VictorJuiz/thesis huggingface dataset:
Entangled Photon Pair Sources based on Periodically Poled Silica Fiber

Entangled photons are a fundamental resource in quantum applications. Broadband entangled photon sources have been used in applications such as high-resolution quantum sensing and wavelength-multiplexed quantum communication. In particular, in fiber-based quantum applications such as long-distance quantum clock synchronization and quantum key distribution in deployed fiber networks, a practical entangled source that is robust and compatible with silica fiber is highly sought after. Periodically poled silica fiber (PPSF) has been demonstrated to be a promising resource of entangled photon-pairs. PPSF uses the induced second-order nonlinearity in poled fiber to generate polarization-entangled photon pairs based on type-II spontaneous parametric down-conversion. The negligible group birefringence of the PPSF ensures high-quality and broadband polarization entanglement without compensation, making it particularly suitable for these quantum applications. The PPSF-based source has a lot of potentials to be tapped because of its high entanglement quality, broadband emission bandwidth, simple structure, and its compatibility with the existing fiber infrastructure. In this thesis, I focus on the development of the PPSF-based entangled photon sources. I first investigate the design and the manufacturing process of the PPSF where I try to produce PPSF with improved performance and innovative properties. Next, I study the compensation-free nature of the PPSF-based polarization entanglement source and discuss the interplay between dispersion, birefringence, emission bandwidth, and polarization entanglement. Based on the theory, a commercial PPSF-based photon-pair source prototype is developed and patented. It has to my knowledge the simplest design of all polarization-entangled sources reported so far in the literature. Furthermore, I broaden the biphoton bandwidth by building a PPSF photon-pair source that emits biphotons at telecom O-band. With more than 24THz bandwidth, the biphotons generated in this source are the broadest of all O-band polarization-entangled photon sources reported to my knowledge. I also propose and experimentally demonstrate a polarization-frequency hyperentangled photon source using PPSF, which provides higher dimensionality by making use of entanglement in multiple degrees of freedom. Overall, this thesis contributes to the development of PPSF technology for practical quantum applications. I anticipate that the PPSF-based photon-pair source will play an important role in the era of quantum technology.

Keywords: Entangled photons
Quantum entanglement
Advisor: Qian, Li
Neurobiological and Computational Approaches to Behavioural Flexibility

Behavioural flexibility is important in a changing environment. Prior experiences are stored as memories which can be utilized to make decisions in novel environments. These memories can promote or reduce behavioural flexibility in novel environments. The hippocampus is intimately involved with learning and memory and its engagement in this process depends on the age of the memory. Taking these ideas into consideration, I developed an automated Y-maze to test behavioural flexibility in response to a variety of changes in the environment. Mice were trained on a random shift paradigm to ensure that they could continuously explore the Y-maze and learn to poke at the end of the arms to receive rewards. Next, they were tested on a textural discrimination paradigm to ensure that they could learn texture-reward associations that were constantly shifting in the maze. In order to indirectly investigate hippocampal contributions to behavioural flexibility we tested how systems consolidation affects flexibility in response to: (1) value changes and (2)changes in the optimal sequence of actions. Mice were trained to obtain rewards in a Y-maze by switching nose pokes between three arms. During training, all arms were rewarded and mice simply had to switch arms in order to maximize rewards. Then, after a 1 or 28 day delay, we devalued one arm, or we reinforced a specific sequence of pokes. We found that after a 1 day delay mice adapted easily to the changes. In contrast, mice given a 28 day delay struggled to adapt, especially for changes to the optimal sequence of actions. Immediate early gene imaging suggested that the 28 day mice were less reliant on their hippocampus and more reliant on their medial prefrontal cortex. Lastly, I used reinforcement learning to understand the possible computations underlying the facilitation of behavioural flexibility seen in these tasks. Model-free and model-based algorithms were trained and tested in virtual environments that paralleled the setup of the Y-maze experiments. I found that model-based algorithms were able to adapt more efficiently to action devaluations and optimal sequence changes suggesting that the hippocampus may be performing model-based reinforcement learning to facilitate behavioural flexibility.

