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Improvement in Dry Age-Related Macular Degeneration with Photobiomodulation
Get PDFIntroduction: This case report describes a finding of dramatic improvement in drusen volume and visual acuity in a 73-year-old patient diagnosed with dry age-related macular degeneration (AMD) undergoing daily home photobiomodulation alongside AREDS-2 supplements. Case Presentation: This is a retrospective review of a case presentation from 2023 to 2024. After 8 months of continuous home photobiomodulation, the patient’s visual acuity improved from 20/30 to 20/20 in the left eye while the right eye stabilized at 20/25. The outer retina was preserved without signs of geographic atrophy, with a robust reduction in the total number and volume of drusen in both eyes, left greater than right, as shown with optical coherence tomography macular cross-sectional scans. Conclusions: These findings support that photobiomodulation has the potential to improve the management of dry AMD and the overall quality of life, consistent with phase III clinical trials. Future studies are warranted to further establish optimized protocols for broader clinical implementation
The Effects of Sleep-Related Breathing Disorders on Heart Rate Variability and Cardiac Arrhythmias During Sleep in Individuals Living with Spinal Cord Injury
Get PDFSleep-related breathing disorders (SRBD) and cardiovascular dysfunction are common secondarymedical conditions that typically alter sympathetic activity after spinal cord injury (SCI). This
prospective cross-sectional study tested the clinically relevant hypothesis on whether moderate-
to-severe SRBD is associated with decreased heart rate variability (HRV) and increased cardiac
arrhythmias compared with mild/no SRBD in individuals with cervical/high-thoracic SCI. This
study included adults living with subacute/chronic, cervical/high thoracic (at T6 or more cranial)
SCI, who were not previously screened for SRBD. All participants underwent a continuous
electrocardiogram paired with an unattended sleep screening test that was used to quantify the
degree of SRBD. Overall, our results suggest that individuals with cervical/high-thoracic SCI who
develop moderate-to-severe SRBD have decreased nocturnal HRV along with reduced PNS
activity, but similar SNS activity regardless of degree of SRBD. This suggests a less adaptive
cardiovascular system in individuals living with SCI and moderate-to-severe SRBDs, implicating
a higher risk for cardiovascular adverse events/diseases.M.Sc
Computational Imaging for Extremely Large Telescopes
Get PDFWhile wavefront sensing and the use of adaptive optics has been an integral part of modern astronomical imaging, recent advances relating to deep-learning, end-to-end optical design, sensor fusion, and differentiable rendering have largely been overlooked. Instead of perceiving the telescope as a monolith, we approach it as a computational camera -- harnessing the deformable mirror of its adaptive optics (AO) system to augment or modify the incoming light as we see fit to both correct for atmospheric blurring and internal aberrations. We can then leverage telemetry and science data typically underutilized by even state-of-the art telescopes and their AO systems to increase sky coverage, image contrast, and science data resolution.
We present new methods for AO system alignment and calibration using continuous on-sky experimental data which can be matched to simulations using an order of magnitude less data. This method has been shown to work even on extremely noisy and misaligned data and used on-site at the 6.5-meter MMT observatory. These calibrations can substantially improve the on-sky scientific performance. We also show a novel method for predictive control of telescope AO systems both in simulation and experimentally. Our technique is based on a pioneering adversarial training method which maintains stability of the servo control loop, enabling telescopes to observe using up to two magnitudes fainter guide stars — opening up larger areas of the sky to natural guide star adaptive optics. Furthermore, we improve contrast for bright observations (such as those of exoplanets) by removing servo-lag from the control loop. Finally, we introduce an end-to-end method for sub-pixel super-resolution of science images by inducing small perturbations on the deformable mirror, achieving up to an 8x resolution improvement. These optimized perturbations can be tailored for any given telescope, allowing under-sampled telescopes to non-destructively extract otherwise discarded science data.
