VictorJuiz/thesis huggingface dataset:
EEG Biomarkers of Reduced Inhibition in Microcircuit Models in Depression
Keywords: Biomarkers
Depression
EEG
Inhibition
Microcircuits

Reduced cortical inhibition by somatostatin-expressing (SST) interneurons has been strongly associated with treatment-resistant depression. However, whether the effects of reduced SST inhibition on microcircuit activity have signatures detectible in electroencephalography (EEG) signals remains unknown. We simulated resting-state activity and EEG using detailed models of human cortical layer 2/3 microcircuits with normal (healthy) or reduced SST inhibition (depression). Healthy microcircuit models showed emergent key features of resting-state EEG, and depression microcircuits exhibited increased theta, alpha and low beta power (4 – 15 Hz). The changes in depression involved a combination of an aperiodic broadband, and periodic theta and low beta components. In both conditions, neuronal spiking showed a spike preference for the phase preceding the EEG trough. Our study thus links SST inhibition level to features in EEG simulated from detailed human microcircuits, which can serve to better identify mechanistic subtypes of depression using EEG, and non-invasively monitor modulation of cortical inhibition.
Rhythmic Sampling Supports Episodic Memory Formation
Keywords: Encoding
Memory
Oscillations

Theta oscillations (3-9 Hz) in the hippocampus have been posited to mitigate the trade-offs between encoding and retrieval by segregating them in time (i.e. at opposite phases). However, there is limited behavioral evidence that humans cognitively cycle in and out of encoding and retrieval states at this rhythm. Here, I adapted the behavioral oscillation paradigm to investigate if episodic memory formation is rhythmic. In the present experiment (n=79) I found that associative retrieval performance oscillated at the theta frequency (5-6 Hz) with respect to a cue-image delay during the time of encoding. This same rhythmicity was not found for an attention task performed during the time of encoding, suggesting rhythmicity in memory formation was found over and above rhythmicity in perceptual processing. These data provide the first evidence demonstrating that human memory formation oscillates at a similar frequency as neural oscillations in the hippocampus known to underlie memory formation.
Factors Associated with Surgical re-Replacement or Transcatheter Pulmonary Valve Insertion of the Second Pulmonary Conduit
Keywords: congenital heart disease
congenital heart surgery
pulmonary conduit
pulmonary valve

Patients receiving a right ventricle-to-pulmonary artery conduit (PC) in infancy will require successive procedures or replacements, each with variable longevity. We sought to identify factors associated with time-related risk of a subsequent surgical replacement (PC3) or transcatheter pulmonary valve insertion (TPVI) after a second surgically-placed PC (PC2). From 2002 to 2016, 630 patients were enrolled after initial valved PC insertion at age
“In the lion’s den, we just want to know”: A Qualitative Exploration of Parents’ Decisions to Pursue Pediatric Whole Genome Sequencing
Keywords: Genomic sequencing
Parent experience
Qualitative methods
Secondary findings

This dissertation aimed to explore how personal, interpersonal, and societal factors influence parents’ decision to pursue whole-genome sequencing (WGS) for their child. Semi-structured interviews were conducted with parents of children with heart conditions who were offered WGS and secondary variants. Transcripts were coded inductively and deductively, using the Social Ecological Model and Kohler’s framework of personal utility. Nineteen participants were interviewed. During decision-making, parents described personal value they expected to gain from WGS. Gaining an understanding of their child’s current and future health was beneficial and acted as a precursor to enabling cognitive, emotional, and behavioural control. However, parents’ enhanced sense of control required a readiness to learn genetic information. Social contexts also impacted parents’ decisions; WGS was valued as a mechanism for mitigating blame and legitimizing disability. Findings shed light on the acceptability of WGS and may inform counselling strategies and health technology assessment.
Examination of Infection Dynamics within a Viral Consortium Infecting the Haptophyte Alga Chrysochromulina parva
Keywords: algae
competition
ecology
freshwater
microbiology
viruses

