VictorJuiz/thesis huggingface dataset:
Sim-Cyberpunk: Serious Play, Hackers and Capture the Flag Competitions

Capture the flag (CTF) is a style of game developed within the hacker community to simulate/emulate the practice of vulnerability research. In a CTF players identify security vulnerabilities in information systems and exploit these flaws to undermine their operations, which gives them access to a “flag” which they score for points used to win a competition. An exploratory study of this game, this dissertation uses ethnographic methods including observation of three CTF competitions and semi-structured interviews with 47 CTF players and designers. Analysis of this data considers the co-constitution of the game through the practices of its designers and players, concerning the values of the hacker community and its linkages to the information security industry whose membership constitutes the preponderance of CTF participants. Utilizing Sara Grimes and Andrew Feenberg’s (2009) theory of “games as sites of social rationalization” this paper argues that CTF has been instrumentalized as a tool of cultural reproduction. This function of CTF is used to discursively shape and sustain knowledge acquisition, identity formation and work in the cybersecurity industry through the affordances of play in alignment with hacker values, translating intellectual capital into social capital through playful game systems.

Keywords: Capture the Flag
Cybersecurity
Game Studies
Hacker Culture
Hacker Studies
Information Security
Advisor: Grimes, Sara
The Relevance of Casimir Ney's 24 Préludes pour L'alto to the Contemporary Violist

Casimir Ney's 24 Préludes pour L'alto are among the most technically virtuosic works available to the contemporary violist. This dissertation explores the 24 Préludes relevance to contemporary violists through an examination of research relevant to Ney's identity, the history of the viola, musical and technical styles of Romantic string playing, viola pedagogy and pedagogical materials, and viola repertoire. Technical requirements existing simultaneously in Ney's writing and the solo, sonata, and concerto repertoire for viola are compared, with the parallels drawn showing frequent commonalities between Ney and music preceding the 24 Préludes to the present. The research conducted for this document suggests study of the 24 Préludes pour L'alto may assist in the development of personal technical ability. A performance guide for all twenty-four works has been included to provide one option to facilitate learning and preparation of the preludes for performance.

Advisor: Elliott, Robin
Theory of Mind Reasoning in Explanation, Plan Recognition, and Assistance: Theory and Practice

With the rapid advancements in the field of artificial intelligence (AI) in recent years, one of the longstanding goals of the field – building AI systems that are able to interact with other agents in social settings – may appear within reach. However, present-day AI systems do not yet demonstrate the social cognitive skills needed to robustly operate in the real world, and in particular in complex social settings involving humans. Research on humans has identified that Theory of Mind – the ability to attribute mental states (e.g., beliefs, desires, and intentions) to oneself and to others – is a precursor to the development of social cognitive abilities that enable most humans to successfully navigate complex social settings. It follows, then, that augmenting AI systems with Theory of Mind capabilities could improve upon their existing social cognitive abilities and get us closer to achieving AI’s aforementioned longstanding goal. In this dissertation, we present a body of work that investigates the role of Theory of Mind in explanation, plan recognition, and assistance and takes steps towards the betterment of social cognitive abilities held by present and future AI systems. Moreover, in much of this dissertation we appeal to the computational paradigm of epistemic planning, which allows us to address or circumvent some of the challenges involved with augmenting AI systems with Theory of Mind. Appealing to epistemic planning allows us to develop computational solutions and demonstrate the feasibility and usefulness of Theory of Mind in explanation, plan recognition, and assistance. Finally, this dissertation employs these computational solutions and integrates them within a robotic system that demonstrates social cognitive abilities in complex real-world settings, as well as a potential to benefit humans with whom it interacts.

