VictorJuiz/thesis huggingface dataset:
Adapting Voices: The Musical Lifeworld of Sean-nós Singing in Carna, Ireland

Carna, a small village in County Galway, Ireland, is a place that is synonymous with the Irish-language traditional song form called sean-nós (‘old style’). Throughout the 20th century, Carna has seen the emergence of particular local people – often singers who have won at national competitions or have hundreds of songs in their repertoire – as the interpreters and narrators of musical practice. In the past, such individuals would be considered exceptional within a diverse community practice that included many singers, musicians, dancers, and storytellers. Today, the situation is quite different. Carna is a community with a smaller, more educated, mobile, and technologically enveloped population and the importance of sean-nós and other traditional practices as everyday entertainment has collapsed. In the wake of declining community practice, the value placed on knowledgeable local singers has increased to the extent that they are considered specialists. This dissertation expands beyond specialists’ narratives of place and local practice by discussing and interpreting the broader musical lifeworld of sean-nós singing in Carna. In particular, it examines the experience of local people that feel excluded and therefore do not participate in organized sessions and events that include sean-nós. The dwindling participation at such events often leads specialists to characterize sean-nós as a practice in decline with a corresponding local rejection of its value to social life. Seeking to complicate this narrative, my study examines how the social value of sean-nós singing, songs, and listening practices remains vital to social engagement and community cohesion despite the outward appearance of decline and disinterest. I accomplish this by contrasting how sean-nós is meaningful to both specialists and people on the margins of local practice and discuss different moments when sean-nós does expressive work in the community. I describe a broad scope of local people, events, and experience to show that sean-nós is a practice that creates webs of significance in numerous aspects of everyday life in Carna. I argue that sean-nós is embedded in local people’s intersubjective experience of place, song, and each other in a way that challenges the frequent focus on specialist knowledge in Irish traditional music studies.

Keywords: ethnomusicology
Ireland
music and place
phenomenology
Sean-nós singing
song tradition
Advisor: Pilzer, Joshua D
The Effects of Asexuality and Selfing on Genetic Diversity, the Efficacy of Selection and Species Persistence.

Understanding the origin, maintenance and distribution of nature’s astonishing diversity of reproductive systems is a major endeavour in evolutionary biology. One of the oldest evolutionary puzzles is the rarity of species that undergo high rates of asexual reproduction or self-fertilization despite their significant benefits over sex and outcrossing. My thesis investigates the evolutionary consequences of asexuality and selfing using experimental evolution, genomic analyses and theoretical modeling. In chapter 2, I performed a mutation accumulation experiment using the facultatively sexual rotifer, Brachionus calyciflorus, under different population sizes with UV-C radiation. Our finding suggests that large effect mutations are relatively common in B. calyciflorus, at least under UV radiation. In chapter 3 and 4, I examined genomic diversity in natural isolates of the facultatively sexual duckweed, Lemna minor, and B. calyciflorus. We found genomic signatures suggesting L. minor reproduces mostly through asexual propagation but also evidence that it reproduces sexually more often than a related duckweed species, Spirodela polyrrhiza. We found that B. calyciflorus possessed low neutral diversity and relatively efficient purifying selection, but anomalies in the data limited the reliability of our results. These chapters are among the few studies that analyze genome wide diversity in facultative sexual species. In chapter 5, I performed simulations of highly selfing populations experiencing selection that fluctuates in magnitude (not in direction) over time. We found that highly selfing populations accumulate deleterious mutations more quickly when selection fluctuates and that mutations fix disproportionately at loci in the genome that responds to fluctuating selection compared to loci that are constantly selected. This highlights the importance of environmental heterogeneity when considering fitness decline and extinction in selfing populations. In chapter 6, I extend a classic species selection model to track the abundance of asexual and sexual species when diversification rates of asexuals decline with age. Our results broaden the parameters space where sexual and asexual species can coexist. In summary, my thesis contributes data related to selection efficacy and genomic diversity of facultatively sexual species, as well as providing novel theoretical insights into the evolutionary fate of asexual and selfing species.

Advisor: Agrawal, Aneil F
Proteomic-based Signature of Brain-related Proteins as Novel Candidate Biomarkers for Alzheimer’s Disease Diagnosis