Keywords: Behavioural Flexibility
Learning
Memory
Reinforcement Learning
Systems Consolidation
Advisor: Richards, Blake A.
Database Representations of English Literature, 1789–99

How are historic texts selected for digitization in mass digital archives? It can be surprisingly challenging to know what is in the databases which now implicitly structure nearly all literary research. These resources, therefore, may operate as “black boxes,” complex equipment whose operations are mysterious to users. Examining the specific institutional histories of four literary databases, I explore how the scholarly practice of historical recovery might adapt to the site of the database. I measure and historicize uneven digitization as it might affect women writers of the late eighteenth century, to shed light on broader processes of textual selection. Specifically, I examine the English Short Title Catalogue (ESTC), Eighteenth Century Collections Online (ECCO), the Text Creation Partnership (TCP), and HathiTrust. I describe the development of these databases from the 1970s to the present. I then compare each database’s holdings of works published in England 1789–99, manually identifying how many works are attributed to women. I find that these databases in fact marginalize “authorless” works, namely, those which are unsigned, attributed to unidentified pseudonyms, or written by corporate authors. To bridge literary and archival understandings of textual value, I present a definition of value as a principle of selection, arguing that a site of textual selection is also a site of textual valuation.

Keywords: digital archives
digital humanities
digitization
eighteenth century
Advisor: Gillespie, Alexandra
Robinson, Terry F
Developing the Breast Utility Instrument to Assess Health-related Quality of Life and Preferences in Patients with Breast Cancer

Breast cancer (BrC) is the most common cancer in women worldwide, however no BrC-specific preference-based instrument exists. BrC and its treatments can impact patients’ health-related quality of life (HRQoL). Understanding HRQoL in women with BrC is therefore important in guiding clinical decision-making, and health policy development. The overall objective of this research is to develop the Breast Utility Instrument (BUI), a BrC-specific preference-based instrument. In this thesis, I select the core items of the BUI derived from the psychometric instrument, European Organisation for Research and Treatment of Cancer (EORTC) quality of life core questionnaire (QLQ-C30) and breast cancer module (BR45), over three studies.The first study includes a scoping literature review of published condition-specific preference-based instruments (CSPBI) which use item response theory and Rasch analysis in their development. Through a comparison of this literature with established frameworks, I present a four phase, 17-step framework for CSPBI development. In the second study, I conduct confirmatory factor analysis on the responses of 408 patients with BrC to the QLQ-C30 and BR45, establishing a 10-dimension structure with good overall fit. In the third study, I first conduct Rasch analysis on each of the 10 dimensions evaluating global model fit, item fit, differential item functioning (age), and unidimensionality. For items that fit the Rasch model, one item was selected per dimension based on breadth of item thresholds, and high patient (n = 81) and clinician importance-ratings (n = 13), and clinical relevance. Based on a priori item selection criteria, I selected: 1) Physical functioning (Trouble taking a long walk), 2) Emotional functioning (Worry), 3) Social functioning (Interfering with social activities), 4) Pain (Having pain), 5) Fatigue (Tired), 6) Body image (Dissatisfied with your body), 7) Systemic therapy side effects (Hair loss), 8) Sexual functioning (Interest in sex), 9) Breast symptoms (Oversensitive breast), 10) Endocrine therapy symptoms (Problems with your joints). This thesis proposes 10-items for the BUI. Future research will estimate patient and community preference-weights and assess reliability and criterion validity of the BUI. The future BUI will improve health care decisions in BrC by incorporating both patient’s own and community preferences.

Keywords: Breast cancer
Confirmatory factor analysis
Health utilities
Health-related quality of life
Rasch analysis
Scoping review
Advisor: Krahn, Murray D
Davis, Aileen M
Sqilxw Educator Rising: Relationality as Methodology in a Social Work Abolitionist Framework

Wai, iskwis (my name is), Percy Lezard. Sqilxw ways, personal introductions come before any other words. I am outma sqilxw I was born into a family of sexʷwrmin̓ (firekeepers). This research demonstrates how I as a sqilxw stamya? educator have been able to survive and thrive, through my sqilxw identity and Indigenous knowledges, in mainstream post-secondary education institutions. I have used myself as both the subject and researcher within the social context of post-secondary social work settings, with an insider’s vantage point to chronicle my own pedagogical transition, using the qualitative methodology of relationality. Through my interpretations and reflections about two post-secondary programs, I use comparison to highlight the complexities of their strengths and inadequacies. This work includes my account as an Indigenous scholar working within a college program grounded in feminist theory, and a university department grounded in an anti-oppression/anti-racism framework. It explores experiences of anti-Indigenous racism, cis-sexism, pushback for my position of solidarity with Black liberation, and oppressions within a disability justice framework. Using the methodology of relationality, I share the experiences I have encountered and the problems I have faced, to facilitate an understanding of the processes of transition. As the genre of qualitative research brings the reader closer to the subculture studied through the experiences of the author, my work serves to provide an evaluation and insights into the cultures of these two learning environments. Data gathering consisted of a reflexive journal, my personal calendar, faculty agendas, staff memos, and reflective analysis. As well, in each of the institutions, I was able to gather support and insight through ceremony and interactions with Knowledge Keepers and Elders. In this way, I was able to reflect upon teachings and to apply Indigenous knowledges to my work. These research tools were used to capture the experiences of my transition. The results of this study were expressed in a personal narrative that comprises of Section 1: Situation, Owing, Questioning. Section 2: How did I come to formulating an Abolitionist Social Work Framework? Section 3: History of Social Work Harms. Section 4: Alternatives Section 5: Vision and closing remarks

