VictorJuiz/thesis huggingface dataset:
Investigation of Genetic and Clinical Heterogeneity in Subtypes of Autism Spectrum Disorder

Autism spectrum disorder (ASD) is clinically and genetically heterogeneous; core symptoms range from mild to severe, and the presentation and severity of co-morbidities vary greatly. Hundreds of genes and genomic loci have been identified to contribute to ASD susceptibility. Several genetic models have been proposed to explain the contribution of rare and/or common variants to ASD susceptibility. Subdividing ASD-affected individuals into more genetically or phenotypically homogeneous subgroups can help elucidate the relationship between clinical and genetic heterogeneity in ASD. In my thesis, I investigate the genetic and clinical heterogeneity in ASD subtypes using extensive phenotype information and rich genetic data from whole-genome sequencing (WGS). First, I developed a robust WGS analysis workflow to apply to subsequent studies. I contributed to identifying ASD candidate gene using a de novo variant approach by compiling a database of de novo variants from 4,807 ASD families. I conducted a comprehensive genetic and clinical characterization of one of these candidate genes, KMT2A, which revealed a characteristic phenotypic subtype of ASD. Lastly, I examined the genetic contribution of rare and common variants in ASD subtypes categorized based on morphology. Although rare variants have different effect sizes, traditional rare variant burden analyses assume they have similar impacts on ASD risk. To address this limitation, I developed a gene set-based rare variant score (GRS), which is a weighted sum of the number of rare variants in ASD-relevant gene sets and noncoding loci, weighted based on effect sizes. Using this approach, I found a greater burden of ASD-relevant rare variants in ASD probands with more morphological anomalies compared to those with fewer anomalies. In contrast, those with fewer morphological anomalies had a significant over-transmission of common variant risk. These findings reveal distinct contributions of rare and common variants in different morphological ASD subtypes, supporting a combined polygenic model for rare and common variants in ASD. The novel GRS method can be applied to future studies to better measure the impact of rare variants on susceptibility to ASD and other complex disorders. Data and WGS methods presented in this thesis will guide clinical genetic testing, genetic counseling and clinical management.

Advisor: Scherer, Stephen W
A Performance Guide to George Rochberg’s Caprice Variations for Solo Violin

The American composer George Rochberg’s Caprice Variations, composed in 1970, draws on a vast array of historical stylistic references from the Baroque to the modern musical periods. For Rochberg serialism, arguably the most influential compositional technique of the twentieth century, could no longer convey the full extent of what he wanted to express in his music. After the death of his son Paul in 1964, he determined to renew his musical language by returning to tonality, yet without abandoning a twentieth-century musical idiom. His Caprice Variations marks one of his first attempts to bring together the two polar opposite worlds of tonality and atonality. This one-and-a-half-hour-long work for solo violin is based on the theme from Paganini’s 24 Caprices for Solo Violin, Op.1, No. 24, and presents a wide range of technical challenges for the violinist. Since the piece is long, difficult to play, and now fifty years old, a performance guide to assist violinists is a useful contribution to the pedagogical literature. With a thorough analysis of the piece, and a consideration of both compositional and violin practice issues, as well as discussions with the original editor of the work and two violinists who have recorded it, my research will offer a complete performance guide for performers, advanced violin students, and violin teachers to assist them in achieving a deeper understanding of the work and a high level of artistic performance. The first and second chapter of this thesis offer a biographical background of George Rochberg and a literature review. In Chapter Three, each variation is approached from a theoretical perspective, analyzing the relationship to the theme and the stylistic references. Chapter Four provides an analytical practice guide for performers. A practical solution regarding technical difficulties is offered, as well as interpretative suggestions. Chapter Five presents interviews with the editor Lewis Kaplan and the performers, Andrew Jennings and Peter Sheppard Skærved, who have recorded the whole work. 美國作曲家羅奇伯格《給小提琴獨奏的奇想變奏曲》創作於1970年，是根據帕格尼尼《二十四首小提琴隨想曲》第24首的主題而創作，曲長約一個半小時。羅奇伯格原為系列主義作曲家，此曲為其回歸到調性音樂的重大轉折，當中運用巴洛克、古典、浪漫、現代以及流行等多種風格，相當迥異於早期的創作風格。 本論文除了分析作曲手法，亦提供按部就班的練習指引，最重要的是，與首演小提琴家、作品編輯Lewis Kaplan以及錄製過完整樂曲的小提琴家Peter Sheppard Skærved 與Andrew Jennings訪談，從而獲得他們與羅奇伯格互動、練習的第一手資料。期望本論文可以對欲學習此首作品的小提琴家有所助益。羅奇伯格《給小提琴獨奏的奇想變奏曲》是二十世紀後期非常重要的作品，此曲象徵作曲家對系列主義的革命，也代表多元風格世代的來臨。本論文將讓音樂學者對羅奇伯格的作曲手法及其影響有深入瞭解，並幫助小提琴家的演奏更臻完美，從而提升此曲的知名度，更為世人所知。

