VictorJuiz/thesis huggingface dataset:
Noninvasive EEG-based Prediction of Infantile Spasms using Deep Learning Networks with Phase Amplitude Cross-frequency Coupling

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.

Keywords: biologically inspired artificial intelligence
deep learning
neural networks
seizure prediction
signal processing
west syndrome
Advisor: Bardakjian, Berj L
Inpatient Rehabilitation Exergames in Children with Cerebral Palsy after Lower Extremity Orthopaedic Surgery

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.

Keywords: exergames
neurotechnology
orthopedic
rehabilitation
Advisor: Fehlings, Darcy
Analysis of Municipal Permitting Systems and Trends in Preparation for Electronic Permitting Implementation

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.

Keywords: building
e-permitting
municipal
Ontario
permit
permitting
Advisor: McCabe, Brenda Y
A Practical Simulation Framework for Thermal Sensation Analysis of Fenestration Designs

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.

Keywords: building design
direct solar radiation
draught comfort
thermal comfort
window design
Advisor: Touchie, Marianne
O'Brien, William
System Similarity, Performance Guarantees, and Asymmetry in Transfer Learning for Robotics

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.

Keywords: Control Systems
Machine Learning
Robotics
Transfer Learning
Advisor: Schoellig, Angela P
Staffing in the Emergency Department: A Discrete Event Simulation Approach

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.

Keywords: Discrete Event Simulation
Emergency Department
Length of stay
Modelling
Nurse workload
Physician workload
Advisor: Carter, Michael
Numerical Simulation of Complex Hydraulic Fracture Development by Coupling Geo-mechanical and Reservoir Simulator

Hydraulic fracturing is one of the standard techniques adopted by oil and gas industries to enhance production in unconditional reservoirs. Reservoir properties and treatment designs have a significant influence on the effectiveness of hydraulic fracturing treatments. Extensive studies on the mechanism of hydraulic fracturing have been conducted to optimize the hydraulic fracturing design. Recent advances in fracture diagnostic technology have brought new insights to the complex fracture geometry. Numerical simulation is an economical approach to investigate the generation of fracture geometry and its effect on post-treatment production enhancement. This work proposes a workflow to study the fracture complexity through coupling the geomechanical simulator Irazu and the reservoir simulator CMG. The geo-mechanical simulator is devised to simulate the hydraulic fracturing process employing the hybrid finite-discrete element method while the reservoir simulator CMG is used for the reservoir post-treatment production forecast.

Keywords: hydraulic fracturing
numerical simulation
reservoir simulation
Advisor: Grasselli, Giovanni
A Model Reduction Framework with the Empirical Quadrature Procedure for High-dimensional Shape-parameterized Partial Differential Equations

This thesis details a goal-oriented model reduction framework for parameterized nonlinear partial differential equations (PDEs), with an emphasis on shape-deformation problems with high-dimensional and non-affine parameter dependence. The framework builds on five technical ingredients: free-form deformation, which provides implicit geometry-independent shape deformations; reduced basis spaces, which provide rapidly convergent approximations of the parameterized solutions; the empirical quadrature procedure (EQP), which provides efficient hyper-reduction for nonlinear PDEs with non-affine parameter dependence; the dual-weighted residual (DWR) method, which provides a posteriori error estimation; and a greedy sampling method based on saturated parameter space assumptions, which provides efficient adaptive training in high-dimensional parameter spaces. This generalized framework enables automatic training of reduced order models that meets a user-prescribed error tolerance for a wide range of continuum mechanics problems. The versatility of this framework is demonstrated for many-query shape deformation problems in acoustics, aerodynamics, and hyperelasticity. The eventual application of this framework is to accelerate many-query problems such as shape optimization and uncertainty quantification.

Keywords: CFD
EQP
FFD
finite element method
model reduction
reduced basis
Advisor: Yano, Masayuki
Evaluating Model Uncertainty to Inform Offset Ratios for the Protection of Freshwater Fish Productivity in Canada

Ecological models allow resource managers to evaluate human impacts on fish and their habitat. However, quantitative methods that incorporate and assess uncertainty in these models are rare. These models require fish life history information, which is often uncertain, and can thus lead to uncertain predictions and pose risks to either the environment or proponent. I utilized a multispecies size spectrum model to evaluate uncertainty surrounding estimates of three fish life history traits: (1) asymptotic weight; (2) the von Bertalanffy growth coefficient; and (3) weight at maturity. I then applied an existing framework for quantifying compensation ratios to achieve “no net loss” (NNL) in the context of a theoretical development project. The results of this study show that asymptotic size and forage fishes have the greatest influence on predictive uncertainty. I recommend that sampling effort be prioritized for these and demonstrate how to account for uncertainty in a precautionary management framework.

