VictorJuiz/thesis huggingface dataset:
Development of a Breast Cancer Cell Microenvironment in Three-Dimensional Hyaluronic Acid Based Hydrogels

Breast cancer cell invasion is influenced by the tumor microenvironment including the extracellular matrix, mechanical properties, stromal cells, and bioactive factors. To elucidate the role of the microenvironment on cell invasion, defined 3-dimensional hydrogel models are required because xenograft models are too complex and 2-dimensional models lack a matrix for cell invasion and often do not recapitulate the appropriate mechanical properties. Breast cancer cell invasion is also influenced by gradients of epidermal growth factor (EGF); however, studying the influence of EGF gradients is challenging due to their transient nature and convoluted in vivo models. In this work, a hyaluronic acid (HA) based hydrogel crosslinked with matrix metalloproteinase (MMP) cleavable peptides (HA/MMPx) was developed to study the role of the microenvironment on breast cancer cell invasion. Specifically, crosslink density, adhesive ligand density, and MMP cleavable peptides were evaluated. Defined EGF gradients were photochemically immobilized into HA/MMPx hydrogels to evaluate the invasion and drug response of breast cancer cells with different EGF receptor (EGFR) expression levels. The crosslink and ligand densities of HA/MMPx hydrogels were decoupled to elucidate their effect on the invasion of MDA-MB-231 breast cancer cells. Increasing crosslink density decreased MDA-MB-231 invasion because more crosslinks had to be degraded for the cells to move through the hydrogel. Increasing adhesive ligand (GRGDS) density did not effect MDA-MB-231 invasion, but did increase cell number. The MMP cleavable crosslinker increased MDA-MB-231 cell invasion relative to a non-cleavable control, confirming that invasion is facilitated by cell-mediated matrix degradation. Immobilized EGF gradients in the HA/MMPx hydrogels differentially affected breast cancer cells with varying levels of EGFR expression: EGF gradients increased the invasion of moderate EGFR expressing MDA-MB-231 cells, decreased the invasion of high EGFR expressing MDA-MB-468 cells, and had no effect on low EGFR expressing MCF-7 cells. The EGFR inhibitor cetuixmab reversed the effects of EGF, decreasing MDA-MB-231 and increasing MDA-MB-468 cell invasion on EGF gradients. With these studies, we developed a versatile platform to study the influence of the microenvironment on breast cancer cell invasion and demonstrated the importance of including microenvironmental factors in culturing platforms when evaluating drugs that target these interactions.

Keywords: Breast cancer
Epidermal growth factor
Gradients
Hydrogel
Invasion
Photochemistry
Advisor: Shoichet, Molly S.
ASCL1 directs the neuronal fate of neoplastic cells in glioblastoma

Tumours represent aberrant organogenesis with growth caused by unlimited proliferation and failure of differentiation of malignant precursor cells. I propose that defects in lineage commitment lock neoplastic cells in a self-renewing state that fuels tumour growth and treatment resistance. Thus, promoting terminal differentiation would limit clonal expansion and attenuate tumour growth. Herein, I identified that a substantial subset of patient-derived glioblastoma stem-like cells (GSCs) express ASCL1 (ASCL1hi GSCs), a proneural transcription factor involved in the generation of differentiated neurons during development and adult neurogenesis. In contrast to low expressing (ASCL1lo) GSCs, ASCL1hi GSCs are competent to undergo neuronal differentiation. The balance between self-renewal and differentiation in ASCL1hi GSCs is governed by Notch signaling, which can be manipulated with small molecules. Blocking Notch signaling in ASCL1hi GSCs increases levels of ASCL1, and leads to loss of self-renewal with neuronal commitment. Critically, even in a neoplastic context, enforced ASCL1 expression in ASCL1lo GSCs rescues neuronal differentiation competency, promotes terminal commitment, and attenuates tumourigenicity in vivo. Induction of ASCL1 results in new sites of open chromatin promoting expression of neuronal target genes, suggesting it functions as a pioneer factor to reorganize the chromatin enabling neuronal differentiation in the neoplastic context.

Advisor: Dirks, Peter B
Adaptive Blocker Cancellation For Wireless Receivers

This thesis targets cancellation of unwanted signals (blockers), one of the most difficult requirements for a wireless receiver. Current state-of-the-art analog filtering ADCs are analyzed and compared in detail. Recognizing that the analog circuitry requires accurate calibration and PVT correction, a digital filtering ADC in the baseband is proposed that has a digitally defined transfer function that is highly reconfigurable and insensitive to PVT variations. A blocker adaptation algorithm is also presented that tracks the blocker in real time and takes approximately 26ms to converge. The proposed architecture is demonstrated in a wireless receiver prototype implemented in 28nm CMOS technology. The measured programmable digital filter provides 34.9dB attenuation of TX leakage and variable attenuation of an additional blocker anywhere in the frequency range 17.5MHz–107.5MHz. The receiver front-end operates at 1.8GHz with a noise figure of 3.9dB, IIP3 of -5dBm, and consumes only 20.4–37.5mW, the lowest among state-of-the-art designs.