Keywords: Epistemic Planning
Plan Recognition
Theory of Mind
Advisor: McIlraith, Sheila Ann
Recycling of LiNixMnyCo1−x−yO2 (NMC) Cathodes from End-of-Life Lithium-Ion Batteries Using Hydrometallurgical and Direct Recycling Processes

Lithium-ion batteries (LIBs) have become a mainstream power source for portable electronic devices and electric transportation due to their several prominent advantages, including high energy density, long storage life, small volume, lightweight, and low self-discharge. With the increasing demand for LIBs, the serious shortage of raw materials for LIB production, and the growing global awareness to protect the urban environment, recycling of postconsumer LIBs has become imperative. In recent years, LiNixMnyCo1−x−yO2 (NMC) cathode material has become the most promising cathode material for LIBs because of its low cost, high discharge capacity, good cyclic performance, and stable structure; thus, its application in electric vehicles (EVs) has been promoted. Since this cathode material will soon enter the recycling stream, it is critical to have an effective recycling process for its handling. The overall objective of this dissertation is to develop novel, efficient, and sustainable hydrometallurgical and direct recycling processes for NMC cathode materials from spent LIBs. This dissertation is focused on 1) recovering lithium, nickel, manganese, and cobalt from NMC cathode material of spent LIBs of an EV via acid leaching; 2) separating all four metals from the leachate after acid leaching using electrodialysis; 3) synthesizing nickel-rich NMC cathode material for LIBs utilizing supercritical CO2; and 4) directly recycling degraded NMC cathode material of spent LIBs from an EV using hydrothermal relithiation combined with sintering. The milestones in this dissertation involve 1) developing, advancing, implementing, and optimizing the leaching, metal separation, coprecipitation, and relithiation steps to improve the hydrometallurgical and direct recycling routes by reducing the environmental impact and enhancing the sustainable development; and 2) elucidating the leaching, electrodialysis, coprecipitation, and relithiation mechanisms using fundamental investigations and kinetic modeling. The potential for social, environmental, and economic impacts through innovations and scientific excellence of this dissertation is immense. The advantages of successful implementation of this research project are twofold: 1) it provides a secure secondary supply for strategic materials that face steep demand growth and potential supply shortfall; and 2) it provides an environmentally sustainable and economic route for waste valorization and resource recovery, which in turn will enable the circular economy.

Keywords: Direct recycling
Electric vehicles
Hydrometallurgy
Lithium-ion batteries
NMC cathodes
Advisor: Azimi, Gisele
At the Mouth of the River: Shame, Secrecy, and Intergenerational Trauma in Newfoundland

In this dissertation, I engage with theories of intergenerational trauma to explore the psychic dynamics of loss and memory in Newfoundland. This inquiry works to unearth the complex historic and social conditions that contextualize ongoing legacies of social injury in Newfoundland. I explore the many ways that Newfoundlanders grapple with the messy contradictions of trauma through aesthetic expression, resilience and love. I ask: in what ways has trauma demanded a kind of suspension between spaces, both temporal and cognitive, in Newfoundland culture? How and why do historic losses define Newfoundland culture, identity, politics and industry today?This dissertation swims in the slippery waters of secrecy, shame and silence that define intergenerational trauma in Newfoundland. Working with theories of trauma, I explore how enigmatic memories move through the generations across relational, embodied, cultural and ecological passageways. By turning to the aesthetic archive of Newfoundland film, folklore and art, this dissertation traces the affective, relational, and sociopolitical legacies of trauma in Newfoundland as they move through somatic, relational, familial, cultural, and ecological passageways. Importantly, I consider how these legacies are rooted in transnational histories that have shaped the cultural landscape of this island, including the Atlantic slave trade, settler colonialism, and resource extraction. In doing so, I propose methods for attuning us to the paradoxical tensions of silence that resound through Newfoundland culture. Such methods lay the foundation for an analysis of the way in which historical contexts such as colonialism, slavery, resource extraction, poverty, rurality, and religion continue to define contemporary Newfoundland life through shame and silence. In this dissertation, I seek a range of modes for listening to transgenerational silences to working through cultural shame and to imagine radical change.