Keywords: 2 Spirit
Abolition
Harm Reduction
Indigenous Knowledge
Radical Relationality
Transgender
Advisor: Walcott, Rinaldo
Liquid Atomization by an Electrostatic Rotating Bell Atomizer and Spray Deposition on Solid Surfaces

In an electrostatic rotating bell (ESRB) atomizer, fluid is driven from a central orifice over the bell-cup’s surface towards its edge by the centrifugal force. After the fluid is ejected, it breaks up into droplets. Images of these spray droplets were captured using a DropSizer while operating the bell-cup at various angular frequencies (ω). After processing the images to obtain the droplet sizes, the Sauter mean diameter (SMD) was found to decrease as the angular frequency was increased. Furthermore, a stretching rate γ ̇=ω^2 R/U ̅, where R is the distance from the axis of rotation, was derived for ligaments ejected from a serrated bell-cup and it was shown that the SMD ∝ γ ̇^(-0.5).To determine how spray droplets cover a surface, images of an ESRB atomizer spraying a 20 wt% aqueous glycerol solution on a vertical glass substrate were captured from behind using a high-speed camera. The fraction of surface area coverage was obtained by processing each image. An analytical model was developed based on probability theory and used to predict, with good agreement, the fraction of surface covered by solely using the rate of droplet impingement and the droplet size. A minimum theoretical film thickness assuming full coverage was derived from the probabilistic model; when divided by the droplet diameter, it was found to be dependent only on the droplet spread factor. Droplet/surface interaction is not limited to spreading and drawback when spray droplets impinge on surfaces that are porous. As such, water was atomized using a full-cone nozzle and sprayed onto various vertical stainless-steel meshes. The mass of liquid that penetrated the mesh was measured using a scale, and images of each mesh surface were captured during droplet impingement. It was observed that droplets that landed near unblocked pores of a mesh were leached by neighbouring pools of liquid, delaying the blockage of some pores. A stochastic model, developed to determine the mass of liquid that penetrates a vertical mesh, compared well with experimental measurements. In the model, the volume required to block a pore was a function of the number of surrounding blocked pores and the mesh’s open-area ratio.

Keywords: Atomization
Coatings
ESRB Atomizers
Liquid Films
Sprays
Surface Coverage
Advisor: Chandra, Sanjeev
Arterial Spin-labelled MRI Analyses to Advance Adolescent Bipolar Disorder Research and Clinical Applications

Cerebral blood flow (CBF) is foundational to brain function in health and disease. Through three distinct analyses, the aim of this thesis is to extend current understanding of CBF in adolescent bipolar disorder and to enable future understanding of CBF in other brain diseases. CBF measurement can interrogate the putative vascular underpinnings of bipolar disorder, however, the extent of CBF changes in the early stages of the disease is unknown. ASL MRI allows non-invasive imaging of brain physiology, including CBF, and is especially valuable when invasive methods are inappropriate, such as in adolescent psychiatry. Yet, technical advancements have only recently supported wider availability of ASL and this thesis focuses on remaining opportunities to: 1) study the multivariate relationships of CBF between brain regions in health and disease and 2) continue technological advancement of ASL workflows for researchers and clinicians alike.In the first study of this thesis, I present an analysis of multivariate patterns of CBF, and their relationship to neuroanatomy, in a large group of adolescents with and without bipolar disorder. The results show differences between adolescents with and without bipolar disorder with respect to patterns of CBF and their correspondence to inter-regional relationships of brain anatomy. In the second study, I identified a multivariate CBF phenotype related to adolescent bipolar disorder. This analysis extends that of the first study by using patterns of CBF in a classification scheme based on participant diagnosis. In the third study, I develop a fast and automated CBF image synthesis algorithm to address a bottleneck in the workflow of advanced ASL MRI. I demonstrate a significant analysis speedup over a standard workflow, show capability of hemodynamic parameter uncertainty estimation, and present preliminary evidence of generalizability to specific acquisition parameters. This thesis employs three distinct ASL analyses to show multivariate phenotypes of CBF in adolescent bipolar disorder, and to support future study of CBF through image processing methods development. Together, these studies act toward understanding the physiological underpinnings of bipolar disorder, develop methods for CBF image analysis and synthesis, and support broad application of ASL in clinical neuroimaging research.