Advisor: Chan Carusone, Anthony
Liscdini, Antonio
In Vivo Role of Hepatic JAK2 and IGF-1 in Atherosclerosis

Non-alcoholic fatty liver disease (NAFLD) is an emerging independent risk factor for cardiovascular disease (CVD). However, our current understanding of the underlying mechanism by which fatty liver per se increases atherosclerosis risk remains unclear and is difficult to delineate due to its common association with other metabolic abnormalities. In this thesis, genetically modified atherosclerosis-prone ApoE-null and Ldlr-null mouse models were used to investigate the essential role of hepatic Jak2 in atherogenesis. I assessed the role of circulating IGF-1 as a mechanistic link between NAFLD and atherosclerosis. In chapter 4, I describe the consequences of deleting hepatic Jak2 on atherosclerosis development and progression. I show that hepatic Jak2-deficiency resulted in profound fatty liver without other confounding cardiovascular risk factors, and this was accompanied by accelerated atherosclerosis with increased plaque macrophages and decreased plaque smooth muscle cell content. Furthermore, I demonstrate that reduced circulating IGF-1 played a causal role in exacerbating atherosclerosis that occurred with hepatic Jak2-deficiency, which was attenuated by pharmacologic or genetic restoration of circulating IGF-1. I next assessed the essential role of hepatic IGF-1 in atherogenesis. In chapter 5, I show that disruption of hepatic Igf1 and reduction of circulating IGF-1 did not phenocopy hepatic Jak2-deficient mice with accelerated atherosclerosis. In fact, hepatic Igf1-deficiency led to a significant reduction in atherosclerosis particularly in female mice. Interestingly, female hepatic Igf1-deficient mice also displayed profound hepatic steatosis with reduced circulating IL-6 and triglycerides. Taken together, the results presented in this thesis reveal a novel mechanistic link between NAFLD and atherosclerosis through hepatic Jak2 that provides atheroprotection. While restoration of IGF-1 partially attenuates the accelerated atherosclerosis in hepatic Jak2-deficient mice, endogenous hepatic IGF-1 does not appear to be essential in atheroprotection. These results illustrate the complexity in the regulation of atherosclerosis that is mediated by hepatic JAK2 signaling. Clear understanding of how hepatic signaling affects atherosclerosis can lead to novel therapeutic strategies to combat CVD.

Keywords: Atherosclerosis
IGF-1
JAK2
NAFLD
Advisor: Woo, Minna N
A Multi-scale Metabolic Model of the Whole-Human Body

Model-based design (MBD) is a well-known approach in the biomedical and health sciences research community. It has a significant impact for answering important questions related to human metabolism, systems pharmacology, precision medicine, epidemiology and public health. Multi-scale modelling is one of the MBD approaches to analyze and study complex biological systems like the human body. However, there are some challenges associated with this approach. For instance, a lack of systematic integration methods, a lack of efficient computational algorithms, and difficulty for model validation. This thesis aims to meet these challenges. First, I present a multi-scale modelling framework that was developed using a dynamic parsimonious flux balance analysis technique. The mechanistic model integrates the metabolomic and genomic data with human physiology. Simulations are performed to demonstrate the computational efficiency of integration algorithm. Then, I use the proposed model to identify biomarkers for inborn errors of metabolism. I explore how the developed model can be used to predict blood alcohol concentrations. Here, in vivo data are integrated with the metabolic model to validate the prediction results. In the next section of the thesis, I develop a mathematical model for low-density lipoprotein cholesterol (LDL-C) regulation in the body. The proposed model integrates the metabolic pathway for cholesterol synthesis, hepatic LDL receptor (LDLRs) signaling pathway, and proprotein convertase subtilisin/kexin type 9 (PCSK9) mechanism to degrade LDLRs at the surface of the hepatocyte cells. Circulating PCSK9 increases endosomal and lysosomal degradation of hepatic LDL receptors, resulting in the decreased ability to clear LDL-C from the circulation. Experimental evidence and previous studies are used to obtain the parameters of the model. The LDL-C model is employed to predict the effect of anti-PCSK9 and statin drugs on LDL-C levels in a certain populations with hypercholesterolemia. In the next part of the research, I develop an algorithm to estimate drug dosage for individual patients with hyperuricemia. The proposed computational algorithm uses the multi-scale modelling framework to create individual disease models. An in silico study shows the potential of proposed modelling framework in precision medicine. Finally, aligned with the research objective, I develop a new modelling framework to capture multiple functions of the liver cells simultaneously. The simulation results show that the developed model has promise with respect to computational efficiency, convergence and robustness. The proposed multi-scale metabolic modelling framework integrating genomic and metabolomic data presented in this thesis should aid biomedical engineers and clinicians to address different health-related problems such as obesity, diabetes, cardiovascular, and genetic diseases.

