VictorJuiz/thesis huggingface dataset:
3D Microgels to Quantify Tumor Dynamics for Identifying Therapeutic Targets

Cancer remains a global problem and still lacks effective therapeutic strategies that can achieve total tumor response. Despite ongoing efforts to identify novel drug targets and treatment strategies, the attrition rate of the current cancer drug discovery pipeline remains the highest of any disease area. This high failure rate can be attributed in part to three realistic cancer features that impact patient drug response and that are not well captured by current preclinical models for drug discovery: 3D tumor architecture, tumor heterogeneity, and the dynamic nature of tumor progression. This thesis aims to identify novel therapeutic vulnerabilities for two dynamic cancer phenomena, cancer invasion and cancer regrowth, by including these cancer features using tissue engineering tools, cancer patient-derived samples, and imaging informatics, that when combined, improve disease biology representation and enable access to novel mechanistic and phenotypic insights. Both approaches leverage the tissue engineered GLAnCE (Gels for Live Analysis of Compartmentalized Environments) platform, which generates thin, uniform, layers of micro-molded gels, termed 3D microgels, that enable high-throughput, high-content imaging of patient-derived samples in a single system. To investigate cancer invasion dynamics, we used GLAnCE to model the tumor-stroma invasive margin, where the interaction between cancer cells and the cancer-associated fibroblast (CAF) population perpetuates a pro-invasive tumor cell phenotype that drives the initial stages of cancer dissemination. Using this approach, we identify a novel epigenetic CAF target that can be used to inhibit the pro-invasive tumor phenotype observed in our model. We also investigate cancer regrowth after treatment dynamics. To do this we initially scaled-up GLAnCE to a 96-well plate format (96-GLAnCE) to improve throughput and enhanced our image-based analysis workflow. Then using 96-GLAnCE, we reveal unexpected dose-dependent variations in regrowth response, and assess the different regrowth phenotypes within and between patient-derived organoids that could have targetable potential. This thesis showcases the power of leveraging complex in vitro tumor models in conjunction with real-time, high-content imaging to explore the contribution of tumor heterogeneity on dynamic tumor biology. More broadly, this approach promises a new path for discovering new therapeutic targets with clinical translatability and greater potential for curative treatment.

Keywords: 3D in vitro tumor model
cancer regrowth
drug screening
image-based analysis
patient-derived organoids
tumor microenvironment
Advisor: McGuigan, Alison P
Borrower Information Environment and Institutional Lending

Institutional (i.e., non-bank) lenders have become major funding providers in the leveraged loan market. Certain loan facilities — institutional facilities — are designed to primarily attract funding from institutional lenders. This dissertation studies the role of borrower information environment and the related information asymmetry problem in institutional lending. Although institutional lenders are the primary funding providers for institutional facilities, they still mostly rely on bank lenders for loan origination. Such market practice embodies less access to borrower private information for institutional lenders, resulting in their information disadvantage compared to bank lenders. In Chapter 1, I find that institutional facilities are more likely to be issued along with a bank facility (thus forming a loan package) when institutional lenders are at a greater information disadvantage. Further, within the same loan package, contractual terms for institutional versus bank facilities can differ. I show that when institutional lenders are at a greater information disadvantage, (1) the spread premium for institutional facilities relative to their bundled bank facilities is larger, and (2) institutional lenders are less willing to delegate their control rights to bank lenders through a covenant-lite arrangement when they have a stronger bargaining power. Taken together, Chapter 1 documents a connection between the “packaged” design of institutional loan deals and the information asymmetry between institutional and bank lenders. Chapter 2 examines the role of accounting quality in the price discovery of institutional loan facilities during syndication. Loan spreads and original-issuance discounts (together forming effective spreads) are first proposed by the lead arranger, and can be subsequently adjusted up or down based on the demand from institutional lenders. In Chapter 2, I show that lower accounting quality is associated with a higher (lower) likelihood that an institutional facility’s effective spread will experience an upward (downward) adjustment during syndication, and associated with a longer time to break into secondary-market trading. I also find that lower accounting quality is related to greater underpricing of the loan as compared to its first secondary-market-trading price. Taken together, Chapter 2 shows that accounting quality affects the efficiency and effectiveness of the price discovery of institutional facilities in the primary market.