Alzheimer’s disease (AD) is the most common type of dementia characterized by the progressive memory loss and cognitive decline, with typical age of onset after 65 years. The main disease hallmarks include extracellular amyloid beta deposits and intracellular neurofibrillary tangles. Brain pathology is reflected in cerebrospinal fluid (CSF) where core biomarkers amyloid beta 1-42, total tau, and phosphorylated tau protein levels are changed relative to cognitively normal elderly. There is a need for novel disease-specific biomarkers that will capture disease more accurately and at an earlier stage, predict disease severity, and be used in research and clinical trial settings for patients’ enrichment and stratification or to monitor drug efficacy. The aim of the present dissertation is to evaluate diagnostic potential of brain-related proteins in CSF of AD patients. The study was focused on proteins with high specificity for brain tissue. Only proteins expressed predominantly in the brain and reliably identified in the human CSF proteome were selected for development of multiplex mass spectrometry-based assay. Candidate biomarkers were then evaluated in AD patients with different spectrum of disease severity and cognitively healthy individuals (in total 154 subjects). This exploratory study suggests APLP1 protein as a promising biomarker for early AD detection. Specifically, the protein was elevated in mild cognitive impairment compared to cognitively healthy individuals (p

Keywords: Alzheimer's disease
Biomarkers
Cerebrospinal fluid
Mass spectrometry
Selected reaction monitoring
Advisor: Diamandis, Eleftherios P
The Immune Impact of Common Sexually Transmitted Viruses and the Vaginal Microbiota: Implications for HIV Susceptibility in African, Caribbean, and other Black Women from Toronto

Genital inflammation is a key determinant of human immunodeficiency virus (HIV) transmission and may increase the availability of HIV-susceptible target cells at sites of exposure. The African, Carribean, and other black (ACB) community is at increased risk of HIV acquisition in Toronto and several genital conditions that increase HIV risk are also more prevalent, including bacterial vaginosis, herpes simplex virus type-2 (HSV-2) and human papillomavirus (HPV) infection. Therefore, we assessed the impact of these three genital conditions on mucosal immune cells and cytokines in the female genital tract of ACB women. Endocervical cells and cervicovaginal secretions were collected by cytobrush and Instead Softcup, respectively. T cells and dendritic cells were assessed by flow cytometry, proinflammatory cytokines and chemokines by multiplex enzyme-linked immunosorbent assay (ELISA), and the microbiota by 16S ribosomal ribonucleic acid gene sequencing. HSV-2 infection was associated with elevated levels of endocervical HIV target cells (CCR5+ CD4 T cells), Lactobacillus-deficient microbiota was associated with elevated proinflammatory cytokines, prevalent HPV infection was associated with Lactobacillus-deficient microbiota, and HPV clearance was associated with higher numbers of Langerhans cells in the female genital tract. These results suggest multiple ways in which genital conditions are associated with factors that have been shown to influence HIV susceptibility and provides novel targets for future HIV prevention strategies.

Keywords: Female Genital Tract
HIV
Infectious Diseases
Mucosal Immunology
STI
Advisor: Kaul, Rupert
Modeling and Analysis of Optical Blur for Everyday Photography

Optical blur obscures image detail due to the camera's optics. The blur appearance depends on the scene's depth, wavelength, as well as the camera. The inference of such information --- optical calibration, image deblurring, and depth estimation -- is of great interest to computer vision. Existing approaches make impractical assumptions about the camera and the scene, and are therefore restricted to lab settings. In this thesis, we propose novel optical blur models towards solving the above inference problems in everyday settings. First, we propose a practical model for lenses with monochromatic optical aberrations, assuming the aberrations can be fully described by Seidel aberrations. Although the model produces realistic 2D blur kernels of complicated appearance, it has very few parameters and thus can be estimated using very limited data. We show specifically that just three blur kernels contain enough information to estimate the lens parameters up to an aperture-dependent scale factor. Second, we study image deblurring for RGB-Infrared imaging. This problem is especially challenging since RGB-Infrared cameras suffer from inevitable chromatic aberration, channel crosstalk, and pixel multiplexing due to the color-filter-array. The coupling of the distortions are critical to deblurring quality but is non-trivial to invert efficiently. We propose a practical image formation model that captures all three distortions while enables fast restoration. Third, we develop an approach to two-frame Depth from Defocus (DFD) in everyday settings. The main challenge here is that the inter-frame motion needs to be estimated in addition to depth from just two images. We propose conditions to control the camera focus to guarantee near-optimal DFD estimation and a method to estimate depth and the motion jointly in local 9x9 patches. This allows us to capture sparse depth map even in non-rigid scenes. Fourth, we propose a method to fuse local DFD results into dense depth and flow maps. The noise, sparsity and ambiguities inherent in DFD makes this problem particularly difficult. We introduce a splined-based prior to enable fusion over great image distances and irregular shaped regions, and to allow explicit reasoning about figure-ground relationships. Our final results exhibits high quality results with crisp boundaries.

