VictorJuiz/thesis huggingface dataset:
Selective Peripheral Nerve Recording Using Simulated Human Median Nerve Activity and Convolutional Neural Networks

It is difficult to create intuitive methods of controlling prosthetic limbs, often resulting in abandonment. Peripheral nerve interface signals can be used to convert motor intent into usable commands. Extraneural Spatiotemporal Compound Action Potentials Extraction (ESCAPE) is a deep learning-based framework that was demonstrated to be effective at discriminating neural sources in animal models. For clinical application, ESCAPE needs to be validated in humans. Using cross-sectional immunohistochemistry images of a human median nerve, a finite element model was generated and used to simulate extraneural recordings. ESCAPE was used to classify naturally-evoked compound action potential (nCAPs) based on source location. Classification accuracy was found to be inversely related to the number of nCAP sources: (3- class: 0.96 +/- 0.03; 10-class: 0.89 +/- 0.07 in low-noise conditions). The performance observed compared favorably to results in animal models. These results demonstrate the promise of ESCAPE for use in human nerves in vivo.

Keywords: convolutional neural network
human
peripheral nerve
selective recording
simulation
spatiotemporal
Advisor: Zariffa, Jose
Safe Motion Planning of Quadrotor Swarms in Cluttered and Complex Environments

This thesis addresses the problem of safe motion planning of quadrotor swarms in cluttered and complex environments. Part one introduces a linearization-free trajectory optimization approach that allows a quadrotor to compute collision-free trajectories to avoid ellipsoidal static and dynamic obstacles (other quadrotors). Using a polar reformulation and an alternating minimization algorithm, we can significantly reduce the conservatism in the swarm behaviour and improve the success rate and per-agent computation time compared to sequential convex programming baselines. In the second part, we extend the approach to enable navigation in complex environments by developing a static obstacle avoidance model that uses Octomap distance queries. Compared to safe flight corridor construction approaches, which decompose the obstacle-free space as convex sets, our approach provides an implicit non-convex decomposition of obstacle-free space, thereby improving the success rate and mission completion time. The proposed approaches are verified through extensive simulation tests and challenging experiments.

Keywords: Collision Avoidance
Motion and Path Planning
Multi-robot motion planning
Navigation in Complex Environments
Quadrotor Swarms
Trajectory Optimization
Advisor: Schoellig, Angela
A4S: Co-designing Scaling and Placement in Stream Processing Systems with Memory-parallelism Curves

A significant challenge in stream processing systems is adapting to workload changes while maintaining throughput and end-to-end latency requirements. Traditional auto-scaling solutions perform CPU scaling by adjusting operator parallelism, which works well for stateless operators. However, these solutions perform poorly for stateful operators because they do not consider the impact of operator memory size and IO operations. Another challenge in existing solutions is that operator scaling and task placement are performed independently, which leads to sub-optimal resource allocation.This thesis presents A4S, a co-designed scaling and placement strategy for stream processing systems that works well for both stateless and stateful operators. The key insight in A4S is that, for achieving a certain throughput, the memory and parallelism requirements of stateful operators are correlated. This insight allows trading memory and parallelism, leading to better scaling and placement. We formalize this correlation with a memory-parallelism curve, which shows the minimum operator memory size needed for a given level of parallelism to achieve a target throughput. These curves provide a set of parallelism choices for operator scaling. Then, task placement chooses a level of operator parallelism and memory size that ensures a target throughput, acceptable end-to-end latency and efficient resource utilization. We show that memory-parallelism curves can be derived from the miss-rate curves of stateful operators. For effective scaling, we need a miss-rate curve estimate of the current workload pattern. Thus, we propose an online method for generating miss-rate curves that has low overhead and provides reasonable accuracy. We have implemented A4S in the Risingwave streaming database. Our evaluation shows that A4S provides more accurate scaling and resource-efficient placement compared to state-of-the-art solutions.