Advisor: Elliott, Robin
The Dynamics of Composer-performer Relationships: A Study of Long-term Creative Collaboration

This dissertation investigates the dynamics of long-term collaborative relationships between composers and performers, particularly percussionists, with the aim to present useful models of artistic collaboration. It surveys the history of the composer-performer relationship in the Western concert music tradition, examining the historically rooted assumptions regarding the roles of composers and performers and the function of the score. It also discusses the importance of composer-performer collaboration throughout the history of Western percussion music, highlighting particularly significant examples of collaboration between John Cage and his West Coast Percussion Ensemble; Karlheinz Stockhausen and Christoph Caskel; Steve Reich, Russell Hartenberger and other members of the Steve Reich Ensemble; as well as Iannis Xenakis, Les Percussions de Strasbourgs, and Sylvio Gualda. An argument is made that composer-performer collaboration has been and continues to be especially important to the development of Western percussion music. This dissertation also looks critically at some of the scholarship on collaborative practices in order to establish a theory and methodology for studying collaboration. Beginning with the argument that artistic creativity is inherently a social process (presented by Howard Becker, Dorothy Miell, and Vera John-Steiner), the implications of this idea for the concept of authorship are discussed. Recent scholarship centred specifically on composer-performer interactions has presented various models and criteria for defining degrees of collaboration. This dissertation summarizes and compares these various approaches, assessing their usefulness for the present study. Finally, this dissertation presents the findings from eight interviews conducted with composers and percussionists who have engaged in long-term collaborations spanning at least a decade. These interviews sought to illuminate how these collaborators began working together, how their working relationships developed over time, how they have communicated about their shared work, and what the effects of long-term collaboration have been on their individual practices. Through a qualitative analysis of these interviews, comparing and contrasting the experiences of the interview subjects, this dissertation presents conclusions regarding what general attitudes and approaches can facilitate artistic collaboration. Furthermore, it addresses how these conclusions lead to a deeper understanding of the roles and practices of both composers and performers.

Keywords: Collaboration
Collaborative
Composer
Creativity
Percussion
Performer
Advisor: Huang, Aiyun
A Beautiful Mind

A Beautiful Mind, is a 20-minute-long orchestral composition in two movements and for the following instrumentation: *2, *2, 2, 2—4, 2, 2, 1—timpani, 2 percussion; harp; and string orchestra. As the title suggests, A Beautiful Mind is an intuitive meditation on the phenomenon of Beauty and its roots in the human psyche. In my own musical experience, I have encountered this sense of beauty in the music of the Romantic era, early Impressionism and folk music of various traditions and moments in human history. In preparing for this composition, I spent quite a bit of time studying the music of European Romanticism. Among the many masterpieces of this era, I have been influenced the most by the colorful timbres and rich layers of Ottorino Respighi’s music and the long, languid continuous phrases in the orchestral works of Gustav Mahler. During the past ten years I have been living in Canada. It was my first extensive living experience outside China, my birthplace. During this time, I have been deeply influenced by the simplicity of the Canadian landscape, its people and their traditions. I find everything here simple and authentic. This connection between authenticity and simplicity is something I have discovered in my new country and have embraced it. Canada’s diverse culture and wide-open spaces have inspired in me a sense of originality and uniqueness that it is easier for an outsider to detect and be inspired by than for people born here who may be so used to it that it becomes invisible to them. Christmas Window, the first movement, was inspired by window displays in Toronto during Christmas time. Everything was so beautiful, and I felt overwhelmed by a sense of longing and beauty. Simple Elegance, the second movement, was inspired by a journey across Canada with my parents. They helped me synthesize our age-old traditions of my native China with the boundless beauty of my new country. A Beautiful Mind is dedicated to my parents and the love of my life, my husband.