Keywords: Bundling
Cov-Lite
Information Asymmetry Between Institutional Lenders and Bank Lenders
Institutional Loan Facilities
Market Flexing
Within-Package Differential Contract Design
Advisor: Hope, Ole-Kristian
Vyas, Dushyant
Meta-perceptions: The What and When of Considering Others’ Impressions of Us

Many theories imply, but never formally test, the roles of meta-perception and much of the empirical work to date has focused on the sources and accuracy of meta-perceptions without fully understanding what function these meta-perceptions serve. The goal of this dissertation is to shed light on the functions of meta-perceptions by exploring what people think about when forming meta-perceptions and how much, when, and why people care about the impressions they make on others in daily life.To explore what people think about when forming meta-perceptions, I first assessed qualitative data on meta-perceptions, self-perceptions, and impressions of others in a single interaction (Study 1) and the content of meta-perceptions in daily life (Study 2). Results demonstrated that, like self-perceptions and impressions of others, people tend to consider the Big Five traits, namely extraversion and agreeableness, when forming meta-perceptions. However, unlike self-perceptions and impressions, people tend to consider global positivity and relational attitudes more when forming meta-perceptions, suggesting that people might use meta-perceptions to gauge others’ attitudes and monitor social connections. Second, I used a latent-variable model to test what goes into trait meta-perceptions (Paper 1). Results revealed that meta-perceptions include attitudes and trait substance, but to varying degrees depending on the trait and acquaintance being judged. Participants’ attitudes about how positively they were seen were related to their attitudes about themselves, suggesting a link between meta-perceptions and identity, and they accurately tracked others’ attitudes towards them, demonstrating that meta-perceptions involve an attitude-tracking system likely for monitoring social connections. To explore if and why people form meta-perceptions, I used experience sampling to capture how much, when, and why people care about meta-perceptions in social interactions across their daily life (Paper 2). Results demonstrated that people generally care about the impressions they make on others, socially connected individuals tend to care more, and people tend to care more when experiencing greater social connection or lower status. Thus, meta-perceptions might function to help people maintain social connections and navigate social hierarchies. Overall, this dissertation reveals that meta-perceptions are important to social functioning and contributes to a framework of the functions of meta-perceptions.

Advisor: Carlson, Erika N
A Comparative Analysis of Quebec and Ontario: How each province approached elementary provincial numeracy curricula and corresponding Faculty of Education accredited Teacher Education programs during the period of 2003-2018

The issue of declining student achievement in elementary mathematics can be correlated to the implementation of the curricula reforms that began in the 1990s. The NCTM standards guiding the reforms called for significant change in teachers’ instructional pedagogy and approach (NCTM 1989, 2000). The Ontario government was increasingly concerned about the downward trend on provincial and international mathematical assessments as “results over the 2003 to 2018 period show a steady decline in Canada’s math scores” (Allison & Geloso, 2021, p.5). Quebec is the only province in Canada that has not experienced decline on national and international elementary mathematics assessments; instead, it continues to maintain its status as one of the highest performing jurisdictions in the world (Brochu et al., 2013).This exploratory descriptive and mixed methods research study aimed to understand, from a comparative analysis of Ontario and Quebec, how each province approached the organization and structure of the elementary mathematics curriculum, and how Faculty of Education programs approached teacher training within this changed context. I undertook a quantitative and qualitative analysis of both provincial curricula utilizing the ‘Model of Numeracy in the Twenty-first Century’ (Goos et al., 2011) for coding through four dimensions: context, mathematical knowledge, tools, and dispositions. This process was followed by a case study that included one Faculty of Education from each province. For this study, I conducted interviews with six key informants (three faculty and or administrators from each university) to examine how faculties responded to the large-scale changes and described the theoretical findings of the curricula analysis. These interviews provided valuable insight into the vastly different training structures each Faculty of Education had for certifying teachers. The study findings highlight four key themes that emerged: (a) differences in Ontario and Quebec student achievement in the area of number sense and numeration; (b) differences in curricula structure (size and complexity); (c) statistical differences by province in the dimensions of context and mathematical knowledge; and (d) differences in the incorporation of problem solving, mathematical tools, theoretical underpinnings and the use of supplementary resources. The findings include implications for theory, policy and practice.