Most importantly, these methods are all designed with current telescopes in mind -- requiring no additional optical hardware or modifications. This expands the science capabilities and lifetime of existing telescopes while also providing direction for the design of future extremely large telescopes and their massive instruments while extracting maximum performance thanks to these computational techniques.Ph.D
Reconstructing the Evolutionary History of Cancer using Single-Cell Sequencing Data
Get PDFIntratumoural heterogeneity (ITH) and evolutionary forces are major factors in cancer development,treatment response and recurrence. To better understand these phenomena, evolutionary history
reconstruction methods have been created to construct cancer trees, graphical objects that indicate
mutation ordering, subclonal genotypes and subclone phylogeny. Existing methods typically suffer
from one of several drawbacks, such as performance drop off when constructing large cancer trees
or failing to report reconstruction uncertainty. To address this, I developed scPairtree, a novel
single cell-based reconstruction method capable of constructing large cancer trees complete with
uncertainty. It incorporates a mutation pairs relationship model with which it constructs a pairs
tensor, an object that stores estimated probability distributions of mutation pair relationships. The
pairs tensor guides a Markov chain Monte Carlo (MCMC)-based tree sampling algorithm such that
tree proposals move poorly placed nodes to more suitable locations. This results in the algorithm
converging on the tree posterior in fewer iterations than comparable MCMC-based methods. I
have also developed a novel tree sampling method by which trees are sampled directly from the
pairs tensor (DFPT), which are then used in importance sampling to infer properties of the tree
posterior. Trees from either method are used to construct a consensus graph, a graphical object
that captures the most likely cancer tree while visually representing uncertainty.
I also present my work constructing a cancer tree for a basal breast cancer in collaboration withDr. Elena Kuzmin. Of particular interest was mutation ordering with respect to chr4p loss, which
had been identified as recurrent in basal breast cancers. Data was derived from both bulk and low
coverage single-cell sequencing performed on samples from a single tumour. I manually constructed
a cancer tree by inferring the haplotype-specific copy number profiles for each single cell, clustering
these cells into subclones, generating pseudobulk data using the clustered single cell data, inferring
subclonal genotypes by performing set analysis on the point mutations called in each sequencing
experiment, and defining heuristics to infer the copy number profile of the most recent common
ancestor of the sampled cells. From the resulting clone tree we identified chr4p copy-neutral loss of
heterozygosity as an early event with additional copy number loss occurring subclonally.Ph.D
“As Many Saints as Stars”: Irish Peregrini in Continental Hagiography (8th-10th centuries)
Get PDFThis dissertation analyzes the representation of Irish saints in hagiographies written on the European continent between the eighth and tenth centuries. Its aim is to further the understanding of how non-Irish hagiographers conceptualized Irish peregrini pro Christo for their continental communities, which also adds to the larger discussion of how Irish influence was perceived on the early medieval continent. It is a close analysis of twenty-one saints’ Lives written about eighteen saints who were portrayed as making the ascetic and lifelong exile known as peregrinatio pro Christo to different communities in western Europe in the Carolingian and the immediate post-Carolingian periods.