Advisor: Hatzis, Christos
Numerical Modeling of Recovery Boiler Deposit Removal under Sootblower Jet Impingement

Deposit buildup on heat transfer surfaces in recovery boilers is undesirable as it lowers the overall boiler thermal efficiency and can result in unscheduled boiler shutdowns. To prevent excessive fouling, sootblowers are used to remove deposits by blowing supersonic steam jets onto them. However, sootblowing is not very effective and can be very expensive, as it consumes 3-12% of the total steam a boiler generates. This thesis aims to better understand the sootblower jet impingement process, and to suggest means of lowering the cost of sootblowing. A numerical model is developed to simulate sootblower jet impingement, and to predict the resulting deposit internal stress by coupling Computational Fluid Dynamics and Finite Element Analysis modeling. The removal mechanism is postulated to be due to the tensile stress induced at the deposit-tube interface. The simulation results are used to evaluate the effectiveness of different sootblowing operating conditions. In addition, a geometric model is developed to assess sootblowing efficiency over the full working cycle. Based on the results on a predefined deposit geometry and tube layout, the maximum possible sootblowing efficiency is calculated to be less than 10%. One reason for the low efficiency is the large gap between tube platens in the superheater, because most steam is wasted by blowing into space. The other reason is that the removal mechanism of using compression to induce a tensile stress is very inefficient. More efficient sootblowing could be achieved by dynamically changing the sootblower translational velocity or steam flow rate based on local sootblowing effectiveness. However, such changes will add significant complexity to the mechanical design of sootblowers. Finally, the overall modeling approach is a framework for analyzing sootblowing effectiveness and efficiency, and can be used to evaluate different sootblowing configurations, deposit geometries and tube layouts.

Keywords: Deposit removal
Fluid structure interaction
Recovery boiler fouling
Sootblower
Supersonic jet impingement
Advisor: Bussmann, Markus
Tran, Honghi
Fiducial i\Inclusive and Differential Cross Section Measurements of the Higgs Boson in the H → ZZ∗ → 4l Channel with the ATLAS Detector

This thesis presents measurements of inclusive and differential fiducial cross sections of the Higgs boson. Cross sections are measured in the fiducial phase space of the H → ZZ∗ → 4l decay channel, where l = e, μ. Measurements are performed using 139 fb-1 of proton-proton collision data produced by the Large Hadron Collider at a centre-of-mass energy of 13 TeV. The dataset was recorded by the ATLAS detector from 2015-2018. To remove detector-related effects on the measurement, the data are unfolded using the detector response matrix. Results are compared to various Standard Model predictions, including the inclusive ggH cross section predicted at N3LO in QCD. The inclusive fiducial cross section is measured to be σfid = 3.28 ± 0.32 fb, and is in agreement with the Standard Model prediction of σfid(SM) = 3.41 ± 0.18 fb. The inclusive fiducial cross section is also extrapolated to the full phase space, with a measured total cross section of σtot = 53.5 ± 4.9 ± 2.1 pb, also in agreement with the Standard Model prediction of σtot(SM) = 55.7 ± 2.8 ± 66 pb. A variety of cross section measurements are also performed for different observables related to the Higgs boson production and decay, including the transverse momentum of the Higgs boson and the jet multiplicity. All measurements are in agreement with the Standard Model.