Keywords: Cultural Studies
Folklore
Newfoundland
Psychoanalysis
Queer Theory
Trauma
Advisor: Georgis, Dina
Ultrasound Jetting and Atomization of Sessile and Impacting Droplets

We present the results of our experimental and theoretical study of the jetting and atomization of a sessile and an impacting droplet subject to an ultrasonic surface vibration. Such high frequency vibrations result in the formation of a liquid jet shooting outwardly from the surface of the droplet, which eventually breaks up into droplets. Part of the liquid remains on the surface, which eventually goes through ultrasonic atomization. We divided this process into three categories of (i) jetting, (ii) jet breakup and liquid layer formation, and (iii) liquid layer atomization, and characterized each one separately. We have developed a model to predict the onset of jetting and jet velocity. The liquid jet may breakup into droplets, the sizes of which were measured and predicted theoretically. The liquid layer remaining on the surface may go through ultrasonic atomization resulting in bimodal droplet size and velocity distributions. Additionally, the effect of parent droplet size on the final aerosol size distribution was studied and theoretical models were proposed to characterize the ultrasonic atomization and liquid breakup (droplet size, ejection threshold, and ejection velocities). It was also shown that the ultrasonic atomization of nanoliter liquid volumes results in the formation of <10 μm mist with the large droplets being cut off.

Keywords: Mass Spectrometer
Ultrasonic Atomization
Ultrasonic Droplet Breakup
Ultrasound Jetting
Advisor: Ashgriz, Nasser NA
Computational Frameworks to Interpret Genetic Abnormalities in Hematologic Malignancies

In the era of high throughput sequencing technologies, the speed of genomic data generation exceeds our abilities to store, analyze and interpret the data without high-performance computing facilities. In hematology, next-generation sequencing (NGS) is being utilized for diagnosis, prognostication, and post-treatment monitoring. Although it is undoubtedly the future of molecular testing and monitoring, computational methods to interpret results at single and longitudinal time points are highly in need. Thus, this thesis is devoted to mining clinically and scientifically meaningful information from NGS data in the context of hematologic malignancies. First, I show how incorporating allelic burdens of mutations can enhance the risk stratification of patients with acute myeloid leukemia (AML). Instead of considering mutations as binary variables, the model considers mutations as continuous variables, considering clonal architecture when predicting the prognosis. Also, I demonstrate single mutation does not determine a patient's risk alone, but the patient's risk depends on the entire mutation profile. Second, I describe computational methods to detect residual leukemia cells remaining post-treatment (termed "measurable residual disease" (MRD)). I show that NGS-based MRD detection is feasible in different subtypes of AML at various time points. In addition, estimating sequencing error rates helps reduce false positives while increasing true positives, thus maximizing clinical relevance. Throughout multiple studies, I describe different approaches to detect NGS-based MRD and to mine clinically meaningful information. Lastly, I present a computational workflow that analyzes single-cell proteogenomic sequencing data to identify relapse-fated subclones from the time of diagnosis in an FLT3-ITD+ AML case. Simultaneous proteogenomic profiles allow the refinement of clonal models relying only on mutation profiles and help identify relapse-fated AML subclones at the time of initial diagnosis. I also describe how copy-neutral loss-of-heterozygosity at chr13q can be accurately detected at the single-cell level and cell surface marker expressions help identify somatic mutations.

Keywords: Acute myeloid leukemia
Cancer genomics
Computational biology
Hematologic malignancies
Machine learning
Measurable residual disease
Advisor: Zhang, Zhaolei ZZ
Adapting Manifold-Based Analyses to Describe How Personal and Task Constraints Impact Lower Extremity Movement Variability During Exercise