Keywords: Comparative Analysis
Elementary Provincial Numeracy Curricula
Faculty of Education
Ontario
Quebec
Teacher Education
Advisor: Vezina, Asima C
The Role of White Adipose Tissue Remodeling in Mediating Burn-Induced Hypermetabolism

Major burns represent one of the most severe forms of trauma due to the magnitude and persistence of an amalgamation of symptoms, including systemic inflammation, glucose and insulin signaling dysregulation and whole-body catabolism, together inducing a hypermetabolic response. Remarkably, hypermetabolism can persist for years after the initial injury, even after full wound closure. Given its pervasiveness, and based on strong correlations between hypermetabolic symptoms and the increased risk of sepsis, multi-organ failure, and death, discovering novel interventions geared towards mitigating hypermetabolism is a top priority to improve patient outcomes. One potential avenue is to target adipose tissue. It is now well-appreciated that adipose tissue is not simply a quiescent lipid storage vessel. Rather, it is profoundly adaptable and possess a wide array of functions that govern systemic metabolism. Moreover, adipose tissue has been implicated as the driving force mediating a diverse spectrum of metabolic pathologies. Thus, we hypothesized that adipose tissue is a central regulator of burn-induced hypermetabolism, and that by reducing its metabolic activity, this may alleviate poor outcomes. We first demonstrated, in both severe burn patients and mouse models of thermal injury, that white adipose tissue (WAT) remodeling, including increased lipolysis, mitochondrial biogenesis, and browning (i.e. the phenotypic switch of adipocytes towards an energy expending state), is initiated by multiple factors, such as adrenergic stimulation and systemic inflammation, and persists long-term. Moreover, this was associated with severe metabolic derangements, such as increased energy expenditure, inflammation and tissue-specific dysfunction. Given this correlative evidence, we next aimed to provide direct support that WAT drives hypermetabolism. Indeed, we showed that WAT can independently induce a systemic dysfunctional state when burn adipose is transplanted into healthy recipients. Remarkably, the dysfunctional phenotype was restored when healthy fat was transplanted into a burn model. This suggests that WAT can independently elicit or improve the hypermetabolic response. Finally, we uncovered a novel mechanism of intra-adipose remodeling, which coordinates an immune-adipocyte crosstalk facilitated by nicotinic acetylcholine receptor signaling. Collectively, this thesis clearly identifies WAT as a dominant mediator of the long-term hypermetabolic response to burns. Thus, future therapeutic interventions should be designed to target adipose metabolism.

Keywords: Adipose Tissue
Burn Injury
Hypermetabolism
Advisor: Jeschke, Marc G
Screaton, Robert A
Anatomical and Functional Characterization of the Larval Zebrafish Periaqueductal Gray Through the Development of Experimental Tools

