VictorJuiz/thesis huggingface dataset:
Vanadium Dioxide for Memory, Oscillators, and Optical Beam Manipulation

Vanadium dioxide (VO2), which exhibits insulator-metal transition, has been utilized to demonstrate a non-volatile memory and a tunable metasurface device. To realize these devices, fabrication techniques were developed. Different dry etching recipes were created for making VO2 micro-wires depending on the material crystallinity. In addition, a post-fabrication technique using current injection was developed to create single-crystal VO2 micro-wires from initially poly-crystalline samples. The electrical properties of VO2 become more favorable after this recrystallization process. First, we present a VO2 memory device that demonstrated optically addressable nonvolatile memory at room temperature. The combination of electrical and optical stimuli was used to write memory, and the device state could be read out as voltage oscillations even after several days. This is the first time, to our knowledge, that non-volatile memory is observed in VO2 at room temperature. This observation suggests the presence of a metastable phase in the VO2. Although probing the physical nature of this phase was outside the scope of the thesis, the non-volatile memory effect was studied phenomenologically using VO2 micro-wire devices. Second, we show highly tunable optical transmission in a VO2 optical metasurface. The device consisted of gold (Au) gratings on a VO2 thin film. The gratings simultaneously served to enhance the optical transmission and as resistive heaters. As current was applied through the Au gratings, the localized area of VO2 became metallic due to Joule heating. By switching between extraordinary optical transmission when the VO2 was an insulator to a high absorptive state when the VO2 was metallic, the transmission was tunable by 33 dB/mm. Furthermore, another metasurface device is proposed with simulations displaying reconfigurable beam steering capabilities while using only digital switching of the VO2 elements. With the development of fabrication processes along with the demonstrations of nonvolatile memory and beam manipulation with VO2, this thesis expands the opportunities for VO2 to be used in new types of computing and flat optics devices.

Keywords: phase change material
phase transition
vanadium dioxide
Advisor: Poon, Joyce K. S.
Exploring the State of Sexual Health Literacy among Young Black Gay and Other Men who Have Sex with Other Men in Toronto, Ontario, Canada

Despite advancements in diagnosis, treatment and prevention for HIV and other sexually transmitted infections (STIs), young Black gay and other men who have sex with men (YBGM) experience significantly higher HIV rates compared to other young gay and other men who have sex with men. While sexual health literature indicates various socio-structural factors (e.g., systemic racism, low income) contribute to these rates, research on YBGM’s sexual health literacy in Canada is sparse. I developed a qualitative study guided by intersectionality and the social-ecological model theoretical frameworks and methodologically informed by Charmaz’s constructivist grounded theory to begin addressing this scarcity. My primary research question was: what is the state of YBGM’s sexual health literacy? My sub-questions were: 1) what or who are YBGM’s sources of sexual health information?; 2) how do YBGM evaluate the information they gather from these sources? and 3) in what ways, if any, are YBGM applying this information in their everyday lives? Twenty-two YBGM aged 16 to 31 years underwent a socio-demographic survey and one-on-one semi-structured interviews. The first manuscript centered on YBGM’s pre-exposure prophylaxis (PrEP) knowledge. My findings revealed that YBGM’s limited PrEP knowledge was due to healthcare institutions’ inability to effectively disseminate PrEP information coupled with the impact of PrEP stigma and their social locations on this knowledge. Manuscript two explored YBGM’s approaches to evaluating the credibility of key sexual health information sources. My findings countered common narratives in the literature that identified sex-ed, same aged peers and family as key sources. Older Black peers were seen as a key source who used ‘testimonials’, a commonly used knowledge dissemination approach in the Black-African diaspora, to share their experiential sexual health knowledge with YBGM. My final manuscript explored the state of healthcare providers’ sexual health communication skills through the lens of YBGM. Participants’ accounts pointed to providers’ inadequate skills and to the healthcare system’s medicalization of YBGM whereby their race, sexual orientation and/or age automatically categorized them as needing HIV and other STI testing even when they sought non-sexual healthcare. We conclude with the study’s implications on sexual healthcare research, policy and practice.