Keywords: Scheduling
Streaming Processing
Advisor: Goel, Ashvin
Thermal Control System Design of Two Microsatellite Missions with Optical Payloads

Smaller satellites are gaining popularity due to their affordability, lightweight design, and faster development time. The development of a satellite requires the consideration of various subsystems, with the thermal control subsystem responsible for regulating the temperature of all spacecraft components. This thesis presents the thermal control system design for two microsatellite missions, one for maritime monitoring and the other to study the circumgalactic medium of nearby galaxies. Both missions included an optical payload, which posed challenges for the spacecraft's thermal design due to the need for strict temperature control to prevent distortions in the optics. Each thermal control system was developed by constructing a thermal model and analyzing multiple scenarios that considered worst-case environmental conditions, spacecraft attitudes and power dissipation. The design was then iterated until all the requirements were met. The results show that a thermal control design is achievable for both missions, primarily using passive thermal control techniques with some active methods.

Keywords: analysis
control
spacecraft
thermal
Advisor: Zee, Robert E
Structural and Functional Characterization of the CRL3/KCTD5 Ubiquitin E3 Ligase Complex with Gβγ

The ubiquitin-proteasome system controls a wide range of normal and pathological processes. In this system, the covalent attachment of ubiquitin to a target substrate protein is mediated by a cascade of three enzymes including a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). In most cases, E3 ligase complexes determine substrate specificity. The multi-subunit Cullin-RING ligases (CRLs) comprise the largest family of E3s in which a cullin protein serves as a central assembling scaffold to bridge substrates to E2 enzymes for ubiquitin transfer. In CRL3 complexes, the C-terminal domain of Cullin3 associates with the RING-finger protein (Rbx1) to recruit the E2, while its N-terminal domain interacts with BTB domain-containing substrate receptor proteins. KCTD5 is a homo-pentameric BTB domain protein that acts as a substrate receptor in Cullin3-associated E3 ligase complexes. Gβγ subunits have recently been identified to be associated with KCTD5. Here, we present the characterization of CRL3/KCTD5 ubiquitin E3 ligase complex required for Gβγ ubiquitination. We report the cryo-electron microscopy structure of a 5:5:5 assembly composed of KCTD5, Cullin3NTD and Gβγ. We also use structure-guided mutagenesis to probe the workings of the complex. Our findings show how a CRL3/KCTD5 complex targets Gβγ proteins for ubiquitination and advance our understanding of how Gβγ complexes are regulated by this post-translational modification.

Keywords: BTB
E3 ligase
Gβγ
KCTD5
Ubiquitination
Advisor: Privé, Gilbert G
Exploring the Role of Leiomodin-1 and Tau in Nodding Syndrome

Nodding syndrome (NS) is a neurological disease associated with tau pathology affecting children in rural communities in Eastern sub-Saharan Africa. One study suggests that infection with the nematode parasite Onchocerca volvulus triggers an autoimmune attack against the human protein leiomodin-1. We tested this hypothesis by studying the distribution of leiomodin-1 in the normal human brain and other human tissues using immunohistochemistry. Our study showed that leiomodin-1 is mostly expressed in cerebral blood vessels, rather than neurons or glia. Our results also could suggest the possibility of leiomodin-1 antibody cross-reactivity between human Purkinje cell membranes and the body wall of C. elegans; a finding explained by the homology between leiomodin-1 and tropomodulin. These data do not support the hypothesis of autoimmunity involving Onchocerca volvulus and leiomodin-1. The present study also established clinicopathologic correlation on six cases of NS with marked tau pathology through both qualitative and quantitative methods of analyses.

Keywords: Epilepsy
Leiomodin-1
Neurodegeneration
Nodding Syndrome
Onchocerciasis
Tau Pathology
Advisor: Pollanen, Michael MSP
The Role of Schema Charge and Permeability in Cognitive Models of Schizophrenia Spectrum Disorders

Cognitive models of psychopathology, including psychosis, highlight key cognitive mechanisms in the development and maintenance of symptoms, including maladaptive cognitive schema and cognitive biases. The current study investigated whether schema charge and schema permeability differ between individuals with schizophrenia-spectrum disorders (SSDs) and healthy controls. Seventeen individuals with SSDs and 16 controls engaged in both an exclusion and inclusion version of Cyberball. Following Cyberball exclusion, one of the computerized players apologized and provided an explanation for the exclusion before including the participant in the inclusion task. Individuals with SSDs endorsed stronger negative schemas and cognitive biases than controls; however, there were no significant interactions with Cyberball conditions. The bias against disconfirmatory evidence significantly mediated the relationship between schema charge and permeability. Though we found mixed results, overall, results support the cognitive theory that negative cognitive schemas are more activated in individuals with SSDs, and they have important relationships with cognitive biases.