Investigation of sensorimotor neural circuitry has evolved tremendously from traditional experimental approaches that relied on electrophysiological recordings and lesioning. Modern optical technologies allow for in vivo cellular resolution monitoring of activity across thousands of neurons, and selective neuronal inhibition or activation with light. Larval zebrafish are apopular model system to investigate neural circuitry using optical approaches owing to their small vertebrate brain and transparency. They also exhibit a diverse behavioural repertoire at early ages, including prey capture and predator avoidance. In this thesis, I take advantage of the experimental benefits offered by larval zebrafish to investigate the periaqueductal gray (PAG), a midbrain region with a variety of functions including the regulation of active and passive responses to threats. Due to the small size of the larval brain, all neurons within the PAG are accessible for near simultaneous recording of activity, an approach not currently feasible in mammals. To investigate PAG function in zebrafish, I first developed an experimental pipeline that allowed for precise visual stimulation, while recording behaviour and neural activity from whole populations of identified PAG cell-types. The two populations I examined express either the rln3a or penka neuropeptide genes, landmarks used in mammalian PAG studies. I found that the populations are partially overlapping, and reside near the cerebral aqueduct. Fluorescent in situ hybridization revealed that both populations are overwhelming GABAergic. Through calcium imaging, I uncovered that roughly half of rln3a neurons, and a small percentage of penka neurons respond to a threatening looming disk visual stimulus. Rln3a neurons displayed similar activity when presented with other decreasing luminance stimuli, with a return to high luminance abruptly terminating rln3a activity. This indicates these neurons can encode environmental light levels. Combined calcium imaging and behavioural experiments demonstrated that both rln3a and penka neurons have increased activity when fish produce fewer swim bouts after expansion of the looming disk. This suggests a role for these neurons in behavioural suppression during visual threats. This partially contradicts the presumed role for inhibitory neurons within the mammalian PAG, and sets the stage for future studies into the functional evolution of this ancient brain region.

Keywords: penka
Periaqueductal gray
rln3a
zebrafish
Advisor: Thiele, Tod R
Algorithms for Self-driving Labs

This dissertation investigates how self-driving laboratories can be improved with the help of machine learning and data management techniques. The first part of the dissertation presents two methods, namely ORGANIZER and RouteScore, that can be implemented in existing self-driving labs. ORGANIZER is a soft- ware framework that enables equipment from multiple labs and locations to work seamlessly together, while RouteScore is a tool that quantifies the cost of synthetic routes, where both human and automated platforms can collaborate. The second part of the dissertation focuses on predicting the outcomes of chemical reactions. This would increase the available chemical space of the self-driving labs, making them more versatile. The chemical reaction were predicted using language models and a molecular representation called SMILES.

Advisor: Aspuru-Guzik, Alan
Investigating the Effect of Microenvironmental Gradients on Tumour Cell Heterogeneity Using a 3D In Vitro Model of Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a high-mortality cancer with no effective treatment options for the majority of patients. Notably, tumour cell behaviour and response to therapy in PDAC is heavily influenced by the characteristic hypoxic and immunosuppressive tumour microenvironment (TME). The emergence of 3D in vitro models that capture a variety of TME features offers a new opportunity for exploring the complexity of tumour-TME interactions in PDAC. Patient-derived organoids (PDOs) have advanced our capacity to model tumour heterogeneity in vitro but lack important microenvironmental components. Conversely, complex 3D in vitro models, such as the Tissue Roll for Analysis of Cellular Environment and Response (TRACER), recapitulate key TME features but have largely been restricted to use with cell lines with limited disease relevance. In this work, we adapted the TRACER platform to facilitate the incorporation of PDOs and create an engineered tissue model that leverages the advantages of both platforms for investigations of tumour biology (TRACER2). We demonstrated that PDOs cultured in TRACER2 establish microenvironmental oxygen gradients and show phenotypic changes in response to this gradient, including changes in cell proliferation, immunosuppressive capacity, and response to gemcitabine treatment. Subsequently, we performed single cell RNA-sequencing (scRNA-seq) of TRACER2, revealing location-dependent changes in the transcriptional patterns of PDOs. Significantly, we demonstrated that microenvironmental gradients, and hypoxia in particular, likely promote a more basal-like transcriptional phenotype in PDAC tumour cells, which has been linked to poor disease prognosis. Taken together, this work demonstrates the value of applying high-dimensional single cell analysis to a complex PDO-based 3D in vitro model of the TME to gain novel insight into tumour-microenvironment interactions. Looking to the future, we believe that this approach will pave the way to identifying novel therapeutic strategies that can meaningfully improve patient outcomes in PDAC.