Keywords: African
Caribbean
Black
HIV
men who have sex with other men
sexual health literacy
STIs
youth
Advisor: Grace , Daniel
Invisible Work and Hidden Labour in Ontario’s Public Education: A Decolonizing Institutional Ethnography of Mothering and Teachers’ Work

This study explores how one institutional text, Ontario’s Parental Engagement Policy (2010), enters into and coordinates the work of mothers and teachers in publicly funded education. An institutional ethnography was conducted based on in-depth interviews with ten mothers and ten teachers of students in Grades 4 to 6 in the Greater Toronto Area (GTA) comprising of the municipalities of Toronto, York, Durham, Peel and Halton. The data was analyzed using Smith’s framework that keeps the institutional ruling relations in view. The findings indicated that Ontario’s Education Act and Parental Engagement Policy operationalized governance through a network of subordinate texts and textually mediated mothering and educational discourse routinely activated through the text-reader dialogic of everyday work. While the efforts of the Ontario policy appeared to invite parents to connect with their children’s teachers to understand schooling and support their children, the data highlighted how the teacher union, the Elementary Teachers’ Federation of Ontario’s professional judgement and professional conduct guidelines subjugate parental engagement by asserting teachers’ expertise over these attempts and efforts. I argue that due to the racist Standard North American Family (SNAF) ideology of Ontario’s Education Act and policy, as well as the power relations of ETFO, mothering work -a valuable contributor to students’ learning outcomes -is largely marginalized and undervalued in GTA schools especially when done by women caught in the intersections of raced-class, immigration trajectories and linguistic hegemonies of socially dominant languages within the North American schooling context. I conclude that ETFO and the Government of Ontario operate as isomorphic organizations with similar relations of ruling that create invisible barriers for parental engagement as well as the advocacy practices of equity-minded, anti-racist teachers. Social change recommendations include community-led, multilingual, outcomes-driven parent advocacy collaborations alongside teacher-led participatory action research to build professional capacity that invites and authentically supports parent partnerships in schooling.

Keywords: Education policy
Institutional Ethnography
Mothering Work
School-Family Partnerships
Sexism and Racism
Teacher Unions
Advisor: Bascia, Nina
Modelling Spatial Location Choice and Transition for a Changing Urban Landscape

This dissertation focuses on the integration of models of spatial location and transportation decision-making that form the core of modern integrated urban models. A conceptual framework for the modelling of household behaviour is developed from the theory of home production. This theory provides a means of integrating individual time-use and household consumption of goods and services in a consistent microeconomic model structure. It is shown that budgetary constraints on time-use and consumption can be used to relate models of long-term location choice with activity-based transportation demand models and macroeconomic models. The dissertation contains six empirical studies that develop elements of the proposed conceptual framework for integrated urban modelling. The first two studies focus on shifts in residential location choice. The first of these studies estimates a residential location choice model that incorporates intra-household negotiations. The second study applies a choice set formation model to a panel of residential location choice data to explore potential shifts in the types of dwellings considered by households. A third location study applies a latent auction approach to establishment location choice. It tests a structural specification of agglomeration using a generalized nested logit correlation structure. The final three empirical studies focus on elements of the home production model. The first of these studies develops a framework for data fusion and synthesis to construct the dataset necessary for the estimation of the home production model. The model is then derived from microeconomic foundations and estimated using this dataset. The final empirical study isolates a component of the home production model; specifically, the relationship between population density and household consumption. Taken together, the components of this dissertation provide a sophisticated framework for the integrated modelling of urban systems and empirical validation of several elements of the framework.