Despite the recent emphasis in the motor control literature quantifying the structure of movement variability, there is a paucity of research applying these concepts in exercise contexts. Measuring the structure of variability surrounding dynamic valgus motion, and how it is impacted by personal and task constraints, can be achieved by adapting Uncontrolled Manifold (UCM) analyses. This thesis aimed to build a foundation for a complementary approach to evaluating the execution of exercise tasks that considers both average movements and movement variability by addressing four main gaps in the literature. First, it is unclear which methods of computing dynamic valgus motion are most related to external knee abduction and external rotation moments. Second, it is unclear how many repetitions are required to monitor the variability surrounding dynamic valgus motion using adapted UCM analyses. Third, although ankle dorsiflexion range of motion (ROM) restrictions can influence the average dynamic valgus motion, it is unclear whether it also impacts the structure of movement variability. Fourth, research has demonstrated that average dynamic valgus motion is more strongly correlated between single-leg exercises. But, no studies have examined these relationships for the structure of movement variability. In Chapter 3, the data demonstrated that computing dynamic valgus motion as the orthogonal distance of the knee joint center from the hip-foot plane (OD) was a relatively better kinematic proxy of external knee abduction and external rotation moments in comparison to Cardan-Euler angles. In Chapter 4, UCM methods were adapted for use with OD. In Chapter 5, the data showed that participants should perform at least five repetitions to obtain saturated variability data for between-participant analyses and at least eight repetitions for within-participant analyses. Chapter 6 demonstrated that individuals’ ankle dorsiflexion ROM had little influence on the structure of movement variability. Chapter 7 found that the task constraints imposed during exercise strongly influence the structure of movement variability. In summary, data from this thesis provide a platform for future research and practice to expand upon a complementary approach to evaluating the execution of exercise tasks by leveraging movement variability data.

Keywords: Biomechanics
Movement Assessment
Movement Variability
Uncontrolled Manifold
Advisor: Tremblay, Luc
Frost, David M
An Investigation on Renewable Carbons as Natural Sources of Fluorescent and Conductive Materials for Smart Device Applications

Controlled carbonization of biomass leads to nano-layered graphitic structures with characteristic crystalline sp2 hybridization with conductive and optical properties. The starting material and processing parameters influence the final chemical and morphological structure of the renewable carbon, which determine its practical applications. Biomasses investigated include various wood, xylem sap and peanut shells. Controlled pyrolysis of several wood species to 800 ˚C yielded photoluminescent graphene clusters with a notable electrical conductivity of 600 S/m and electromagnetic interference shielding effectiveness of 47.7 dB at 12 GHz. This is due to the renewable graphitic carbon’s material graphene-graphite composite, since graphene is known to be highly conductive due to its high carrier mobility. Catalytic graphitization with iron nitrate nanoparticles successfully showed the formation of single crystal graphitic carbon structures in black spruce (Picea mariana) at temperatures between 300-800 ˚C and conductivity of 850 S/m. This P. mariana renewable carbon was applied as the cathode of a coin cell battery. To reduce processing temperature further, hydrothermal pyrolysis was performed at 180 ˚C on xylem sap. A characteristic crystalline sp2 carbon was observed in hydrochar xylem syrup. When UV light is shone on the carbon, by the “naked eye” it can selectively detect Fe3+ ions and pH. A chemo sensor was designed based on logic gates, which can displace traditional metal-oxide-semiconductor field-effect transistor (MOSFET) based circuits. Additionally, multiple thermogravimetric comparisons were performed using several model-free and model-based kinetic analyses, where activation energy and pre-exponential factors were determined during the decomposition process. Peanut shell graphitic carbon was applied as an electrode in a Li-ion coin cell battery, yielding a specific capacity of 220 mAh/g and 100 % columbic efficiency for 800 cycles. Thus, these findings on renewable carbon will open a new frontier in sustainable bio-electronics and energy materials manufacturing.