Keywords: Aquatic science
Fish
Fisheries
Modeling
Offsetting
Uncertainty analysis
Advisor: de Kerckhove, Dak
Chu, Cindy
Associations between the Spatiotemporal Distribution of Kawasaki Disease and Environmental Factors: Discovering Clues into the Elusive Etiology of a Complex Disease

Kawasaki disease is an acute vasculitis of childhood which may lead to coronary artery aneurysms, and is the most common cause of acquired heart disease in children in developed countries. The etiology remains unknown, but is currently felt to be the result of a dysregulation and hyper-stimulation of the inflammatory system occurring in genetically and developmentally susceptible individuals after exposure to one or more unidentified infectious or environmental trigger(s). The aim of this thesis was to determine how variations in the incidence of KD in Canada are spatiotemporally associated with the incidence of infections and atopic conditions, wind and weather components, pollution and aeroallergens. We established that immunomodulation may be influenced by pollution and habitual exposure to aeroallergens. We proposed that fungal and algal spores, viral gastrointestinal and bacterial lower respiratory tract infections may trigger KD. These findings add to the etiologic framework for KD.

Keywords: Etiology
Kawasaki disease
Advisor: McCrindle, Brian W
Public Perception of the Scope of Practice of Oral Maxillofacial Surgeons in Ontario

Purpose: Investigate and compare the General Public’s, General Dentists’ and Primary Care Physicians’ level of knowledge of the scope of practice of Oral and Maxillofacial Surgeons (OMS). Materials and Methods: A mail-out survey of the General Public, General Dentists and Primary Care Physicians in Ontario, Canada. Survey consisted of a screener along with 24 clinical scenarios. Responses between groups were compared to identify any significant differences between subjects with P value set at 0.05. Results: The majority of Dentists (100%) and Primary Care Physicians (95.5%) have heard of OMS, in contrast only 73.7% of the General Public (p

Keywords: Oral Surgery
scope of practice
Advisor: Lam, David
Teaching Electronic Medical Record (EMR) Data Discipline to Clinical Trainees: A Canadian Pilot Study

Evidence suggests that patients whose electronic medical records (EMR) are documented with high quality data obtain higher quality care. However, most clinicians do not routinely document with this data discipline, and to date how to instruct this has not been clear. In this study, the key components of such an educational session for Canadian family medicine trainees were determined, with a particular focus on improving trainee awareness of the importance of data discipline and their understanding of data consistency. We piloted our developed session in three academic teaching sites and found no statistically significant difference when comparing two instructional methods – exploratory case simulations versus didactic only. However, trainee performance in general was satisfactory, suggesting robust immediate learning regardless of teaching method. Trainees also confirmed a strong desire for education on data discipline. Going forward, the educational session can be improved, become embedded in curricula, and evaluated using real-world EMR data.

Keywords: data quality
electronic medical records
medical education
Advisor: Shachak, Aviv
Assessing the Viability of Wideband Transmission of Pulse Width Encoded Data Over an Inductive Link for Wireless Neural Implants

To date, there are no clinically available cortical neural implants which wirelessly transmit the full neural signal at an adequate data transfer rate while managing power dissipation limits. The current work addresses power consumption and data bitrate requirements using wideband transmission, omitting the use of a constant carrier wave, and short impulses to transmit pulse width modulation encoded data, transmitting more effective bits per cycle. An inductive link is used, reducing power consumption compared to radio frequency transmitters. 1 Msample/s transmission rate with 6 bits of resolution is demonstrated, providing proof-of-concept for a system that transmits the full neural signal outside the body. Such a system enables extracorporeal processing of the neural signal, potentially lending itself to applications such as brain-computer interfaces and diagnosis and treatment of neurological disorders. The intelligence of the system can be adjusted according to scientific advancements, without being limited to processing power onboard the implant.

Keywords: implant
neural
wireless
Advisor: Popovic, Milos R
Genov, Roman
Investigating the Sufficiency of Chronic Hippocampal Hyperactivity for the Development of Alzheimer’s Disease Pathology

Memory loss is the primary symptom of Alzheimer’s disease (AD), a devastating neurodegenerative condition with no cure. Recent studies have highlighted the importance of hyperactivity, particularly in the hippocampus, during early stages of AD progression. We hypothesized that chronic hippocampal hyperactivity (CHH) would be sufficient to cause AD pathology and memory deficits in wild-type mice. CHH was induced by virally expressing an excitatory receptor (hM3D(Gq)) in hippocampal CA1 pyramidal neurons, chronically activated by administration of clozapine N-oxide (CNO) in their drinking water. Some CHH mice that reached the 19-month timepoint developed beta-amyloid and hyperphosphorylated tau immunoreactivity in the ventral CA1 and lateral entorhinal cortex, respectively. Furthermore, 6 months of CHH led to impaired spatial and recognition memory, and increased anxiety-related behaviour. These findings suggest that CHH may be sufficient to cause aspects of AD, highlighting the importance of future investigations to potentially improve prevention, diagnosis, and treatment.