Viruses are ubiquitous in freshwater and are crucial for nutrient cycling in all aquatic systems. However, little is known about the interactions of freshwater algal viruses and their hosts, or the ecological dynamics of complex systems with multiple pathogens. Here, I investigated these dynamics in a consortium of viruses and virophages infecting Chrysochromulina parva, a freshwater haptophyte alga. Cultures of C. parva were grown and subjected to sequential rounds of lysis. Community composition was assessed using quantitative PCR assays specifically targeting each virus. Viral titre was determined by Most Probable Number assays. All known lytic agents were outcompeted within four rounds by another, unknown, lytic agent or agents. This study provides the first data on inter-virus competition for any viruses of aquatic primary producers, allowing us to generate further hypotheses about the complex ecology of algal viruses, and the coexistence of multiple viruses parasitizing the same host.
Visualizing Insider USB File Exfiltration Anomalies: A Financial Services Case Study
Keywords: File Activity Monitoring
Insider Security Monitoring
Interactive Dashboard
Participatory Design
Security Visualization
User Research

Data exfiltration by insiders (or people masquerading as insiders) is a major threat for organizations that store and use highly confidential data. Standard cybersecurity methods using firewalls and perimeter strengthening measures fail against insiders, and machine learning methods for anomaly detection generate large numbers of false alarms. I worked with domain experts in a large Canadian financial services company and developed new security visualization technology through a Participatory Design (PD) approach. The resulting File Activity Real-Time Investigation Dashboard Application (FARIDA) is usable for a range of stakeholders, allowing experts to quickly review large amounts of data and enabling non-technical investigators to participate in early stages of the anomaly detection process. This research is a first step towards more general use of visualization tools to monitor sensitive data, and demonstrates how human factors approaches can beneficially supplement the development of AI methods in cybersecurity, using data exfiltration as an example.
Use of Machine Learning Classifiers based on Visual Metrics in Children with Acquired Demyelinating Syndromes
Keywords: Machine learning
Multiple sclerosis
Optical coherence tomography
Pediatric

Multiple Sclerosis (MS), an inflammatory degenerative disease and the visual pathway is a key target in the search for a reliable and easily obtainable diagnostic biomarker that can aid the diagnosis. The objective of this study was to investigate the utility of machine learning (ML) based on optical coherence tomography (OCT) features to identify children with MS and other ADS. In this cross-sectional study a total of 512 eyes from 69 (neyes = 138) healthy controls and 187 (neyes = 374) children with ADS were included. Random forest classifier with recursive feature elimination identified MS with 80% accuracy. A set of eight retinal features were identified as the most important in this classification. In conclusion, this study demonstrated that ML classifiers can be used to diagnose MS in children based on structural OCT measures alone with high accuracy, sensitivity and specificity.
Computational Analysis of Druggability and Genetic Variability of SARS-CoV-2 Pocketome
Keywords: Amino acid conservation
Coronavirus
Druggability
SARS-CoV-2
Structural bioinformatics
Structural biology

Emerging novel coronaviruses (CoVs) and new variants of SARS-CoV-2 are a major public health threat. One therapeutic strategy to face this challenge is to develop broad-spectrum CoV inhibitors, also known as pan-CoV drugs by targeting a druggable and conserved binding site of CoV proteins. Therefore, we performed a systemic analysis of seventeen SARS-CoV-2 protein structures and mapped their binding sites in a quest to determine the most conserved druggable sites. We then analyzed the variation of residues lining the SARS-CoV-2 drug-binding pockets across 27 α- and β-CoVs and across thousands of SARS-CoV-2 samples from COVID-19 patients. Our findings indicate that the most promising targets for developing pan-CoV drugs include the catalytic site of non-structural protein 12 (nsp12; RNA-dependent RNA polymerase) and the RNA central channel of non-structural protein 13 (nsp13 helicase). Lastly, we present our data on an interactive web portal (https://www.thesgc.org/SARSCoV2_pocketome/) to allow users to view the individual proteins.
Hybrid Nanometal Morphing Structures
Keywords: Hybrid structures
Morphing
Propeller
Structural design

