VictorJuiz/thesis huggingface dataset:
Optimizing Repetitive Transcranial Magnetic Stimulation for Major Depressive Disorder

Repetitive transcranial magnetic stimulation (rTMS) is a well-established and effective intervention in MDD, with an advantageous side-effect profile over medication. Unfortunately, widespread adoption of rTMS has been impeded by several obstacles limiting clinical accessibility, including high costs of acquisition and operation, technical challenges because of the current complexity of the procedure, and the lack of validated and scalable biomarkers to help predict treatment outcome. To address these issues, we explored novel rTMS delivery methods, including parabolic coils with broad stimulation areas allowing easy targeting, safe and well-tolerated low-frequency 1 Hz stimulation delivered on the most affordable FDA-approved rTMS devices, an open-room setting allowing a single technician to attend to multiple patients, custom-made equipment reducing costs, and performed schedule optimization using treatment acceleration. We subsequently attempted to maximize effects by optimizing stimulation parameters. Lastly, we researched heart rate variability (HRV) as a potential biomarker to predict treatment outcomes. Our initial chart review studies helped us determine that the use of parabolic coils combined with 1 Hz rTMS was safe and well-tolerated in the treatment of MDD. Our second study showed that accelerated 1 Hz rTMS with parabolic coils was also safe, well-tolerated. We also showed that an open-room setting was feasible and that our custom-made rTMS equipment was reliable. Given the limited clinical effects observed in those studies, we researched an even more intensive accelerated 1 Hz rTMS protocol in our third study and found evidence of increased effectiveness. Lastly, we did not observe any significant association between baseline pre-treatment resting-state HRV and clinical outcomes. In the final part of this thesis, we summarize our findings and discuss their implications for the treatment of MDD. We conclude by discuss the various limitations inherent to this preliminary work and potential future directions. Given its established efficacy in MDD and its lower side-effect profile compared to medication, efforts should be made to make rTMS more accessible. Our work proposes several ways to improve rTMS by simplifying procedures to reduce costs and therefore potentially increasing accessibility at the community level, increase clinical effects and help with patient selection.

Keywords: Brain stimulation
Neuromodulation
Neurostimulation
rTMS
TMS
Transcranial Magnetic Stimulation
Advisor: Blumberger, Daniel
Unlocking Dynamic Cameras for Visual Navigation

The ability of a mobile robot to navigate reliably in an unknown environment depends on the information perceived from its surroundings, usually available in the form of measurements from sensors. However, most of the current sensor configurations assume a static rigid transformation between the sensors, placing many limitations on its performance, especially when undergoing high dynamic motion profiles. A Dynamic Camera consists of a camera mounted to an actuated mechanism such as a gimbal and offers several advantages compared to the static case. However, In order to accurately relate information across these cameras and other sensors, a precise time-varying extrinsic calibration needs to be determined. In this dissertation, I present novel methods to calibrate a Dynamic Camera to other sensors such as static cameras and IMUs. First, I analyze a Dynamic Camera Cluster system, and present an information theoretic Next-Best-View formulation that directly minimizes the uncertainty on the calibration parameters and test the resulting calibration in a visual-inertial odometry application. Second, I present a novel analysis of the redundant parameters in the calibration system when joint angle values to the actuated mechanism are unavailable and propose a novel minimal parameterization to resolve the degeneracies. Third, I present the online calibration between a Dynamic Camera and an IMU, and analyze the observability properties of the calibration parameters. I perform extensive tests in simulation and in the real world, consisting of a 3-DOF gimbal and a 5-DOF manipulator, demonstrating our ability to recover an accurate calibration, thereby allowing Dynamic Cameras to be used in visual navigation applications.