Keywords: arterial spin labelling
bipolar disorder
cerebral blood flow
deep learning
magnetic resonance imaging
Advisor: MacIntosh, Bradley J
On the Regulation of Metabolic Flux by Small Molecules

Metabolism is precisely coordinated around the goal of balancing fluxes to maintain robust growth. Hierarchical regulatory mechanisms for controlling metabolic fluxes, from transcriptional regulation of genes to direct modulation of enzyme activity by small-molecule regulation (SMR) have evolved to achieve this goal. While SMR is ubiquitous in metabolism, the organizational principles of the networks formed by SMR interactions and their generalized role in metabolic coordination is not well understood. In particular, questions such as which metabolites are optimal regulators, which reactions are optimal targets of regulation, and what information is communicated via this form of regulation remain open. Answering these questions is essential to uncovering the fundamental constraints that have shaped metabolic evolution, and a systematic understanding of such constraints is required for forward engineering of metabolic systems. In this work, a constraint-and structure-based approach is taken to addressing these questions. First, multi-omics data from Escherichia coli and Saccharomyces cerevisiae are used to show that flux sensing arises due to thermodynamic constraints on consuming reactions, so some metabolites always carry information about upstream rates. These data suggest that a standard Gibbs free energy of at least -4 kJ/mol for any consuming reaction is sufficient to make substrate flux sensitivity likely. Since flux-sensitive metabolites carry information about fluxes, they are optimal controllers of the fate of upstream flux via feedforward regulation. Next, a reconstruction of the genome-scale E. coli SMR network (SMRN) is used to show that higher-order regulatory structures, namely incoherent feedforward loops, are conserved. These loops are structured and tuned to use flux-sensitive metabolites to distinguish between flux distributions and provide differential control of supply and demand fluxes in different metabolic states. Finally, the SMRN is re-cast as a thermodynamic network to show that indeed regulators are most often substrates of thermodynamically constrained reactions. Mechanistically, this is because they maximize information transfer in the conditions in which information would normally be lost. Maximization of information transfer is thus hypothesized as an underlying design principle of SMR.

Keywords: Allostery
Constraint-Based Modelling
Information Theory
Metabolic Engineering
Metabolic Regulation
Thermodynamics
Advisor: Mahadevan, Radhakrishnan
Catherine Malabou's Dangerous Supplement

I am interested in cases in which life’s very viability seems to rest on the destruction of what life, up to a certain point, has been. How can destruction itself be salvific? How might one save oneself, or be saved, precisely by leaving oneself, or by being forced or prompted to leave oneself, behind? As a means of engaging with these questions, I undertake an in-depth examination of Catherine Malabou’s hydra-headed conception of transformation: ‘plasticity.’ Malabou associates plasticity with the production of a ‘way out’ of constraining or subjugating situations precisely when these situations are characterized by an absence of a way out, yet often the subjects she describes as undergoing plastic processes seem worse off for changing. I suggest that this is because they undergo a form of change that is incompatible with the forms of continuity and marks of alterity (traces of the shaping influence of others and otherness) which characterize an alternative type of radical change highlighted within the continental tradition. Malabou, I show, relinquishes the resources she needs to think forms of change which would be radical yet salvific through her rejection of concepts central to Derrida’s discourse (the ‘trace’ and its variants). I indicate why the form of change the latter help render intelligible (‘autoimmune’ change) is central to projects of resistance, as these are construed by Foucault and feminist theorists who have taken Foucault’s key tenets seriously. I argue that this is a form of change Malabou’s theoretical apparatus must accommodate if its own emancipatory promise is to be borne out, and that, to reanimate its promise, we must supplement ‘plasticity’ with the Derridean resources Malabou casts off. Malabou’s own theoretical commitments, I show, constrain her to think this form of change for the sake of her framework’s coherence. Beyond this, ‘plasticity’ will only effectively subvert certain contemporary forms of power if its meaning is broadened in the ways I’ve described. To make this point, I consider, in my final chapter, how plasticity rejoined with autoimmunity can help us politicize depression when contemporary depression discourse (a form of power) does otherwise.

Keywords: Catherine Malabou
Continental Philosophy
Depression discourse
Derrida
Feminist Philosophy
Foucault
Advisor: Comay, Rebecca