The demand for increasing the efficiency of aircraft has led to the pursuit of improved and novel structures. Hybrid structures with morphing capabilities aim to address this through the use of materials with high specific strength, improved manufacturing techniques, and the ability to change shape during flight. A quadrotor propeller was chosen as a proof of concept design for a morphing hybrid structure. This thesis investigates the implementation of morphing via mechanical actuation into various propeller designs, weighing the benefits and tradeoffs for each. A NACA 2412 airfoil was optimized for two separate flight conditions, and various designs were conceptualized for implementation. A design was selected for a finite element analysis to determine the viability of morphing within the structure.
Evaluation of an Electroencephalography Source Imaging based Brain-computer Interface for Youth with Brain Lesions
Keywords: brain-computer interface
EEG source imaging
movement decoding

Brain lesions are the underlying cause of many neurological disorders that lead to physical impairments and disabilities. Brain-computer interfaces (BCIs) have been proposed as an access technology for these individuals since they allow users to communicate using only their brain activity. While electroencephalography (EEG) is one of the most popular BCI modalities due to its affordability and non-invasive approach, it suffers from low spatial resolution and does not account for unique anatomical features present in BCI users with brain lesions, resulting in suboptimal decoding accuracies. This thesis evaluated the classification performance of an EEG source imaging (ESI)-BCI system that incorporates anatomical information from magnetic resonance imaging (MRI) to estimate electrical activity in the brain based on measured scalp potentials. We investigated the offline classification performance of an ESI BCI and EEG BCI in decoding left- versus right-hand motor execution and motor imagery tasks in 9 youth with brain lesions (cerebral palsy and brain injury). Generally, the classification accuracy of the ESI BCI was comparable to that of an EEG BCI. The ESI BCI showed an 8.68±7.84% improvement in one participant for the motor execution task (p
Development of a Novel Computer-aided Design Experiment Protocol for Studying Designer Behaviours
Keywords: CAD
Computer-Aided Design
Design Research
Designer Behavior

Computer-Aided Design (CAD) is indispensable for modern engineering endeavors. The craft of creating CAD models requires extensive experience and expertise. Unfortunately, most traditional CAD training remains focused on declarative knowledge and not higher-level thinking. Studying expert usage could provide insights into the elements of effective CAD modelling. As the first step towards decoding CAD expertise, a novel experimental protocol was developed to capture and characterize designer actions during modeling. The study will serve as a foundation for future CAD design research. The protocol was tested with an experiment of 19 participants of varying skill levels. Event plot visualizations and hidden Markov Models revealed differences between two groups of performance-segmented participants, with the experts adopting a more consistent and organized modelling approach. Compared to existing methodologies, the automated processes developed for this study leverages automatic data collection and analysis to significantly reduce the time and effort required toperform design experiments
Experimental-numerical Determination of the Lorentz and Magnetostriction Mechanism in the Periodic Permanent Magnet Electromagnetic Acoustic Transducer on Steel
Keywords: EMAT
Lorentz
Magnetostriction
Nondestructive Testing
Ultrasound

This thesis determines the relative strength of magnetostriction to Lorentz within the Periodic Permanent Magnet Electromagnetic Acoustic Transducer (PPM EMAT) on steel, which is designed to induce only the Lorentz mechanism. As both mechanisms operate at the same frequency and wavelength, the ratio between Lorentz and magnetostriction is determined through an experimental-numerical method. Another EMAT, which only induces magnetostriction, is constructed to operate at the same wavelength and frequency. In addition, it replicates the magnetic conditions underneath the PPM EMAT that cause magnetostriction. A series of experiments are conducted with both EMATs in a pitch-catch configuration, finding that magnetostriction is significant only at the transmitter. A magnetostriction model is developed specifically for the PPM EMAT, and 3D Finite Element simulations predict EMAT performance. It is found that magnetostriction reduces the output of the PPM EMAT transmitter output by an average of 29% across multiple input current tests.
Accounting for Unpredictability in Autonomous Driving Behaviour
Keywords: Autonomous Vehicles
Behavior Models
Inverse Optimal Control
Inverse Reinforcement Learning
Motion Planning
Self-driving Cars