Advisor: McGuigan, Alison
The Role of Programmed Germline Mitophagy in mtDNA Quality Control

Mitochondrial DNA (mtDNA) is subject to high mutation rates and undergoes little recombination, making it susceptible to the accumulation of mutations. To prevent deleterious mutations from being inherited, the female germline has evolved a special, conserved quality control mechanism that has thus far remained poorly understood. Through a large-scale RNAi screen, I uncover a novel programmed germline mitophagy (PGM) that drives mtDNA quality control in the female Drosophila germline. I show that PGM requires the mitophagy receptor BNIP3, mitochondrial fission factors, and members of the Atg1 complex, but not the canonical mitophagy factors Pink1 and Parkin. Surprisingly PGM is not induced by the presence of deleterious mtDNA, but rather is developmentally triggered in germ cells upon entry to meiosis through the inhibition of the Target Of Rapamycin Complex 1 (TORC1). I also identify the translation regulator, Ataxin-2, as required for PGM. Detailed structure-function analysis demonstrated that Ataxin-2 inhibits TORC1 predominantly through its PAM2 domain, suggesting translational activation is required to inhibit TORC1. By coordinating the timing of PGM with meiosis, I reveal that mtDNA quality control, the mechanism that maintains mtDNA integrity across generations, is developmentally and genetically coupled to meiosis, the mechanism that maintains nuclear genomic integrity across generations. The precise role of PGM in mtDNA selection is yet to be fully understood, but could involve turnover of mtDNA or mitochondrially-encoded proteins. This work also identifies numerous new mtDNA quality control factors and reveals a generalizable strategy for mtDNA quality control applicable across species, tissues, and disease states.

Keywords: Drosophila
mitophagy
mtDNA
oogenesis
quality control
Advisor: Hurd, Thomas R
Middle Eastern Refugees in Europe: The Polarization of Affect through Digital Remediations of Migration as Crisis

This dissertation reads the contemporary political polarization through an affective network, attending to the various manufactured anti-Muslim, multidirectional traumatic and humanitarian sympathetic responses that have accompanied representations of the migratory “crisis,” and exploring the European reactions toward war refugees fleeing the Middle East over the last decade (2012-2022). I bring both poles—humanitarian gestures and alternately patriotic disavowals of migrants—under scrutiny when thinking how technological advancements in communication utilize visual culture to unveil and influence public opinion on social, economic, cultural, and political issues. The first two chapters discuss fearful and sympathetic approaches in depicting refugees and migrants by scrutinizing echo chambers, social media, online videos, television coverage and film festival circuit. Following theories of Sara Ahmed and Tony D. Sampson in approaching fearful and populistic discourses, I argue that conjoining refugees with crises has become a “stuck” association that amalgamates specific events with those narratives shaping governance decisions and border policies. The 2015 European migrant “crisis” is a prominent illustration of this, as it has since been used to justify economic problems and political shifts. Additionally, the “crisis” came to espouse some of the empathetic humanitarian narratives, criticized by Lilie Chouliaraki and Tijana Stolic, that have circulated since the traumatic events of World War II, but also inspired populistic and nationalistic attitudes reminiscent of those towards terrorism, which have led to the problematic treatment of Middle Eastern and Muslim identities in the aftermath of 9/11. A way to move beyond these polarizing remediations is through the refugees’ own accounts of their trauma, as well as their migratory and war experiences, analyzed in the last chapter of this dissertation. There, affect and trauma as theorized on by Michael Rothberg, emerge as the most suitable theoretical languages for addressing the refugee “crisis” because their micropolitics are able to measure intensities and disappearances of affective sensations in the network. Consequently, the analyses produced here look at different media and their affective capabilities to create polarizing viral and immunologic responses to the migration discourse.

Keywords: 2015 refugee crisis
affect studies
digital hate
humanitarianism
political polarization
trauma studies
Advisor: Fenner, Angelica