Keywords: Genome-scale Model
Human Metabolism
Inborn Error of Metabolism
Multi-Scale Modelling
Precision Medicine
Quantitative Pharmacology
Advisor: Mahadevan, Radhakrishnan
R. Cluett, Will
Modelling Hospital Surge with Data-Driven Discrete Event Simulation

Many Canadian hospitals run at or near capacity, frequently experiencing congestion due to surges in demand. “Surge Protocols” that formally define when and what kind of operational steps can be taken to alleviate congestion are routinely in use. Decisions across the hospital, regarding bed capacity and allocation, staffing levels, and the surgical block schedule influence the frequency and severity of congestion, which in turn manifests in high bed occupancy, delayed admissions, a crowded Emergency Department, surgical cancellations and increased use of surge protocols. A generic, data-driven, discrete event simulation is presented that helps hospitals assess the impact of hospital wide decisions and surge policies on each area of the hospital. The model was developed in cooperation with two hospitals, and then applied at two additional hospitals.

Keywords: generic discrete event simulation
Healthcare
Hospital modelling
Operations Research
Surge modelling
Advisor: Carter, Michael W
Advancing Microfluidic Assays toward Personalized Multiple Myeloma Cancer Therapy Selection

Cancer treatment selection is hindered by a lack of personalized data, relying instead on empirical evidence to justify treatment selection. For multiple myeloma (MM), a hematologic cancer, treatment selection is complicated by the occurrence of drug resistance, and patients have been observed to respond in an unpredictable fashion. To address these challenges, there is a need for more personalized treatment selection methods. Since the 1950’s, tools and assays for testing individual patient samples with a variety of drug treatments, called chemosensitivity and resistance assays (CSRAs), have been under development. There are currently no CSRAs approved for clinical use due to a lack of data supporting improved clinical outcomes compared to current empirical methods. A lack of improved clinical outcomes has been linked to limitations associated with the tools and methods used to perform these assays, as they require higher quantities of patient sample than some patients can provide, and they do not sufficiently mimic in vivo conditions. To address these limitations, my objective was to produce several individual advances for a platform previously developed to study MM. Using microfabrication and device material characterization, poly(dimethylsiloxane) (PDMS) drug absorption and its impact on cytotoxicity assays was studied. Diffusion modelling and analysis was performed alongside physical experiments to confirm near-uniform soluble factor diffusion across microsystems. Cell population heterogeneity measures were used to study the effects of varying cell population to assess the feasibility of reducing cell seeding populations. Finally, the importance of accurately mimicking in vivo drug treatment concentrations was assessed by comparing two approaches for analyzing cytotoxicity assay data. The combination of these advancements positions the platform for further application in clinical studies, and to further our basic understanding of MM, with a specific focus on disease progression and drug resistance.

Keywords: Co-culture
CSRA
Microengineering
Microfluidics
Multiple Myeloma
personalized
Advisor: Young, Edmond WK
Coupled Education and Labour Markets

This thesis combines two major projects: a dynamic and a two-dimensional extension of an existing coupled labour and education matching market ([13] and [27]). The first extension addresses the dynamics of the distribution of skills in a population over many generations. Two overlapping generation models are proposed: the first assumes complete information, which allows (and requires) all generations to be solved simultaneously, while the second assumes incomplete information, forcing the competitive equilibrium at each subsequent generation to be found iteratively. Both models combine a labour and an education matching problem. The skill distribution for each generation of adults is determined from that of the previous generation by the educational matching market. We present conditions for the sequence of adult skills to converge. Next, we study the asymptotic which is specific to each model. For the incomplete information model we prove that, if the sequence of wage functions over the generations converges, the limiting steady state solves the steady state model of [13], which allows for an explicit formulation for solutions of [13]. To study the limiting society of the complete information model, we introduce a new steady state model, which includes a discounting factor to reduce the impact of future generations relative to how far in the future they are. The second extension provides proofs for certain results stated in the study of the steady state model when individuals’ skills are two dimensional [27] and presents more rigorous proofs for some of their results. In particular, we prove strong duality and existence of solutions, following [13].