Autonomous Vehicles (AVs) need to behave like humans when interacting with them.We define unpredictability of surrounding drivers as a measure to take into account for trajectory planning and use Maximum Entropy Inverse Reinforcement Learning (IRL) to demonstrate that incorporating unpredictability into a lane change reward function provides insights on human driving behaviour. We first evaluate the IRL algorithm on a Linear Quadratic Regulator proof of concept. Then we use the IRL algorithm to model reward functions for conducting a lane change maneuver in a highway setting. We investigate whether the unpredictability of surrounding traffic will have an effect on the behaviour of the lane changing car by learning two reward functions from human data, a baseline reward function and a reward function that incorporates unpredictability. Our evaluation confirms that incorporating unpredictability results in modest improvements in explaining the behaviour of human drivers and can result in human-like AVs.
Structural Design, Analysis, and Validation of Next Generation Small Satellite Platforms
Keywords: Aerospace
Engineering
Finite Element Analysis
Satellite
Spacecraft
Structural Analysis

The rapid development of small satellite technologies and the lowering cost of launch services have spurred the next generation of satellites allowing more organizations access to space. The Space Flight Laboratory is positioned on the frontier of the New Space market with their advanced and versatile microsatellite platforms. Specifically, the flight proven DEFIANT platform and the new SPARTAN platform will push the envelope of small satellites in low Earth orbit. This thesis will explore the development of the structural subsystem for the new SPARTAN platform and the NorSat-4 spacecraft using a modified DEFIANT platform. The entire process to create a robust spacecraft structure is presented starting with the design and layout of the structural components. The structure is then assessed through a series of finite element analyses to verify the structural requirements. Lastly, the verification of the physical spacecraft structure is performed through a series of vibration tests.
Meaningfulness of Effort: Scale Construction and Validation
Keywords: Meaning
Mental effort
Personality traits
Scale construction

Effort is often viewed as costly but recently our understanding of effort has shifted to allow for its rewarding aspects. The current studies seek to explore effort as a source of meaning in peoples’ lives. Using established methodologies, I developed and tested a scale measuring the meaningfulness of effort across five samples. This scale captures people that obtain meaning purely from their own efforts. Through a combination of comparing structural equation models and regression models, the Meaningfulness of Effort Scale was shown to be distinct from measures such as trait industriousness and conscientiousness. Results indicate that people high in meaningfulness of effort enjoy benefits in both their general and work life, such as psychological well-being and workplace satisfaction. They also achieve higher status jobs and report higher levels of income. Further, people higher in this trait find effortful tasks to be more meaningful and they perform better on cognitive tasks.
Neck Muscle Vibration and Visual Background Information Influence Separate Processes of Goal-Directed Aiming Movements
Keywords: Motor Control
Neck Muscle Vibration
Neck Proprioception
Sensorimotor Processes
Upper-Limb Pointing
Visual Context Information

When performing reaching movements towards a target, humans utilize sensory stimuli arising from the body and the environment. Manipulating proprioceptive cues (e.g., neck muscle vibration; Roll et al., 1991) and manipulating visual background cues (e.g., dots on the aiming board; Coello Magne, 2000) have both been independently shown to influence endpoint position during target aiming. The current study investigated the separate and combined contributions of neck proprioception and visual background cues on the control and performance of upper-limb pointing movements. Overall, posterior neck muscle vibration yielded closer movement endpoints and lower height during limb trajectories, while background information also yielded closer movement endpoints but with less mediolateral deviation during limb trajectories. Significant interactions between Vibration and Background were not found during limb trajectory analyses which may suggest that neck proprioception and visual background information are independently used across the separate phases of online control (Elliott et al., 2010).
From Hospital to Home: Providers’ Experiences of Collaboration when Facilitating Care Transitions across Palliative Care Settings
Keywords: collaboration
palliative care
patient discharge
qualitative research
transitional care