Keywords: Calibration
Drones
Dynamic Cameras
Gimbal cameras
State Estimation
Visual SLAM
Advisor: Waslander, Steven L
Point-of-care Detection Platforms for Metabolic Biomarker and Infectious Disease

The metabolic and protein biomarkers are the most significant detection targets for the point-of-care disease diagnosis and healthcare. The chronic diseases are among the world’s leading causes of mortality, and the COVID-19 pandemic is continuously burdening the global health, especially impacting the low-income, resource-limited regions. Accurate point-of-care detection of biomarkers is an important monitoring strategy for chronic disease development. Early detection of infectious disease outbreaks can reduce the ultimate size of the outbreak and the overall morbidity and mortality due to the disease, in which diagnosis plays an important role. As available diagnostic technologies require well-trained personnel, expensive equipment and complex assay procedure and consume a large amount of time in medical laboratories, there is an urgent need for low-cost portable platforms that can provide fast, accurate, and ideally multiplexed diagnosis of infectious diseases at the point of care. This thesis reports on the design, fabrication, and demonstration of electrochemical point-of-care detection systems for metabolic and protein biomarkers. Rapid results have been achieved by employing electrochemical enzymatic reactions on devices with simple fabrication and preparation. The systems have demonstrated high sensitivity and specificity comparable to state-of-the-art laboratory tests. The works reported in this thesis show strong potential to lead to portable systems for point-of-care diagnosis.

Keywords: COVID-19
Electrochemical biosensing
Flexible electronics
Point-of-care diagnosis
Advisor: Liu, Xinyu
How Gospel Pianists Learn Black Gospel Music: Developing Gospel Music Education in Postsecondary Institutions Beyond Choral Music

The purpose of this study was to create a foundation for the inclusion of gospel piano instruction in the curriculum of postsecondary institutions. Critical Race Theory (Bell, 1987, 1995; Dumas, 2013, 2016; Ladson-Billings, 1998; Yosso, 2005) was used as a theoretical underpinning to interrogate the existence of anti-Black racism in music education and the ways in which Black music, history, culture and voices have been historically silenced in music curriculum. Narrative Inquiry (Clandinin, 2020; Connelly & Clandinin, 1990; Creswell & Guetterman, 2019; Downey & Clandinin, 2020) was used to explore the lived experiences and perspectives of eight professional Black gospel pianists. In conjunction, autoethnography (Davis & Ellis, 2010; Reed-Danahay, 1997) was used to explore the lived experience and perspective of the researcher while engaging in private gospel piano lessons. The study was guided by the question, ‘How can the traditions and practices of learning to play piano in the Black gospel style be used to enrich the curriculum of music in postsecondary institutions?’ The data was gathered through semi-structured interviews and autoethnography experience tracking forms. Findings revealed five broad themes suggesting how postsecondary music institutions can be enriched by including gospel piano in the curriculum: (1) Developing Aural Musicianship and Improvisational Skills; (2) Developing Well-Rounded Musicians; (3) Embracing Diversity; (4) Developing Community Partnerships; and (5) Expanding Gospel Music Programs. These findings provide valuable insights into the practices of learning Black gospel piano and may be used to inform the inclusion of gospel piano in the curriculum of postsecondary music institutions. This integration into the postsecondary curriculum may expand existing gospel music programs or introduce new gospel music courses with the purpose of diversifying music curricula and dismantling anti-Black racism in music education.

Keywords: anti-Black racism
aural musicianship skills
critical race theory
gospel piano pedagogy
narratives of learning gospel piano
university gospel music curriculum
Advisor: Dolloff, Lori-Anne
A Temporal Study of Palestinian Cinema