Advisor: McCann, Robert J.
A Case Study in Meaning-making in a University-level Expressive Writing Class

In this dissertation, I address this concern and extend the literature on writing-reading connections by examining literacy in an expressivist classroom. The study sought to answer three questions: 1) What is each student’s understanding of reading, writing, and editing before, during, and after taking Expressive Writing? 2) How does each student conceptualize the roles of reader, writer, and editor, and how do these concepts change over the life of the course? 3) What are the characteristics of each student’s writing at the beginning, middle, and end of the course? To answer these questions, I observed a section of Expressive Writing at the University of Toronto Mississauga, wrote a series of case studies detailing the experiences of three students, and analyzed writing students produced for the course. The study showed that Expressive Writing connects reading and writing through editing. The course taught students editorial technique and strategy, and by learning how to edit, students learned new ways of reading, writing, and discussing a text. My observations indicate that the course influenced the students’ writing by compelling them to write for an actual rather than imagined audience and to alter (or edit) their texts to appeal to their audience. By the end of the term, the students I observed worked with editors to produce “clear” prose that “connected” readers to the writer. The students saw the editor as essential in helping them to relate to their readers. This dissertation provides support for the argument that reading and writing are inextricably connected, with editing and the role of the editor as the connective tissue. Educators must teach reading and writing together, as two parts of single communication circuit.

Keywords: Composition
Editing
Editorial practice
Expressivism
reading-writing connections
writing instruction
Advisor: Stagg Peterson, Shelley
Placefull Spaces: Queer Women and Non-Binary Artists Resisting an Emptied Stage

For marginalized queer artists, inequitable distribution of and access to performance space impact both the development process and production of artistic works. While a lack of ongoing or resident performance space for women’s productions in Canada has been documented (see, for example, Rina Fraticelli; Rebecca Burton; and Michelle MacArthur), less research has been conducted on queer women’s and non-binary artists’ experience of space in the industry. Theatre and performance scholars (see, for example, Gay McAuley, Una Chaudhuri, Jill Dolan, and Laura Levin) have provided the groundwork for exploring the relationship among theatre sites, identities, and productions; and queer geographers such as Natalie Oswin, Julie Podmore, Catherine Nash, and Kath Browne have developed invaluable theories and methodologies to unsettle the assumed neutrality of space. However, few scholars have brought these fields together, particularly in the context of performance in Canada. This doctoral project applies queer and feminist theories of geography to queer women’s and non-binary artists’ performance to explore how insecure and inequitable access to physical space affects both experiences of finding one’s place in the theatre industry and articulations of an imagined place on stage. The germinal Western conceptions of the stage as placeless or “empty” (Brook) work to neutralize the theatre space by assuming all creators, performers, and audience members are easily oriented within it. For marginalized bodies, which are simultaneously hyper-visualized and unseen in dominant cultural spaces, the necessary conditions to access placelessness may be unobtainable, or may be experienced as a form of violent erasure of histories. Through a process of “unmapping” venues and close description and analysis of performances, this doctoral study questions how an intentional engagement with space and place on stage can actively destabilize the presumed universality and neutrality of performance space and combat broader gendered spatial inequities. Focusing on performances and events in Toronto, Ontario and Vancouver, British Columbia, this project develops a theory of “placefullness” as a means of understanding how artists actively resist spatial inequities in the theatre and performance industry in Canada.

Keywords: Lesbian theatre
Queer geography
Queer theatre in Canada
Queer women
Theatre space
Advisor: Goldstein, Tara
Medical Explanations in Evolutionary Medicine, Network Medicine, and Medically Unexplained Physical Symptoms

This dissertation is a philosophical exploration of the limits of medical explanations. I examine three case studies to explore these limits: evolutionary medicine, network medicine, and the medically unexplained. Evolutionary medicine and network medicine exemplify modern attempts to develop new explanatory strategies in clinical research and practice. They are burgeoning, nascent fields that challenge our conventional understanding of health and disease. I am critical of the former and optimistic about the latter. I argue that the ultimate explanations posed by evolutionary medicine are pragmatically and epistemically inadequate as medical explanations. Explanations that appeal to our ancestral past are speculative, often based on adaptationist assumptions, and empirically suspect—we cannot rely on them to develop medical interventions. Network medicine aims to map the connections between the causes of disease and pathophenotypes. It has the potential to reconceptualize diseases as emergent topologies of these networks. I discuss the role of mechanisms in these models and how multi-level, context-sensitive networks aim to be empirically robust. Medically unexplained syndromes, in contrast, are an obscure class of illnesses that cannot be explained by somatic biomedicine. Like complex chronic diseases, these syndromes are a thorn in the overwhelming success of medical progress. Patients with unexplained syndromes are often diagnosed with psychiatric illnesses, and I argue that it is an epistemic injustice to pathologize such gaps in medical knowledge. Rather than diagnosis these conditions by exclusion, we need to embrace epistemic humility when confronted with such medical uncertainty. This dissertation adds to the literature on medical explanations, exploring their unique virtues and clinical implications.

Keywords: epistemology
evolutionary medicine
medically unexplained physical symptoms
network medicine
philosophy of medicine
scientific explanations
Advisor: Walsh, Denis