Keywords: Choice modelling
Econometrics
Integrated urban models
Land use
Transportation engineering
Advisor: Nurul Habib, Khandker M.
Discourse-conditioned wh- in situ in L1 Francilian French and as Acquired by Advanced English- and Mandarin-speaking Learners

This dissertation first tests Hamlaoui’s (2011) hypothesis that the use of wh- in situ (SVQ) in colloquial French is conditioned by givenness, specifically, that in situ questions should be favoured when the non wh- portion (SVC) is discourse-given. It then examines first language (L1) influence on the second language acquisition (L2A) of wh- variation in French in two advanced learner groups with typologically distinct L1s: Mandarin, a wh- in situ language, and English, a language that requires obligatory wh- fronting. As concerns the L2 acquisition of wh- variation, our main hypothesis predicts L1-based syntactic influences, namely, the over-dependence on canonical SVQ order for L1-Mandarin and fronted variants for L1-English speakers. To test the hypotheses for both native speakers (NSs) and L2 learners, we conducted a study involving three participant groups (15 NSs, 10 Sinophones, and 10 Anglophones). The principal task was an Oral Discourse Completion Task in which each item elicited a wh- question for a discourse-context intended to favour either a fronted wh- or an SVQ variant. Consistent with Hamlaoui’s hypothesis, NSs used more in situ questions when the SVC portion was given. Importantly, they also preferred SVQ when the SVC portion was not given, which may potentially be attributed to participants’ motivation to be sociostylistically appropriate. We raise the possibility that sociostylistic factors can override discourse-related factors in NSs’ use of the target structures. Regarding the L2 learners, neither group was overly dependent on the canonical wh- order of their L1, and contrary to our prediction, the L1-English but not the L1-Mandarin group’s performance was target-like. We propose that the infelicitous use of fronted wh- variants by the L1-Mandarin group in discourse-given contexts can be explained with reference to L1 influence (namely, a strong preference for the canonical SV sentence order in Mandarin) and the more restricted input of these learners’ academic setting that contrasted with the work setting of the English group, which included exposure to sociopragmatically correct input beneficial to L2 discourse development. Accordingly, our study also highlights the essential role of input quality in the L2A of variable syntactic structures.

Keywords: discourse
English
French
Mandarin
second language acquisition
wh- variation
Advisor: Steele, Jeffrey W
Convergence Rates of Random Discrete Model Curves Approaching SLE Curves in the Scaling Limit

Recently, A. Kempannien and S. Smirnov provided a framework for showing convergence of discrete model interfaces to the corresponding SLE curves. They show that given a uniform bound on specific crossing probabilities one can deduce that the interface has subsequential scaling limits that can be described almost surely by L\"owner evolutions. This leads to the natural question to investigate the rate of convergence to the corresponding SLE curves. F. Johansson Viklund has developed a framework for obtaining a power-law convergence rate to an SLE curve from a power-law convergence rate for the driving function provided some additional geometric information along with an estimate on the growth of the derivative of the SLE map. This framework is applied to the case of the loop-erased random walk. In this thesis, we show that if your interface satisfies the uniform annulus condition proposed by Kempannien and Smirnov then one can deduce the geometric information required to apply Viklund's framework. As an application, we apply the framework to the critical percolation interface. The first step in this direction for critical percolation was done by I. Binder, L. Chayes and H.K. Lei where they proved that the convergence rate of the Cardy-Smirnov observable is polynomial in the size of the lattice. It relies on a careful analysis of the boundary behaviour of conformal maps and their discrete analytic approximations as well as a Percolation construction of the {\it Harris systems}. Further, we exploit the toolbox developed by D. Chelkak for discrete complex analysis on isoradial graphs to show polynomial rate of convergence for the discrete martingale observables for harmonic explorer and the FK Ising model to the corresponding continuum objects. Then, we apply the framework developed above to gain a polynomial convergence rate for the corresponding curves.