Keywords: aberration
calibration
depth from defocus
image restoration
optical blur
Advisor: Kutulakos, Kiriakos N.
Trends and Outcomes of Carotid Artery Revascularization in Ontario, Canada: A Population-Based Analysis

Introduction: Evidence for the safety and efficacy of carotid-artery stenting compared with endarterectomy is accumulating from randomized controlled trials. However, data on utilization trends and long-term outcomes of carotid revascularization strategies in real world practice are lacking. Methods: We first conducted a multicenter validation study to assess the accuracy of carotid-artery revascularization coding in Ontario health administrative databases. We then identified a retrospective population-based cohort of individuals who underwent carotid endarterectomy or stenting in Ontario, Canada (2002-2015). We used time-series analyses to examine temporal changes in the utilization rates of carotid revascularization procedures, and compared long-term (up to 13 years) and 30-day outcomes of carotid endarterectomy versus stenting overall and by operator specialty. Results: Carotid-artery revascularization procedures were coded with high accuracy in administrative databases (positive predictive value, 87-99%; sensitivity, 90-93%). Overall, 86% of patients underwent endarterectomy and 14% stenting. The rate of endarterectomy decreased by 36%, whereas carotid-artery stenting increased by 72% during the study period. Rate of the composite outcome of 30-day death, stroke or myocardial infarction plus any stroke during 13-year follow-up was higher with stenting (16.3%) compared with endarterectomy (9.7%) (adjusted hazard ratio, 1.57; 95% confidence interval, 1.43-1.73). In the endarterectomy group, the risk of 30-day stroke or death was higher among patients treated by non-vascular surgeons (4.0%) compared with vascular surgeons (2.9%) (adjusted odds ratio, 1.32; 95% confidence interval, 1.08-1.62). Operator specialty was not associated with adverse outcomes after carotid-artery stenting. Conclusions: Although the utilization of carotid-artery stenting has increased, stenting carries a 1.5-fold higher risk of long-term events compared to endarterectomy. Vascular surgeons appear to perform endarterectomy at the lowest event rates. While non-randomized, these results raise potential concerns about the interchangeability of carotid endarterectomy and stenting in the context of actual clinical practice, and may have implications for local referral practices and policies.

Keywords: carotid revascularization
carotid stenosis
clinical epidemiology
health services research
stroke
vascular surgery
Advisor: Al-Omran, Mohammed
Promoting Financial Management Activities After An Acquired Brain Injury: Enhancing Assessment Evidence

The purpose of my dissertation was to provide guidance for evidence-based financial management assessment in acquired brain injury rehabilitation. The objectives were to (1) synthesize current financial management assessment instrument literature, and (2) qualitatively examine the real-world financial management actions and behaviours of adults with brain injury. I conducted three studies. In the first study I used systematic search and instrument content analysis methods to identify 88 different instruments that include financial management items. Of these, eight instruments were identified as being potentially advantageous to the comprehensive observation- based assessment of financial management. However, two areas of financial management were missing from these eight measures: budgeting and monitoring of spending. In the second study I used systematic assessment instrument review methods, including an evidence critical appraisal, to critique the eight select instruments identified in the previous review and content analysis. Five of the eight measures had moderate volumes of low-risk of bias evidence for construct validity (hypothesis testing); two instruments had limited evidence for test-retest reliability; and all instruments lacked content validity and responsiveness evidence. In the third study I used qualitative inquiry and grounded-theory methodology to develop the Financial Management Activity Process conceptual framework. This framework was created from interviews with adults with brain injury and close-others who help with financial activities. It highlights the use of personalized financial management strategies that account for the person, activity, and environment factors facilitating or limiting activity completion. Together, the studies highlight that current financial management instruments require more investigation prior to endorsement. Also, instruments’ need refinement to address all current relevant areas of financial management. Strategy use may be a salient consideration in developing new instruments, as it was relevant to the everyday financial management actions and behaviours of adults living with acquired brain injury. Further instrument development and research is needed.

Keywords: assessment
brain injury
cognitive impairment
finanial management
instrumental activities of daily living
measurement
Advisor: Dawson, Deirdre R
Tablet Technology for Neuropsychological Testing and fMRI