Keywords: Cognitive Biases
Cognitive Models of Psychosis
Cognitive Schemas
Psychosis
Schizophrenia
Advisor: Best, Michael W
Automated Hand Function Assessment from Egocentric Video after Spinal Cord Injury

Background and Objective: Hand function assessments in a clinical setting are critical for upper limb rehabilitation after spinal cord injury (SCI) but are unable to accurately reflect performance in an individual’s home environment. When paired with computer vision models, egocentric videos from wearable cameras provide an opportunity for remote hand function assessment. This study presents a novel computer vision model for predicting clinical hand function assessment scores from egocentric video. Methods: SlowFast, MViT, and MaskFeat models were trained and validated on a custom SCI dataset, which was annotated with clinical hand function assessment scores. Results: An accuracy of 0.551±0.139 and F1 score of 0.547±0.151 was achieved on the 5-class classification task. An accuracy of 0.724±0.135 and F1 score of 0.733±0.144 was achieved on a consolidated 3-class classification task. Conclusion: This novel algorithm, for the first time, demonstrates that automatically evaluating the quality of hand function from egocentric video is feasible.

Keywords: Computer vision
Hand function
Rehabilitation
Spinal cord injury
Advisor: Zariffa, Jose
Cannabis Self-Administration in the Human Laboratory: A Scoping Review of Ad Libitum Studies

Cannabis self-administration studies may be helpful for identifying factors that influence cannabis consumption and subjective response to cannabis. Additionally, these paradigms could be useful for testing novel pharmacotherapies for cannabis use disorder. This scoping review aims to summarize the findings from existing ad libitum cannabis self-administration studies to determine what has been learned from these studies as well as their limitations. We reviewed cannabis smoking studies, focusing on subjective response and self-administration behavior (e.g., smoking topography). A systematic search was conducted using PubMed and Embase from inception to October 22, 2022. Our search strategy identified 26 studies (Total N = 662, 79% male) that met our eligibility criteria. We found that tetrahydrocannabinol (THC) concentration significantly affected subjective response to cannabis in some but not all studies. In general, cannabis self-administration tended to be most intense at the beginning of the session and decreased in later parts of the session. There were limited data on cannabis self-administration in adults older than 55. Data on external validity and test-retest reliability were also limited. Addressing these limitations in future ad libitum cannabis self-administration studies could lead to more valid and generalizable paradigms, which in turn could be used to improve our understanding of cannabis use patterns and to help guide medication development for cannabis use disorder.

Keywords: ad-libitum
cannabis
human laboratory paradigms
scoping review
self-administration
Advisor: Sloan, Matthew
Telling the History of Female Sexuality in Greco-Roman Exhibitions by Synthesizing Curatorial Dreaming and Critical Fabulation

This thesis will critically engage with the absence of female sexuality within Greco-Roman history exhibitions. Throughout this study, a methodological axiom will synthesize Shelly Ruth Butler and Erica Lehrer’s methodology of "curatorial dreaming" with Saidiya Hartman's "critical fabulation" to provide an example of how museums can adopt alternative techniques of displaying underrepresented histories to tell impossible stories from the past. By ushering in a way to explore the history of women's sexuality in Greco-Roman antiquity, this thesis will highlight how museums can engage with the societal perceptions of female eroticism in the past so that it may become better understood in the present. Therefore, this thesis will develop Hartman's method of critical fabulation in a theoretical museum context to demonstrate its use of expanding the contemporary understanding of available historical evidence by fabulating the history of sexuality within Greco-Roman exhibitions to encompass a greater female perspective.