Advisor: Sain, Mohini M
Lu, Zheng-Hong
“The Right Story”: Discursive Strategies in Gender-Affirming Healthcare Access

Despite strides towards a less pathological and diagnostic-centered approach to transgender healthcare, many policies continue to present barriers in accessing gender-affirming medical support that may provide individuals with greater ease in their embodiment. Research on transgender speakers’ linguistic practices in healthcare interactions has shown that practitioners’ prerequisites for granting access to this kind of care remain largely based on criteria presented in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders. This practice of evaluation has led to an impression within trans communities that accessing gender-affirming care is a test, where patients must “do” their gender or present their identity in a particular way. Meeting this expectation may feel especially imperative and dehumanizing for non-binary transgender people, as individuals who do not identify as either, or exclusively, masculine or feminine. Presenting a gender positionality outside of the binary has historically meant losing access to care, and as a result, non-binary patients often find themselves using different language to describe their experience than they would in other contexts, simply to gain access to much-needed care. As an intervention in the inequity of doctor-patient communication in this setting, this dissertation considers the metalinguistic (“talk about talk”) observations of non-binary people regarding their gender-affirming healthcare interactions in Ontario. Rather than considering non-binary patients’ practices as straightforward acts of capitulation to medical expectations, their performances in these high-risk interactions are a means to contest their marginal status within the healthcare system. Participant-collaborators express numerous strategies to simplify or obscure their non-binary identities in their pursuit of care, such as the flexible use of identity labels, vocal pitch modulation, the intensification and historicization of experiences of suffering related to gender identity, and avoiding asking questions about their care so as not to compromise doctors’ impressions of their certainty about medical transition. This dissertation thus shows how linguistic performances are a crucial part of the gender-affirming care process; in other words, whether patients get the access that they need often depends not just on what they say, but how they say it, and what they strategically omit.

Keywords: discourse analysis
language and healthcare
sociocultural linguistics
trans linguistics
Advisor: Hachimi, Atiqa
Design of a Multiparameter Islet-on-a-Chip Device to Measure the Functional Variability of Individual Pancreatic Islets

Pancreatic islets are small micro-organs responsible for glucose-stimulated insulin secretion, which occurs in two phases; a rapid first phase burst followed by a sustained second phase. Islets are commonly studied ex vivo using assays that have poor temporal (>5 min) and spatial (multiple/bulk islets) resolutions. Bulk measurements are highly susceptible to uncoordinated responses, poor treatment penetration and often lack multiparametric capability. These limitations are especially exacerbated by the functional variability of pancreatic islets. The magnitude, rate, and timing of first and second-phase insulin secretion are highly variable between islets. We postulate that this variability is important to the normal function and dysfunction of islets. Hence, studying islets individually can help overcome the limitations of bulk islet studies to enhance our knowledge of functional variability. Our goal here was to measure O2 consumption rates and insulin secretion from individual pancreatic islets with a high spatiotemporal resolution. To achieve this goal, we combined microfluidics with an O2-sensitive probe and biochemical assay. We first developed O2 microsensors using SU-8 microwells to digitize the O2 measurements and a polydimethylsiloxane-based sensor to enhance oxygen diffusion. We fabricated our microfluidic platform out of polymethylmethacrylate to limit diffusion and permeation of external O2 from saturating our measurements. We combined the O2 microsensors and platform to measure islet OCR simultaneously with Ca2+-activity. Glucose-stimulated O2 consumption of individual mouse islets was found to be biphasic with the timing independent of cytoplasmic Ca2+-influx. Finally, we developed an on-chip fluorescence anisotropy immunoassay to measure c-peptide secretion as a surrogate for insulin from individual mouse islets. In this study, we designed a novel islet-on-a-chip that mixes islet effluent with the assay reagents to be imaged downstream of the islet. We showed that islets respond to glucose at varying times with different magnitudes of secretion. Future directions include combining the O2 and c-peptide sensor into the islet-on-a-chip. Overall, this thesis reveals the power of individual islet measurements, which show how current methods have been undermining islet variability. The tools engineered in this thesis provide an individual islet approach to further characterize islet metabolism and to understand the intricacies of healthy and unhealthy islets.

Keywords: Fluorescence Anisotropy
Insulin Secretion
Islet-on-a-chip
Microfluidics
Oxygen Sensor
Pancreatic Islets
Advisor: Rocheleau, Jonathan V