Advisor: Kim, Junchul
Takehara-Nishiuchi, Kaori
Identifying the mRNA Targets of the RNA-binding Protein TIA-1 in Human Neurodevelopment

TIA-1 is an RNA binding protein that is implicated in neurodevelopment. I conducted RIP-seq on lysates from three in vitro stages of neurodevelopment: human embryonic stem cells (hESCs), neural progenitor cells (NPCs), and cortical neurons, to identify TIA-1 targets during neurodevelopment. Despite minimal changes in TIA-1 expression or localization, TIA-1 binding efficiency decreases over neurodevelopment. RIP-seq identified 2365 TIA-1 targets in ESCs, 846 NPC targets, and 330 neuronal targets. ESCs targets included genes associated with neurodevelopment and autism, which were not bound in neurons. I validated TIA-1 binding to two mRNA targets critical to neurodevelopment, UBE3A and MECP2, using RIP qRT-PCR. These results provide insight into the network of TIA-1 targets during neurodevelopment and provide a first step towards defining the functional role of TIA-1 in neuronal differentiation. They suggest that TIA-1 regulates neurodevelopmentally relevant transcripts in early stages of development, but that this regulation decreases during neuronal differentiation.

Keywords: neurodevelopment
RIP-seq
stem cells
TIA-1
Advisor: Ellis, James
Understanding of Palliative Care among Members of the Public

Introduction: Palliative care (PC) aims to improve the quality of life of patients and caregivers. We examined the public’s knowledge and attitudes about PC. Methods: A survey was distributed by e-mail to the Canadian public. Participants were >18 years old, could comprehend English or French, and resided in Canada. Results: Of 1518 participants (52% female), 56% had limited or no knowledge of PC. Of those who had heard of PC, 60.1% were unaware that PC could be incorporated early in the illness. Initially, 56% were fearful of a referral to PC; after reading the definition of PC, this percentage was reduced to 41%, and degree of fearfulness was reduced in 46% (p

Advisor: Zimmermann, Camilla
Moisture Diffusion through Nanoporous Membrane and Protective Vents: Characterization and Modelling

Porous membranes are widely used in various industries. Outdoor electronics that generate significant heating commonly use protective vents to allow free thermal expansion and contraction of air within their enclosure aimed to prevent pressurization. Fibrous membrane may be installed as a protective vent to stop contaminants and foreign particulate from entering the electronic enclosure. A challenge frequently encountered with these breathable vents is that moisture can easily permeate through them and diffuse into the electronic enclosure. If the internal relative humidity approaches saturation point, the risk of condensation intensifies. Formation of liquid water can potentially damage the electrical components or lead to a short-circuit. In this thesis, moisture transmission through a commonly used protective nanofibrous Gore-Tex vents was studied in various ambient conditions and a model was developed to estimate the internal relative humidity of a select electronic enclosure by calculating the moisture permeation rates in a transient environment.

Keywords: Gore-Tex
Moisture permeation
Moisture transmission
Nanofibrous membranes
Porous membranes
Advisor: Chandra, Sanjeev
An Integrative Analysis of the Effects of Neonicotinoid Pesticides on North American Hummingbirds

Neonicotinoids are neurotoxic systemic insecticides applied extensively worldwide. The impacts of neonicotinoid exposure on invertebrates are widely studied, however effects on essential vertebrate pollinators like hummingbirds have received little attention. My study into the effects of imidacloprid, a common neonicotinoid, on hummingbirds integrates lab-based and field-based assays with emphasis on cellular, systems, whole-organism, and behavioural levels. Within 2 h of exposure, hummingbirds exhibited a significant depression in energy expenditure (up to 25% +/- 11%). I did not observe effects on feeding behaviour, immune response, or cholinesterase activity in the lab, or stress hormone deposition in feathers collected in the field. I also determined that hummingbirds excrete imidacloprid quickly (elimination half-life of 2.1 h +/- 0.1 h) relative to other bird species. Hummingbirds exist on narrow energy margins, especially during migration and breeding seasons. Therefore, changes in their metabolism following exposures to imidacloprid observed herein could bear important energetic consequences.

Keywords: dose-response
hummingbirds
imidacloprid
integrative biology
neonicotinoid pesticides
Advisor: Welch Jr., Kenneth C.
Identifying Cases of Spinal Cord Injury/Disorder in an Ontario Primary Care Electronic Medical Record Database

Currently, little health system information exists on the longitudinal course of spinal cord injury (SCI). The increasing availability of information from electronic medical records (EMR) offers an opportunity to fill this gap. An initial keyword search of all eligible records in a database of primary care EMR in Ontario, Canada, was conducted to identify possible cases of SCI. A random sample of possible cases was selected (n=803) and reviewed using a structured chart review process. 126 validated cases of SCI were identified and this reference standard cohort was used to develop and test potential algorithms. The optimal algorithm uses a combination of free-text keywords and ICD-9 codes, with a sensitivity of 70.6%, a positive predictive value of 89.9%, and an F-score of 79.1%. This cohort can be linked with administrative data to study longitudinally the health status and health care utilization of this population.

Keywords: Case identification
EMR
Spinal cord injury
Advisor: Jaglal, Susan B