Keywords: ATLAS detector
fiducial cross section
H4l
Higgs boson
high energy physics
Advisor: Teuscher, Richard
Hierarchical Data Storage And Processing on the Edge of the Network

Current wireless mobile networks are not able to support next-generation applications that require low latency or produce large volumes of data that can overwhelm the network. Examples include video analysis applications, wearable devices, safety-critical applications, and intelligent smart city systems. The use of servers on the wide-area cloud, however, is also not an option as these applications require low response times, or involve the processing of large volumes of data from many devices. To address these challenges, edge computing proposes the addition of computation and storage capabilities to the edge of the network. This thesis generalizes edge computing into a hierarchical cloud architecture deployed over the geographic span of a network. The vision supports scalable processing by providing storage and computation along a succession of datacenters positioned between the end device and the traditional wide area cloud datacenter. I develop a new deployment and execution platform called CloudPath based on the Function as a Service (FaaS) model that supports code and data mobility and distribution by enforcing a clear separation between computation and state. In CloudPath applications will be composed of a collection of light-weight stateless event handlers that can be implemented using high-level languages, such as Java. In this thesis, I also develop a shared database abstraction called PathStore that enables transparent data access to the hierarchy of cloud and edge data centers. PathStore supports concurrent object reads and writes on all nodes of the database hierarchy and its extension called SessionStore adds session consistency (read your own writes, monotonic reads/writes) for mobile applications. Finally, I implement a geo-distributed query engine that exploits the hierarchical structure of our eventually-consistent geo-distributed database to trade temporal accuracy (freshness) for improved latency and reduced bandwidth.

Keywords: Cloud Computing
Distributed Databases
Distributed Systems
Edge computing
Path Computing
Advisor: de Lara, Eyal
Theatre of Truth: Performing Public Religious Disputation in Seventeenth-century Europe

This dissertation examines the practice of public religious disputation in early seventeenth-century Europe. It takes a transnational approach, examining disputations in France, England, and the Low Countries between 1598 and 1625. This approach highlights the ways in which common social and political circumstances created a climate for frequent disputations, but also how religious controversy was communicated across political boundaries. It argues that these debates were part of a wider culture of performance and became especially prevalent in religiously-divided communities where performances of religious unity like Corpus Christi processions had become contested. These disputations took the practice of academic disputation, still well regarded by both Catholics and Protestants as an effective method of inquiry, and relocated it in the homes of lay hosts. The lay audience thereby became active participants in the performance, debating clergy and performing their own religious identity. Disputations then became the subject of a more public debate as rumours about them spread and clerics exploited oral and manuscript communications networks and printing presses to vaunt their victories and denigrate their opponents, making use of negative stereotypes to solidify religious divisions. State actors, seeing the utility of disputation in shaping public opinion, also sought to organize disputations in an effort to legitimize their religious policies. An examination of these disputations therefore contributes to our understanding of how religious divisions were framed and communicated in the early modern public sphere.

Keywords: Early Modern Europe
Performance
Public Sphere
Religious Coexistence
Religious Disputation
Advisor: Cohen, Paul
Assessing and Training Reactive Stepping for Individuals with Incomplete Spinal Cord Injury or Disease

Individuals with incomplete spinal cord injury or disease (iSCI/D) experience more falls than people with other neurological conditions, and one of the leading causes of these falls is impaired balance. The objective of this work was to determine how reactive stepping, a strategy used to recover from balance perturbations and therefore prevent falls, can be assessed and trained in this population. The first study found that behaviour measures from the Lean-and-Release test, a safe and standardized measure of reactive stepping ability, were reliable and valid among 26 individuals with chronic iSCI/D. The second and third studies report the findings from a randomized clinical trial involving 20 individuals with chronic iSCI/D. The second study found that Perturbation-based Balance Training (PBT), a method of training reactive stepping using repeated unexpected perturbations, did not result in greater improvements on the behavioural response of the Lean-and-Release test compared to Conventional Intensive Balance Training (CIBT), although both groups improved over time. The third study found that the PBT group may have experienced fewer falls and had a longer time to first fall than the CIBT group during the six months following training. The fourth qualitative study explored the perspectives of the participants in both balance training programs. Through a conventional content analysis four themes were identified: 1) benefits of participating, both psychological and physical, 2) increased awareness of how body, behaviour, and environment play a role in balance control, self-management strategies and fall avoidance, 3) desire for challenge and continual progress towards goals, and 4) unique aspects of PBT. These findings indicate that reactive stepping is feasible to assess and train as part of iSCI/D rehabilitation, and that while PBT may not improve reactive stepping ability beyond conventional approaches, using perturbations may reduce fall rates for individuals with iSCI/D.