Keywords: Classical Studies
Critical Fabulation
Curatorial Dreaming
Gender and Sexuality
Museum Studies
Women's Studies
Advisor: Keilty, Patrick
Mihalache, Irina D.
Exploring the Utilization of a Wellness Framework for Children and Young People with Intellectual and Developmental Disabilities within Adaptive Sports Programs

Introduction: Children and young people with Intellectual and Developmental Disabilities (IDD) have unique abilities and challenges that affect their health and wellness. Adaptive sports programs offer important opportunities to support their wellness. Objective: To explore the integration of a Wellness Framework into adaptive sports programs tailored for children and young people with IDD. Methods: 1) A rapid scoping review using Wellness Framework principles to provide a summary of sports coaching strategies to support the wellness of children and young people with IDD in a sports setting. 2) An explanatory sequential mixed-method study using non-participant observation to describe if and how the Wellness Framework principles were integrated into real-world adaptive sports programs run by Special Olympics. Results: The Wellness Framework was both supported in the literature and real-world sports programs and has been demonstrated to be a useful tool to help children and young people with IDD live their most meaningful lives. The summarized list of strategies to support the wellness of children and young people with IDD may be helpful for supporting their overall wellness if implemented by sports staff. Discussion: Sports coaches and health promotion staff have opportunities to purposefully integrate the strategies identified through both the scoping review and observational study to support the wellness of children and young people with IDD.

Keywords: Adaptive
Coach
Intellectual or developmental disabilities
Sports
Well-being
Wellness
Advisor: McPherson, Amy C
The Creation of a New Payload Operations Planning Software for Complex Small Spacecraft Mission Operations

As small spacecraft become more capable, so too does the complexity of their operations. Searching for potential concurrent observation or access opportunities and ensuring they are compatible with one another may become tedious and repetitive for operators to manually compute. Currently available commercial-off-the-shelf tools that automate this process are capable but expensive. To address this problem, a new payload operations planning tool has been developed by the Space Flight Laboratory to handle the deterministic aspects of mission planning, such as: detecting observation opportunities, validating observations in a schedule, and generating lists of commands to be sent to satellites. This lightweight tool is generalizable to any Earth-observing mission configuration, and can support complicated observation geometries. Opensource libraries were used to reduce the overhead for development as they decrease the amount of code that must be newly created and maintained. Functionality has been compartmentalized through a containerized service-based architecture. In this way, new functionality can be added or replaced as needed. To enhance usability, a user may interact with the tool through a browser-based user interface. This thesis outlines the features of the Payload Operations Planning Software, as well as details about its architecture and development.

Keywords: Aerospace
Operations
Planning
Software
Advisor: Zee, Robert E
The Role of Omega-3 Polyunsaturated Fatty Acids in Adipose Tissue Inflammation: a Longitudinal Analysis in the PROMISE Cohort

The role of adipose tissue (AT) as the initiating organ of the sub-clinical inflammation phenotype characterizing obesity-associated chronic disease is being actively investigated. Pre-clinical evidence suggests that n-3 PUFAs modulate AT inflammation, although human data are limited and inconclusive. This thesis aimed to (1) map existing literature on n-3 PUFAs and AT inflammation in healthy humans in a scoping review; and (2) investigate longitudinal associations of circulating levels and dietary intake of n-3 PUFAs with AT-specific biomarkers using data from a cohort study of Canadian adults at high risk for type 2 diabetes. The scoping review documented inconsistent findings in published studies (n=25), as well as considerable heterogeneity in important methodological features. Cohort analysis indicated significant inverse associations of circulating n-3 PUFAs, more specifically EPA, DPA, and DHA, with AT-specific biomarkers. Collectively, these results suggest n-3 PUFAs may have a beneficial effect on modulating AT inflammation in humans, although additional well-designed studies are needed.

Keywords: Adipose Tissue Inflammation
Epidemiology
Fatty Acids
Obesity
Observational
Omega-3
Advisor: Hanley, Anthony AJH
Mixedness in Motion: Challenging Contemporary Narratives of Mixed-Raciality and Physical Movement through Aesthetic Mixedness

Although often celebrated as a sign of a post-racial society, Mixed-race identities are incompatible with the racial categories constructed by Whiteness and coloniality/modernity, regardless of how these are reconfigured within our current society. Race as a social construct is inseparable from the body and thus movement; therefore, a relational and interdisciplinary analysis is required. Entering the gap in research on Mixedness and physical movement in Canada, this study deployed focus group interviews and arts-based creation workshops with eight (8) Mixed-race participants to explore racial identity and physical movement. Findings revealed insights into how to reconceptualize what it means to be Mixed-race beyond colonial/modern and neoliberal constructions and explore negativity and paradox to reveal new possibilities for Mixedness and physical movement.