In each chapter, I investigate specific traits used to promote the holiness of these saints, and I scrutinize whether any of those traits can be designated as uniquely “Irish”. By distinguishing what was characterized as “Irish” in certain saints’ Lives, this project historicizes how the continent understood the Irish, and, subsequently, how they viewed the influence of the Irish on the continent. Chapter One explains how the saints’ Irish origin was portrayed, and therefore how much the hagiographers knew about Ireland. Chapter Two outlines the patterns through which the hagiographers exemplified the peregrini pro Christo status of their saints, particularly the ascetic and almost otherworldly nature of such an exile. Chapter Three looks at how some saints were depicted as monachi and some as clerici, depending on what kind of community the saints created or integrated into on the continent and the audience for which the vita was written. Chapter Four surveys the scholarly attributes of the saints, considering that the Lives were written at the time when prestigious Irish scholars were living, working, and teaching in continental monastic centers. Chapter Five concerns the interactions and status each saint had with external authority figures beyond their communities: popes, bishops, nobles, and kings. Each continental hagiographer in this corpus developed a Life to exemplify an Irishman’s sanctity, and this analysis argues that there is significance to the patterns the writers used.Ph.D
The Thread in the Labyrinth: Entanglements of Legacy, Matter, and Meaning in End-of-Life Care
Get PDFThis dissertation explores the practices of legacy in end-of-life care through an ethnographic study of a community-based hospice in Toronto, Canada. Drawing on interviews with hospice clients, volunteers, staff, healthcare providers, and bereavement industry professionals, alongside observation, the study examines how legacy is made, experienced, and understood by those who are dying and those who care for them. The central research questions ask: What does legacy mean for people who are dying and their carers? How do hospice volunteers shape, and become shaped by, their participation in legacy activities? And how do these practices resist, reinforce, and revise dominant assumptions about death and dying? Guided by agential realism, this dissertation conceptualizes legacy not as a fixed representation of self to be preserved, but as a dynamic, emergent process shaped through intra-actions among people, objects, environments, and histories. Findings are organized through the metaphor of the labyrinth, offering a layered and processual account of how legacy emerges through intra-action, relation, and transformation. In “walking inward”, the analysis begins with an exploration of how legacy takes shape through intra-actions between people and things and the apparatuses through which legacy takes shape. At “the centre”, the focus turns to diffraction and agential cuts, examining how legacy is refracted through multiple perspectives and shaped by institutional and structural boundaries that determine who has access to legacy work and under what conditions. In “walking outward”, the analysis emphasizes entanglement and response-ability, showing how legacy continues through others, especially volunteers who carry forward the traces of those for whom they cared. Across these stages, legacy is revealed not as something fixed or stable, but as a relational phenomenon that emerges most vividly when the self recedes, allowing legacy to take on a life of its own. By reframing legacy in this way, the dissertation challenges representationalist and ego-centric models common in end-of-life care, offering more ethically responsive and materially attuned possibilities for practice and policy.Ph.D
Goodness-of-Fit Tests via Entropy-Based Density Estimation Techniques
Get PDFGoodness-of-fit testing remains a fundamental problem in statistical inference with broad practical importance. In this paper, we introduce two new goodness-of-fit tests grounded in entropy-based density estimation techniques. The first is a boundary-corrected empirical likelihood ratio test, which refines the classic approach by addressing bias near the support boundaries, though, in practice, it yields results very similar to the uncorrected version. The second is a novel test built on Correa’s local linear entropy estimator, leveraging quantile regression to improve density estimation accuracy. We establish the theoretical properties of both test statistics and demonstrate their practical effectiveness through extensive simulation studies and real-data applications. The results show that the proposed methods deliver strong power and flexibility in assessing model adequacy in a wide range of settings
Closing the Gap Between Design and Operation: A Mixed-Methods Post-Occupancy Evaluation of Passive House and EnerPHit Multi-Unit Residential Buildings in Cold-Climate Canada