Research shows that many patients with advanced illness prefer to receive care and die in their homes; therefore, transitions from acute care to community settings are common. However, while many studies have examined the patient and caregiver experience of this transition process, few studies have focused on the provider’s perspective. This qualitative study explored interprofessional and interorganizational collaboration among providers when transitioning patients from hospital to home in the context of palliative care. Four themes were elucidated that reflect providers’ experiences of collaboration within and across palliative care settings. Key barriers include a perceived lack of formalized leadership roles and having continuously changing inpatient providers involved during discharge planning, inconsistent communication during patient handovers, and insufficient system-level infrastructure to support information sharing across settings. The findings of this study reveal several opportunities at the organizational and broader health system levels to better assist providers in supporting these types of transitions.
Comparison of the Epidemiology, Disease Characteristics, Treatment, Outcomes, and Late Effects of Osteosarcoma and Ewing Sarcoma in Adolescents and Young Adults, treated in Ontario Pediatric versus Adult Cancer Centres: An IMPACT Cohort Study
Keywords: Adolescent and young adult
Event-free survival
Ewing sarcoma
Locus of care
Osteosarcoma
Population-based cohort

Background: Location of cancer therapy (LOC) may impact outcomes in adolescents and young adults (AYA) with osteosarcoma or Ewing sarcoma. Objectives: To compare differences in demographics, disease/treatment characteristics, survival and late effects in a population-based cohort of AYA with bone tumours treated in pediatric versus adult centres. Methods: We used administrative health databases to identify Ontario AYA (15 - 21 years old) diagnosed with osteosarcoma or Ewing sarcoma between 1992 - 2012. We compared patients by LOC using appropriate statistical methods. Results: 137 patients were diagnosed with osteosarcoma (47 pediatric, 90 adult) and 84 with Ewing sarcoma (38 pediatric, 46 adult). Pediatric centres had higher clinical trial enrolment rates and cumulative chemotherapy doses. Five-year event-free and overall survival rates were 47% and 58% in osteosarcoma and 43% and 56% in Ewing sarcoma. LOC did not impact survival. Conclusion: Outcomes in osteosarcoma and Ewing sarcoma did not differ by LOC
Defects in Autophagy are Implicated in a Mecp2-mutant Mouse Model of Rett Syndrome
Keywords: Autophagy
MECP2
Mouse model
Rett syndrome

Rett syndrome (RTT) is a rare neuro-metabolic disorder, with most cases caused by de novo mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). Although several metabolic pathways have been implicated in RTT pathology, much of the underlying biology behind the disorder remains unknown. Interestingly, perturbations in the autophagy pathway, which has not been well studied in RTT, are consistent with many of the metabolic features of RTT pathogenesis. I found multiple lines of evidence for impaired autophagy in Mecp2-mutant mice, in vivo and in mouse embryonic fibroblasts. Systemically, autophagy is elevated prior to outward metabolic phenotypes, but is defective following aberrant lipid accumulation. Together, these results show that autophagy is abnormal in Mecp2-mutant mice and suggest that certain autophagic cargo are affected more than others. My findings highlight the similarities RTT has to other neurological and metabolic disorders with autophagic defects, providing exciting new insight.
The Cost-effectiveness of Early Physical Medicine Rehabilitation (PM) Consultation for Trauma Patients in a Level 1 Trauma Centre in Canada
Keywords: Cost-Effectiveness
Health Technology Assessment
Physiatry
Physical Medicine Rehabilitation
Trauma

BACKGROUND: Physical Medicine Rehabilitation (PM) consultation at Level 1 trauma centres improves clinical outcomes in major trauma patients. Cost-effectiveness evaluation of this intervention is lacking, but important for healthcare payers. PURPOSE: Assess incremental cost for providing PM consultation, per quality adjusted life year (QALY), from single public health payer perspective. METHODS: Probabilistic Markov model incorporating clinical trial data, administrative data and published literature to estimate incremental cost and effect over a life-time horizon. RESULTS: For major trauma sustained at age 18, incremental cost of providing PM consultation was $5,297. Incremental effect was 0.18 QALY. The incremental cost effectiveness ratio (ICER) was $29,428/QALY. Incremental effect increases with increased age, decreasing the ICER to $16,150/QALY for trauma sustained at age 75. CONCLUSIONS: PM consultation is associated with increased cost and increased QALY. Across all age groups, the ICER falls below a $50,000/QALY threshold, indicating PM consultation is likely a cost-effective intervention.