This dissertation discusses how time is reckoned with and represented in Palestinian cinema through a thematic and formal analysis of select Palestinian films. I argue that a defining feature of Palestinian cinema is its preoccupation with understanding, both in the context of Palestine as well as on a universal scale. These films utilise singular qualities of the cinematic medium to reflect on Palestinian history, depict the experience of the present moment, and speculate about the future. In each chapter I engage with the representations of the past, the present, and the future respectively, while also problematising any assumption that temporal vectors can be understood conclusively and in isolation. I show that while Palestinian cinema is deeply and unavoidably concerned with the experience of historical trauma, its films attempt to make sense of how history and its experience are narrativized and rendered coherent in spite of unavoidable ambiguities. This can be detected in the formal qualities of the films I discuss by way of a focus on media and the creation of historical records. I demonstrate how the films are shaped formally and thematically by the conditions of occupation and the regimentation of time and space, or, in other words, how their depictions of temporal and spatial experiences directly emerge from the conditions of life in Palestine. While the spatial consequences of occupation, symbolised by images of the Separation Wall as well as checkpoints, tend to be the focus of most analyses, I show that it is not only space but also time that is divided, and attentiveness to time and temporality is equally essential and rewarding. Working my way towards the future in a nonlinear manner, I conclude the project by showing how Palestinian cinema anticipates and speculates about the future, particularly how it acknowledges uncertainty and contends with utopian impulses through the concept of Sumud/steadfastness while also imagining Palestine beyond the present moment’s political impasse

Advisor: Fenner, Angelica
The Utility of Second-Tier Genomic Sequencing for Hereditary Cancer Syndromes: A Mixed-Methods Study

Background: Identification of patients with hereditary cancer syndromes (HCS) is important to detect high-risk patients who become eligible for surveillance and preventive surgeries that reduce cancer risk or detect it earlier, reducing morbidity and mortality. Standard panels only identify 10-20% of HCS patients. Genomic sequencing (GS) may identify more high-risk patients; however, evidence demonstrating utility of GS in HCS is lacking. Methods: This mixed-methods thesis aimed to explore the utility of second-tier GS for HCS. The first study explored clinician-reported utility of GS for HCS and other indications through a qualitative study using semi-structured interviews with Canadian clinicians with GS experience. Transcripts were thematically analyzed using constant comparison. The second study evaluated clinical utility of second-tier GS for HCS through chart review and survey conducted for cancer patients undergoing GS in an RCT. Charts were reviewed to extract diagnostic yield and management changes data. The final study explored patient-reported utility of cancer GS results by conducting a qualitative study using semi-structured interviews with patients who received second-tier GS as part of the aforementioned RCT. Transcripts were analyzed using constant comparison, similar to aim 1. Finally, a narrative approach was used to integrate quantitative and qualitative data. Results: All three studies suggest that GS provides limited utility above standard panels in HCS patients. The first qualitative study found that cancer clinicians attributed minimal utility from second-tier GS, who emphasized that the additional low/moderate penetrance results identified would not change management. The second study revealed that second-tier GS identified pathogenic results in 10% of patients, most in low/moderate penetrance genes with minimal actionability and at the cost of a high VUS rate of 90%. Findings from the third study indicated that patients centered their perceptions of utility of GS results on whether they changed management. Consequently, patients without management changes perceived anxiety and became hypervigilant, experiencing harms. Conclusions: As a second-tier test, GS provided limited utility for cancer patients and may be triggering harms. Our findings call for practice interventions to support patients receiving uninformative results from cancer genetic testing and for research to establish the utility of first-tier GS in HCS.

Keywords: Clinical utility
Genome sequencing
Health services research
Health technology assessment
Hereditary cancers
Mixed-methods research
Advisor: Bombard, Yvonne
Laupacis, Andreas
Yoga in the Mokṣopāya