Keywords: Aesthetics
Mixed-Race
Mixedness
Physical Cultural Studies
Physical Movement
Research-creation
Advisor: Joseph, Janelle
The Relationship between Dispositional Mindfulness and Psychological, Cognitive, and Functional Outcomes following Mild Traumatic Brain Injury

Most individuals who sustain a mild uncomplicated Traumatic Brain Injury (mTBI) recover within 1-3 months. However, a significant proportion consistently report ongoing cognitive, psychological, and somatic sequelae, which can be functionally disabling and hinder active participation in society. This study examined dispositional mindfulness as a targetable protective factor as it pertains to psychological, cognitive, and functional outcomes in the post-acute stage. 45 litigating individuals with persistent symptoms in the post-acute stage following mTBI completed a neuropsychological assessment, including current and retrospective, pre-injury ratings of the Five-Facet Mindfulness Questionnaire. Mindfulness was significantly associated with depression and anxiety but not with attention or working memory. Lower mindfulness was observed in individuals who had returned to work compared to those who had not. Pre-injury mindfulness significantly predicted scores on the Psychiatric Impairment Rating Scale, with higher Observing scores predicting worse functioning. Future research employing experimental and longitudinal designs can further elucidate these relationships.

Keywords: cognition
dispositional mindfulness
functional disability
mindfulness
return to work
traumatic brain injury
Advisor: Zakzanis, Konstantine K
Segal, Zindel V
Biomimetic Optogenetic Stimulation of Ventral Tegmental Area GABAergic Projections to the Tegmental Pedunculopontine Nucleus is Sufficient to Elicit Artificial Naïve Opiate Reward

Morphine injections into the Ventral Tegmental Area (VTA) produce reward behaviour. Lesions of the Tegmental Pedunculopontine Nucleus (TPP) block these rewarding effects in formerly drug-naïve animals. We hypothesize TPP-projecting VTA GABA neuron circuits produce morphine reward in previously opiate-naïve animals. We employed optogenetics to activate TPP-projecting VTA GABAergic neurons in real-time place preference (RTPP) paradigms. GAD65-cre mice expressing a high fidelity channelrhodopsin in the axon terminals or cell bodies of TPP-projecting VTA GABA neurons received biomimetic laser stimulation that replicated the action potentials of a VTA GABA neuron firing trace recorded from a mouse acutely injected with morphine. Stimulation of the cell bodies or axons of this TPP-projecting VTA GABA population (and not other projection populations) led to reward responses, even during dopamine antagonism. This work indicates dopamine-independent direct projections from VTA GABA neurons to the TPP may underlie the rewarding effects of morphine in previously naïve mice.

Keywords: Behaviour
Biomimetic
Opioids
Optogenetics
Pedunculopontine nucleus
Ventral tegmental area
Advisor: van der Kooy, Derek
The Influence of Shelter on the Establishment of the Invasive Dandelion, Taraxacum officinale, at its Northern Range Limit

Invasive species represent a threat to many ecosystems but are nearly absent from arctic and subarctic Canada. The subarctic town of Churchill, Manitoba, has an unusually high number of invasive species due to the presence of a grain port and railway, but few of these species have spread to the surrounding tundra. I am attempting to understand why one of these species, common dandelion (Taraxacum officinale), currently is restricted to town, focusing on the tendency of buildings to provide shelter and, thus, allowing it to persist. I surveyed the distribution of T. officinale and a native congener, T. lacerum, relative to existing structures. My results show that T. officinale's distribution is influenced by the availability of human-created microclimate more than that of T. lacerum. These results suggest T. officinale may spread beyond these refuges as the climate continues to warm.

Keywords: Climate Change
Dandelion
Plant invasion
Shelter
Subarctic
Taraxacum
Advisor: Kotanen, Peter M.