Keywords: Physical therapy
Postural control
Reactive balance
Rehabilitation
Spinal cord injuries
Advisor: Musselman, Kristin
Mansfield, Avril
Dynamic Response and Containment of Blade Shedding in Gas Turbine Engines

In this thesis, the problem of blade shedding in aviation gas turbine engines (GTE) is investigated analytically, numerically and experimentally. The work is divided into three integrated sections. The first is concerned with the dynamic response of traditional metallic blades and advanced metal matrix composite (MMC) blades accounting for their geometric and material nonlinearities, and mode coupling effects. The transient response of traditional metallic blades under a periodic contact load and decaying centrifugal force field is obtained by modeling the blade as a rotating tapered Timoshenko beam. The dynamic behavior of realistic advanced MMC blades is determined using a unified beam formulation and micromechanics homogenization scheme. The second is concerned with blade shedding experiments. A novel instrumented scaled down test rig is designed and developed using dimensional analysis to ensure its dynamic equivalency with a GTE. This test rig is used to study the interactions of a released blade with a single trailing blade and a fully bladed disk. The third is concerned with the finite element (FE) analysis of blade shedding to examine the containment capability of various containment ring designs and propose a new improved system. This comprehensive study includes fundamental planar impact studies, and blade shedding analysis of a fan disk with single-ring and dual-ring designs. The outcome of this work reveals that the lateral displacement of a blade due to a decaying centrifugal force field is an order of magnitude higher than that observed at constant rotational speeds. A significant increase in the natural frequency and reduction in weight can be achieved with the use of MMC blades. Remarkably, the experimental results confirm the FE predictions of a typical fan disk. They clearly show the influence of the trailing blades on the trajectory of the released blade, large deformation of the trailing blades and confinement of the released blade at the tip of the trailing blades. The proposed dual-ring design composed of ductile frontal aluminum ring and backing Kevlar ring with an interfacial gap has the potential to successfully arrest the released blade within the confines of the ring.

Keywords: blade shedding
blade vibration
containment
dynamic response
experiment
gas turbine engine
Advisor: Meguid, Shaker A.
A Foucauldian Discourse Analysis of the Construction of Canadian International Pharmacy Graduate (IPG) Professional Identities and Subjectivities

This research explores the construction of professional identities and subjectivities of former international pharmacy graduates or IPGs. It is a study of the reprofessionalization of pharmacy practice in the Canadian context and the resocialization of IPGs into a profession that is in transition. My thesis adopts a bricolage approach in which I theorize professional identity construction through the theoretical lenses of Michel Foucault, Stuart Hall, Judith Butler and the race and space literature. These related theories facilitate the understanding of professional identity construction through the take up of professional discourses and the ‘translation’ experiences of internationally-trained professionals navigating discursive border crossings while integrating into the host country’s labour market. A Foucauldian governmentality approach was employed to analyze an archive of professional journals to determine how the profession governs its members to become the ‘right’ type of pharmacist at this time in the profession’s history. I also analyzed interview data from 17 participants examining the multiple discourses that former IPGs adopt to construct their professional subjectivities. The study reveals that former IPGs readily take up professional discourses in becoming a ‘Canadian’ pharmacist and that the process of identity construction for racialized professionals requires conducting oneself ‘professionally’ when managing racist encounters in the workplace.

Keywords: Foucault
immigrant
international pharmacists
pharmacy
professional identity
resocialization
Advisor: Muzzin, Linda