This thesis aims to elucidate the Yoga of the Mokṣopāya, a philosophical story-text from tenth century Kashmir in which the sage Vasistha imparts teachings to the young Lord Rama on the illusory nature of the world and the path to liberation. In the Mokṣopāya we find a unique nondual idealist philosophy that teaches that the entire world is a dream of the cosmic mind—nothing is fundamentally real—and professes to convey the ultimate truth of all established philosophies while adhering to none in particular. The Mokṣopāya is most popularly known in its later recension as the Yogavāsiṣṭha—a well-known and important text of nondual Vedānta which has been transmitted, translated, and commented upon over the centuries––however, the Yogavāsiṣṭha has significant textual corruption which took place during the transmission of the Mokṣopāya sometime after it was composed. This dissertation draws upon the work of the Mokṣopāya project and the nearly complete critical edition of the Mokṣopāya which presents scholars with a unique opportunity to study this unknown nondual pre-Advaita Vedānta tradition. I suggest that the Mokṣopāya is a Yoga text grounded in a unique and idiosyncratic nondual Sāṃkhya system of knowledge with a strong Yogācāra Buddhist influence and similarities to early Haṭha Yoga. In fact, I suggest that a similar historical context could have led to the development of both Haṭha Yoga and the Mokṣopāya since many common elements are found between the two traditions. Specifically, the Mokṣopāya shares elements with Haṭha Yoga that include the raising of kuṇḍalinī, the intonation of the syllable OṂ, the central focus on prāṇa and kumbhaka, a doctrine of siddhis, a goal of jīvanmukti or embodied liberation, a notion of immortality in the body, a practice of conscious Yogic dying, a doctrine of the prāṇa-sun which is fire that consumes the apāna-moon which is water in a centre in the core of the body, and descriptions of yogins retreating to clean and beautiful but simple Yogic huts or caves to practice nirvikalpa samādhi on animal skin seats in the lotus posture with the openings of the body closed off to keep the flow of prāṇa inside.

Keywords: advaita
Buddhism
emptiness
Hinduism
Rāma
Yoga
Advisor: Raman, Srilata
Hanneder, Jürgen
Towards Understanding Heterogenous Interactions in Photocatalysis

Photocatalytic materials are an interesting subset of nanomaterials capable of converting light into chemical energy. The basis of any heterogeneous photocatalytic reaction involves a redox driven transformation of a small molecule by a semiconducting material, often colloidal nanoparticles. Several questions remained surrounding the physical interactions at play, notably in interactions between small molecules and the colloidal nanoparticle. Herein, four studies aimed at improving our understanding of the photocatalytic process are provided. The first study investigates how conventional 1D NMR can be utilized to follow the progress of photocatalytic reactions. NMR provides a number of advantages over traditional techniques and allows for more environmentally relevant reactions to be studied. Next, the first application of comprehensive multiphase (CMP) NMR to catalytic systems, revealing that molecules transiently interacting with the surface of the nanomaterial appear to be those preferentially targeted by photocatalysis. CMP NMR provides a more holistic approach to studying photocatalysis overall owing to its ability to monitor reactions without sample preparation. The next study discusses a series of TiO2- Nitrogen Doped Graphene Quantum Dot (NGQD) nanocomposites as potential solar photocatalysts. These species show an improved ability to harvest visible light and show increased photocatalytic performance. This improvement appears to multifaceted being due to both a Z-Scheme heterojunction present at the interface of the composite and increased organic retention provided by the NGQDs. The Z-Scheme architecture allows for the highly oxidizing valence band holes of TiO2 to be retained during charge transfer while the organic retention of the NGQDs allows for higher turnover of photocatalytically generated intermediates and a higher degree of interaction between the small molecules and TiO2. Finally, a framework to study photocatalysis of mixtures was used to monitor the degradation of a 2 dye system ii using both TiO2 and g-C3N4 catalysts. Within model system containing Methyl Orange and Methylene Blue dyes, a catalytic enhancement in Methyl Orange’s degradation in the presence of g-C3N4 was found to be caused by increased surface adsorption and secondary homogeneous photosensitization processes. Contrarily, in the presence of TiO2, Methyl Orange’s catalytic degradation was hindered due to competition for photogenerated radical species.