Advisor: Binder, Ilia
PDT-SPACE: Automatic Interstitial Photodynamic Therapy Planning and Optimization

Photodynamic Therapy (PDT) is a minimally invasive oncology treatment that uses light-activated photosensitizers to destroy tumors locally. It has been approved for a variety of superficial tumor indications such as the skin. For deep-seated tumors like brain glioma, the treatment (via interstitial light illumination with fiber optic probes) is yet to be approved due to several challenges that hinder its efficacy. Much of the research to improve interstitial PDT’s (iPDT) therapeutic index has been directed towards developing targeted photosensitizers. However, another factor that highly affects iPDT efficacy is the light penetration inside the tissues, especially when the tumor is surrounded by extremelysensitive healthy tissues such as white matter in the brain. This thesis introduces PDT-SPACE, an open-source software for automatic iPDT planning. We present novel computer-aided design (CAD) algorithms to allocate powers to a set of light diffusers and determine the location and lengths of those diffusers in order to minimize the damage to surrounding organs-at-risk (OAR), while maximizing the damage to the tumor. We also generalize the power allocation algorithm to generate tailored power profiles for cylindrical diffusers to better conform the light distribution to the tumor shape and further decrease the damage. We simulate our methods onnine virtual brain tumors constructed from glioblastoma multiforme (GBM) MRI images taken from the cancer imaging archive. Through the various optimizations presented, we show that the treatment plans generated by PDT-SPACE can reduce damage to OAR by more than 70% on average compared to state-of-the-art techniques, while destroying at least 98% of the tumor. Additionally, we present several techniques utilizing machine learning to generate robust treatment plans that take into account inter-patient variations of tissue optical properties. These robust treatment plans are more adaptable to the biological uncertainties of individual patients. Finally, we show how PDT-SPACE serves as a prospective methodology to analyze the effect of different combinations of optimization parameters on iPDT efficacy for various oncological indications while avoiding the technical difficulties that come with in-vivo direct measurements. We present different treatment plans (each with its own trade-off) to treat bone metastasis resulting from colorectal cancer recurrence.

Keywords: Computer-aided Designs
Optimization
Photodynamic Therapy
Treatment Planning
Advisor: Betz, Vaughn
Differentiation of Murine and Human Embryonic Stem Cells on Acellular Lung Scaffolds and Extracellular Matrices

Lung diseases are a leading cause of death worldwide. Due to a lack of knowledge of the underlying pathophysiological mechanisms and absence of treatment, lung transplantation is one of the few live-saving options at the end stage of disease. Although the number of donor lungs for transplantation has increased, the demand is exceeding organ availability. To palliate this situation, one promising avenue is the use of decellularized whole-lung scaffolds to bioengineer a functional lung for transplantation. An ideal cell source to recellularize the cell-free lung scaffolds would be a multipotent cell line that combined with the intrinsic differentiation capacity of the scaffold ECM that would properly repopulate the denuded lung. In Chapter 3, we investigated the hierarchical differentiation process of multipotent ES-derived endoderm cells into proximal airway epithelial cells on acellular lung scaffolds. We found that differentiation of ES-derived endoderm on decellularized lung scaffolds towards airway epithelium proceeds via TP63+ basal cell progenitors and tracks a regenerative repair pathway. Our findings support the use of airway basal cells for repopulating the proximal airway side of an acellular lung scaffold.Another approach to lessen the burden of lung diseases is to develop organotypic models that can be used to study pathogenesis and optimize treatment, including cell therapy. To model distal (alveolar) lung disease with alveolar organoids using pluripotent stem cells we need to reproduce the alveolar niche. In Chapter 4, we investigated whether replicating the cellular and matrix environment of the alveolus enhances the differentiation of human lung progenitor cells into alveolar type 2 (AEC2) cells. We found that a 3D organisation and mesenchyme-derived chemical cues were key for the differentiation of ESC into AEC2 while matrix-derived cues were inhibitory. A lot remains to be done prior to modeling distal lung disease, but understanding the role of all constituents of the alveolar niche will bring us closer to it.