Abnormal behaviour may be a warning sign of underlying brain disease. Neuropsychological (NP) tests - behavioural tasks that very commonly involve handwriting and drawing - are widely used in the clinic to detect abnormal brain function in a variety of brain diseases. Task-based functional magnetic resonance imaging (fMRI), a method for noninvasively mapping the brain activity that underlies specific behaviours, can possibly help to inform use of NP tests, and to improve their sensitivity and specificity. Task-based fMRI typically involves peripheral devices that are used to present sensory stimuli and record behavioural responses. Such devices (e.g. video projectors, key pads for detecting button presses) must be designed for compatibility with fMRI procedures, including operation at the very high magnetic field of the MRI system without introducing electromagnetic interference. The common fMRI-compatible devices are insufficient for evaluating many NP tests, however. Consequently, an fMRI-compatible tablet, including a touch-sensitive surface, was developed in the Graham laboratory to enable fMRI studies of NP tests that involve writing and drawing responses. In its original prototype, the tablet did not enable individuals to see their hand while performing writing and drawing actions. This missing feature, termed “visual feedback of hand position” (VFHP), may make it difficult for certain patient populations to interact easily with the tablet during task-based fMRI. The interactivity of the tablet thus should be improved before proceeding to map the brain activity of specific NP tests. This thesis focuses on developing a real-time system to integrate VFHP with the tablet in an augmented reality display, including simple computer graphics to present visual stimuli and tablet responses, and merged streaming video of the hand as it manipulates a stylus during writing and drawing behaviour. First, the new tablet prototype is developed and validated in the context of a writing task that involves copying sentences, showing that tablet interactivity is enhanced when VFHP is included. Second, the prototype is used to perform the first characterization of the brain activity in a control population of young healthy adults as they perform a novel NP test that was specially designed to detect and evaluate writing impairments in patients with Mild Cognitive Impairment and Alzheimer’s Disease. Third, the impact of adopting the tablet with and without VFHP is studied for a group of young healthy adults as they undergo fMRI while performing the trail making test (TMT), an NP test that is commonly used to assess the frontal lobes of the brain. Finally, future directions of this research are discussed, including use of this new tablet technology to assess patients with brain diseases in task-based fMRI trials.

Keywords: fMRI
Neuropsychological tests
pen-and-paper test
visual feedback of hand position
Advisor: Graham, Simon J
The Artist as Literary Character in the Works of Anton Chekhov

The present dissertation considers the methodology of Anton Chekhov’s literary ethics by focusing on the figure of the artist in his work. There are two general strategies he employs in depicting this figure. The first regards his engagement with typicality in characterizing the artist, and the second regards the reflexivity of the artist, which is to say the artist’s actions on the fictional plane draw attention to the author’s actions on the meta-fictional plane. The concern with typicality vis-à-vis the artist is more prominent in his earlier stories and is the focus of the first part of the dissertation. Chapter One addresses typicality in the genre of the physiologie in France and its Russian counterpart, the fiziologicheskii ocherk. This discussion lays the groundwork for Chapter Two, which addresses Chekhov’s move towards the complicated type in a trio of stories showcasing artists published in short succession in February 1886 – “An Actor’s Death” (“Akterskaia gibel’”), “Requiem” (“Panikhida”), and “Anyuta” (“Aniuta”). The reflexive quality of the figure of the artist, which we also find in the three aforementioned stories, is more prominent in Chekhov’s later stories and is the focus of the second part of the dissertation. How an artist sees is of particular importance to Chekhov. Chapter Three examines the visual artists in his mature work to determine the components of artistic vision he sets forth, namely serdechnost’, temporal and sensory specificity, and indeterminacy. Chapter Four analyzes the actress. From his early days as a writer, he was attentive to the power dynamics in the theater. His sympathy towards the actress in stories such as “Requiem” (“Panikhida”) and “A Boring Story” (Skuchnaia istoriia”) is noteworthy. Yet, as Chapter Four argues, he moves beyond sympathy in The Seagull (“Chaika”) to invest Nina, an actress, with the power of self-representation.

Advisor: Orwin, Donna
Changes in Growth Factor Responsiveness during In Vitro Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes

Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) offer a promising source of non-proliferative CMs that can be used to identify conditions that stimulate heart regeneration. Realizing this potential requires efficient methods to generate matured hPSC-CMs that do not readily respond to exogenous cell cycle stimulation. Therefore, the goal of this project was to mature hPSC-CMs and test their cell cycle response in growth factor screens. Alignment on nano-grooved substrates was the first method investigated to mature hPSC-CMs. While aligned tissues formed and established functional syncytia, strong contractions resulted in tissue detachment from the substrate. Next, 3D aggregate suspension was explored as an approach to mature hPSC-CMs. Following 4 weeks in suspension, hPSC-CMs displayed a more mature morphology, gene expression profile, and electrophysiology. Importantly, matured hPSC-CMs were unresponsive to growth factor stimulation for cell cycle induction. Following stimulation of aggregates with bFGF and HRG for 24h, immature hPSC-CMs initiated DNA synthesis, while matured hPSC-CMs did not. Interestingly, both immature and matured hPSC-CMs exhibited ERK activation in response to stimulation. A significant increase in expression of cyclin dependent kinase (CDK) inhibitors, with a corresponding significant decrease in expression of most cyclins and CDKs, is a likely explanation for this result. To test the effect of 40 additional growth factors on cell cycle response, a screening platform was developed. The screen revealed overlapping and distinct hits in immature and matured hPSC-CMs. Transferring screening results to 3D, however, resulted in no effect in matured CMs, which was found to likely be the result of dedifferentiation in 2D, highlighting the need to perform cell cycle stimulation assays in a 3D environment that supports a mature CM state. Overall, these results provide insights into the development of adequate model CMs and experimental assays for discovering treatments that induce CM cell cycle re-entry for regenerative purposes.

Advisor: Zandstra, Peter W