Keywords: Heterogeneous
Photocatalysis
Pollution Remediation
TiO2
Advisor: Goh, Cynthia
Translating Ismaili Muslim Experience in Canada: Integrative Choral Pathways of Belonging

This study explores possibilities for blending choral forms of singing with traditional Ismaili Muslim devotional recitations. In particular, the focus is on finding new musical translations as a means of interpreting tradition and negotiating belonging in Canada. In music education scholarship, Muslim musical traditions can often be portrayed in ways that delimit the communities represented. In doing so, Islam may be inadvertently positioned as a problem to be addressed. Furthermore, there is a paucity of scholarship in music education that illustrates the importance of sound and music in diverse Muslim cultures. This study aims to further the conversation. I propose an “enlightened encounters” theoretical framework that draws together post-colonial, indigenous, educational social justice, and Ismaili literature. Autoethnography and narrative research methods foreground the transformative impacts of integrative vocal practices on retranslating Muslim experience in new contexts. Key findings include: 1) Blended sound and music can play a significant role to feel faith and embody cultural knowledge; 2) Integrative vocal practices can provide the possibility of avenues for Ismaili youth to navigate delicate relationships of belonging within their own traditions, as well as in the larger cultural context; 3) Engaging in participatory communal activities can provide youth with safe spaces for receiving, translating and interpreting knowledge; 4) Music and sound can have a powerful impact on reconnecting spirituality with life.

Keywords: Choral music
Intercultural translation
Ismaili Muslim
Muslim cultures
Soundscape
Zikr
Advisor: Dolloff, Lori-Anne
Structure of the Human VPS33B/VPS16B Complex

In humans, variants affecting expression/function of VPS33B or VPS16B (VIPAS39) can cause arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, a rare neonatal lethal condition with symptoms affecting many organ systems. These proteins form a VPS33B/VPS16B complex which is required for many cellular processes, including the production by bone marrow megakaryocytes of protein-carrying alpha granules, which are absent in the platelets of ARC syndrome patients. Previous students in the Kahr Lab studied the VPS33B/VPS16B complex by a variety of means, including negative-staining electron microscopy (EM), which yielded the dimensions and overall shape of a complex with two lobes resembling a dumbbell. However, key aspects of the complex including the molecular weight, composition and subunit arrangement remained elusive. My work demonstrates that human VPS33B/VPS16B is a pentameric complex containing two molecules of VPS33B and 3 of VPS16B. Negative staining EM imaging of avidin-labeled complex showed the VPS33B subunits present in opposing lobes, oriented in trans. Analysis of the effects of VPS16B truncations revealed that a central domain of this subunit is required for stable assembly of the complex. This work significantly advanced knowledge of the structure and composition of VPS33B/VPS16B, providing details that point to key insights into the potential cellular functions of this complex. I also developed a reliable, scalable and easy-to-modify expression system for recombinant human VPS33B/VPS16B, a library of mutated and truncated complexes, and a TEV-protease cleavable version of VPS33B that will support future research into VPS33B/VPS16B function.

Advisor: Kahr, Walter HA
Pigment Cells Model Lineage Regulation and Cell Clearance in the Planarian Schmidtea mediterranea

Billions of cells are replaced in adult humans every day, yet many of the mechanisms of cell turnover are still poorly understood. In particular, the clearance of dead cells by engulfment, a processed termed “efferocytosis”, remains mysterious. In this thesis, I investigate cell turnover using the freshwater planarian Schmidtea mediterranea, a model organism that undergoes constant cell turnover as an adult and is capable of regenerating all of its organs and tissues. Using light-induced ablation of pigment cells, I first characterize the pigment lineage as a model for cell clearance. Next, I investigate the molecular mechanisms of efferocytosis in planarians, and find that the highly conserved engulfment receptor CED-1/Draper/MEGF10 is not conserved in planarians. Instead, I demonstrate that a related gene, megf6, and the extracellular matrix component hemicentin both function to restrict the stem cell compartment by maintaining the integrity of the basement membrane. Finally, by tracking planarian pigment cells following light exposure, I demonstrate that apoptotic cell corpses are transported to the gut, where they are engulfed by gut phagocytes and excreted from the animal. The planarian ortholog of the conserved engulfment gene CED-12/ELMO is required for efferocytosis of pigment cells by gut phagocytes. Together, these results provide the first insight into the mechanisms of cell clearance in planarians.

Keywords: Cell death
Efferocytosis
Phagocyte
Planarian
Regeneration
Stem cells
Advisor: Pearson, Bret J