Keywords: Acellular scaffold
Alveolar organoid
Epithelial cells
Pulmonary disease
Regenerative medicine
Stem cell
Advisor: Post, Martin
Modeling the Mechanistic and Therapeutic Roles of Allele Specific Copy Number Alterations in Cancer

Aneuploidy, loosely defined as an imbalance of chromosomes, is found in ~90% of all solid tumors and can affect ~33% of the genome ranging from focal aberrations to an entire chromosome or chromosomal-arm. Despite this overwhelming prevalence and severity, copy-number based biomarkers are typically represented at the gene-level and any allelic imbalance is largely ignored. In this thesis, I explore the mechanistic and therapeutic roles of allele-specific copy-number (ASCN) aberrations in cancer and how it compares to an absolute copy-number analysis. I illustrate the mechanistic relevance of ASCN profiles by using a multi-omic and meta-analysis approach to uncover a highly conserved copy-neutral loss-of- heterozygosity pattern in pancreatic neuroendocrine tumors (PANETs). By inferring molecular timing of the somatic mutations in the context of purity and ploidy, I proposed an evolutionary model for a subset of aggressive PANETs that is initiated by mutation of MEN1, ATRX and DAXX. These insights aid in disease risk stratification and guide the way for exploring clinically relevant therapeutic vulnerabilities. I developed two strategies to gauge the therapeutic relevance of ASCN profiles. First, I describe CCLid, a method I developed to cross-validate the genetic identity and karyotypic similarity of 1,497 unique cell lines found in three large pharmacogenomic datasets. I show that genetic drift is widely prevalent between cell lines and that genetic drift occurs between molecular profiles of the same cell line within a single dataset. Second, I employ a deep learning algorithm that utilizes these ASCN profiles to predict cancer-type and drug-response across these same datasets. I use a Hilbert space-filling curve to map the ASCN profiles of these cell lines to a compressed 2D visualization for use in convolutional neural networks. In comparison to a total copy-number predictor that utilizes either gene- or bin-level features, I found that the ASCN encoding can better predict both cancer-types and drug-response. These results suggest that an ASCN approach can be used to boost other molecular profiles to provide a cohesive view of biological mechanisms guiding tumorigenesis, as well as effectively used to improve the performance of predictive models that use copy-number features.

Keywords: Aneuploidy
Biomarkers
Cancer
Copy-number
Pharmacogenomics
Advisor: Pugh, Trevor J
Haibe-Kains, Benjamin
Optimal Control and Mean-Field Game Approaches in Renewable Energy Markets

SREC markets are market based systems designed to incentivize the production of energy from solar means. A regulator imposes a floor on the amount of energy each regulated firm must generate from solar power in a given period and provides them with certificates for each generated MWh. Firms offset these certificates against the floor and pay a penalty for any lacking certificates. Certificates are tradable assets, allowing firms to purchase/sell them freely. This thesis investigates the problem of optimal behaviour for both regulated firms and regulators in SREC markets by leveraging techniques from stochastic control, mean field games, and principalagent games, accounting for the costs the agents regulated by SREC markets face, and their interaction amongst one another. The thesis contains three main parts, with increasing levels of complexity. In the first, we study the optimal control problem faced by a single agent optimizing their behaviour within an SREC market. We propose a model for the firm’s costs and for the prevailing SREC price, which incorporates generation costs, trading costs, and price impacts. Using the Stochastic Maximum Principle, we obtain optimality conditions for said firm’s optimal behaviour. We develop a numerical algorithm to obtain their optimal controls, conduct myriad experiments, and validate our theoretical optimality conditions. Following this, we consider the possible interactions regulated firms may have on one another, by simultaneously solving for all regulated firms’ behaviour to obtain a Nash equilibrium, using tools from mean field games and variational analysis. This requires approximating an SREC market, which has finite regulated agents, with an infinite-player version; however, we show that such an approximation is justified, and the optimal firm behaviour for the infinite-player market satisfies an -Nash equilibrium property in finite population samples. Finally, we flip the perspective by considering the goals of the regulator in SREC markets, and studying their optimal design. We study this from a theoretical and numerical perspective, imposing a parametric family of possible market designs to make the numerical analysis tractable, as the theoretical analysis does not yet allow for complete solutions.

Keywords: emissions markets
mean field games
stochastic control
Advisor: Jaimungal, Sebastian