatial inhibition of CRISPR activity. One particular Acr of interest is AcrIIC1, which binds to the highly conserved HNH domain of various Cas9 orthologs, thus making it an ideal scaffold for generating a mutagenesis library. Thus, the goal of this project is to use directed evolution to develop a platform for the design of protein-based inhibitors against any desired Cas9 species. Insights from this project will be used to further understand CRISPR-Cas9 mechanisms, anti-CRISPR biology, and the evolutionary arms race between bacteria and bacteriophages.
Electromagnetic Surface Treatments for Improving Ground Penetrating Radar
Keywords: Artificial Magnetic Conductor
Ground Penetrating Radar
High Impedance Surface
Resistively Loaded Dipole
Tunable Surface

Autonomous vehicle development and research has recently become a focus many vehicle manufacturers with billions of dollars of investment in recent years. It is shaping the future of the transportation industry. An open problem facing autonomous vehicles surrounds the development of a robust suite of sensors that is able to safely and reliably operate in all weather and road conditions. This thesis investigates the potential of localizing ground penetrating radar as a piece of that sensor suite while simultaneously demonstrating an approach to constructing an LGPR's antenna array by incorporating an artificial magnetic conductor with a resistively loaded dipole. This antenna array has a reduced profile and improved gain performance compared to the current implementation. Such an improvement in gain and profile reduction will allow such a sensor to be more easily incorporated into a vehicle's design and provides a potential road-map to further reduce the size of such arrays.
Noninvasive EEG-based Prediction of Infantile Spasms using Deep Learning Networks with Phase Amplitude Cross-frequency Coupling
Keywords: biologically inspired artificial intelligence
deep learning
neural networks
seizure prediction
signal processing
west syndrome

Around one in 2,500 children develop West Syndrome where 90% develop infantile spasms within the first year of life. Being able to predict the onset of a spasm has the potential to greatly improve the lives of infants with epilepsy since treatment or care can be given by a caregiver prior to the event. In the literature, several seizure prediction algorithms have been developed, giving relatively mediocre sensitivities and specificities. This study improves on these metrics by applying several deep learning networks in combination with the phase amplitude cross-frequency coupling feature derived from scalp electroencephalography. All of the networks contain a convolutional neural network, where variants include the use of a multi-stage state classifier, biologically plausible filters for pre-processing, and a recurrent neural network for post-processing. Overall, the networks are able to produce high accuracies (99%) and significant latencies (10 min.). Explanation techniques are used to validate these models.
Inpatient Rehabilitation Exergames in Children with Cerebral Palsy after Lower Extremity Orthopaedic Surgery
Keywords: exergames
neurotechnology
orthopedic
rehabilitation

Children with Cerebral Palsy (CP) often require lower extremity orthopaedic surgery, with recovery consisting of pain and fewer opportunities for social interaction. The Liberi Exergames, a multi-player exergame powered by pedaling a stationary bicycle and using game-controllers, may provide opportunities for children with CP to cycle, decrease pain and enhance well-being. The objectives were to assess the feasibility of incorporating exergames for children with CP and to explore pain and well-being. Ten children with CP recovering from lower extremity orthopaedic surgery were recruited; the first five received physiotherapy (“comparison group”), and the next five received 15 exergame sessions and physiotherapy (“case group”). Questionnaires evaluating pain and well-being were administered. All feasibility indicators were met, reduced pain scores were reported for both groups, and improved well-being scores were reported for the case group. This project provides the basis for developing larger studies to evaluate exergames for inpatient pediatric orthopaedic populations.
Analysis of Municipal Permitting Systems and Trends in Preparation for Electronic Permitting Implementation
Keywords: building
e-permitting
municipal
Ontario
permit
permitting

Ontario municipalities have complex permitting systems that have been shown to result in lengthy delays. These delays have been getting worse over the years, and municipalities are looking for ways to reduce them. Based on international experience, electronic permitting (e-permitting) has been shown to improve efficiency, and many municipalities in Ontario are looking to adopt such technologies and processes. To do this, it is important to evaluate the current permitting landscape in the province and identify what municipalities need to consider before adoption. This thesis investigates the permitting trends that Ontario municipalities are experiencing and explores the economic circumstances that may impact these trends. Additionally, the permitting data of an Ontario municipality is thoroughly analyzed to identify potential issues in permitting timelines. Finally, a municipality’s plans review process is scrutinized to develop a series of considerations for municipalities interested in e-permitting.
A Practical Simulation Framework for Thermal Sensation Analysis of Fenestration Designs
Keywords: building design
direct solar radiation
draught comfort
thermal comfort
window design

Buildings with highly glazed envelopes have gained popularity over the past decades. Though it is known that these buildings are less energy efficient, few attempts have been made to investigate their effect on thermal comfort apart from surveys. The gap between research and the industry arises because predicting thermal sensation is labourious and lacks suitable tools. In response, a simulation framework, which is the novelty of this work, is designed to reduce such effort. Direct solar radiation and ankle draught effects are considered since they have been shown to increase warm and cold sensation, respectively. Example applications using visualization and sensitivity analysis techniques suggest that window size increases both warm and cold sensation levels, which are also positively correlated with window overall solar heat gain coefficient and U-factor, respectively. The results from the example applications provide insights into how different window designs can affect thermal sensation within a similar context.
System Similarity, Performance Guarantees, and Asymmetry in Transfer Learning for Robotics
Keywords: Control Systems
Machine Learning
Robotics
Transfer Learning

In robotics literature, transfer learning has been proposed in learning-based control frameworks to leverage existing experience from a source robot or task to accelerate or improve the learning process on a target robot or task. It is often assumed without analysis that incorporating prior experience will be beneficial. For robotics applications, inappropriately transferring experience can be unsafe or inefficient. This thesis presents two approaches to this problem. First, we propose an experience selection algorithm based on a dynamics similarity characterization to select source experience that best improves target robot performance. Second, we derive an upper bound on the tracking error of a target robot using an inverse dynamics module from a source robot, and demonstrate how the bound can guarantee a performance improvement on the target robot prior to conducting transfer. We further illustrate that inverse module transfer is asymmetric. We demonstrate both approaches in quadrotor trajectory tracking experiments.
Staffing in the Emergency Department: A Discrete Event Simulation Approach
Keywords: Discrete Event Simulation
Emergency Department
Length of stay
Modelling
Nurse workload
Physician workload

Emergency department (ED) crowding is a significant problem resulting in longer length of stays (LoS), wait times, poor patient outcomes, and higher mortality rates. A major cause of ED crowding is improper staffing. This thesis proposes to address this issue by developing a discrete-event simulation model of the Scarborough General Hospital ED. It uses what-if analysis to find the staffing bottleneck and evaluate the impact of altering nurse and physician staffing on LoS, wait times, and utilization. Results indicate that physicians were the bottleneck; the largest reductions to overall LoS and utilization rates could be achieved by adding a physician shift to match either the daytime or evening peak arrival times. LoS could also be improved by altering the current physician schedule to match patient arrivals. Nurse utilization was affected by the physician schedule. With proper staffing, the hospital can greatly increase ED flow, while decreasing nurse and physician utilization.