Get PDFHigh-performance building standards, including Passive House and EnerPHit, aim to deliver substantial energy savings, yet discrepancies between modelled and operational outcomes lead to performance gaps. This thesis examines the energy performance gap through a mixed-methods post-occupancy evaluation of two multi-unit residential buildings (MURBs) in Hamilton, Ontario: Building A, an EnerPHit-certified deep retrofit, and Building B, a newly constructed Passive House certified building. One year of utility and sub-metered data was compared with Passive House Planning Package (PHPP) predictions under standard (for both Buildings A & B) and Canadian-adjusted assumptions (for Building A only). At the whole-building scale, Building A consumed 86% more total primary energy than predicted under Canadian conditions, with ventilation systems operating at twice their design airflow and significant additional loads in non-metered categories, while the space conditioning and DHW performance aligned with the PHPP model. Total Building B consumption was similar to the total PHPP energy use but recorded space conditioning demand was 158% above modelled values, driven by elevated cooling loads linked to occupant behavior and control sequences, while DHW performance was overestimated in PHPP model by 33%. System-level analysis revealed unmonitored loads, labelled as “Other”, and ventilation are the dominant contributors to performance gap in Building A, while in Building B, space conditioning is the major contributor. Semi-structured interviews with designers, contractors, and operators identified recurring drivers of these gaps, including commissioning limitations, operational constraints, and design challenges, and highlighted the importance of integrating operational realities into early design, maintaining rigorous quality control, and supporting adaptive building management strategies post-occupancy. The findings provide evidence and practical directions for improving alignment between design intent and measured performance in cold-climate Canadian MURBs.M.A.S
Patient Reported Pain Burden after Diagnosis of Gastrointestinal Cancer: Identifying Factors Associated with Symptom Screening and Moderate-to-Severe Pain Outcomes
Get PDFGastrointestinal (GI) cancers impose a significant burden on patients. Pain, as one of the most common and distressing symptoms, remains inadequately managed despite advances in cancer care. Patient reported outcome measures have emerged as powerful tools in eliciting patient’s experiences and managing symptom burden. A retrospective analysis of patients diagnosed with GI cancers between 2011-2019 and registered at an Ontario Regional Cancer Center was conducted to 1) identify factors associated with receiving symptom screening at diagnosis (T0) and in follow-up (T1) and 2) examine factors associated with reporting moderate-to-severe pain in follow up.
Among 84,867 patients, only 8.6% received symptom screening at both diagnosis and follow-up and baseline pain scores at diagnosis was the most significant factor associated with the odds of experiencing moderate-to-severe pain in follow-up. This thesis identifies key areas for improvement in current symptom screening practices, while advocating for the importance of timely assessment and proactive symptom management.M.Sc
Verification, Validation and Payload Identification of a Hardware-in-the-loop Simulation Platform for In-orbit Systems
Get PDFThis thesis discusses the development of a hardware-in-the-loop simulation platform for emulating the contact of rigid bodies in orbit, such as an active debris removal mission of a Deorbiter CubeSat in low Earth orbit. The hardware-in-the-loop simulation platform, called the Mission Analysis Robotic Kit II (MARK-II), is located in Brampton at MDA Space’s Dynamic Robotic Emulation and Mixed Reality laboratory and features a custom serial manipulator that is equipped with a Force-Moment-Sensor (FMS) to emulate the contact dynamics of free-floating bodies. The motion of the Deorbiter CubeSat is simulated in MARK-II software, and the force or moment measured by the FMS accelerates the simulated CubeSat according to the programmed inertia. The tip of MARK-II carries a CubeSat attachment mechanism payload that emulates CubeSat motion and reacts to contact as if it were an in-orbit inertial body. MARK-II is verified and validated according to the testing needs of the Deorbiter CubeSat, which indicate that the MARK-II FMS does not accurately measure the contact force and moment required for testing the Deorbiter CubeSat due to sensor noise, gravity, and payload dynamics. To address this, the FMS is replaced with a more accurate FMS model and two algorithms are proposed to estimate the mass, centre-of-mass position, and moment of inertia tensor of the payload. The first algorithm uses joint telemetry data to estimate payload parameters. The second algorithm uses the FMS and an Inertial Measurement Unit (IMU) attached to the payload to calculate the payload parameters, which is more accurate for estimating payload parameters according to experimental results. The payload mass and inertia parameters are utilised in a Kalman filter that fuses sensor data from the FMS and the IMU to filter out payload gravity and dynamics and accurately measure the contact wrench on the payload. Experimental results show that the proposed Kalman filter successfully filters out sensor noise and the weight and dynamics of the payload while preserving accurate measurement of the contact force and torque.M.A.S