VictorJuiz/thesis huggingface dataset:
The Contribution of LncRNAs to Tip-Stalk Patterning in the Vascular Endothelium
Keywords: angiogenesis
endothelial cells
flow
hypoxia
long non-coding RNAs (lncRNAs)
vascular endothelium

The functional properties of the vascular endothelium are diverse and heterogeneous between vascular beds. This is especially evident in angiogenesis. Specialized endothelial cells (ECs), called tip and stalk cells, coordinate a highly choreographed cascade of events regulated by both exogenous and endogenous regulatory inputs. The most potent activator of angiogenesis is vascular endothelial growth factor (VEGF). As such, it is the most common therapeutic target in diseases in which angiogenesis is dysregulated. However, these treatments have varying degrees of efficacy. In the last decade, work on non-coding RNAs, especially long non-coding RNAs (lncRNAs), indicates that they are important regulators of the gene expression paradigms that underpin angiogenesis. Here, we sought to better understand the contribution of lncRNAs to tip-stalk signaling. Through scRNA-seq of HUVEC, we found a distinct population of tip-like cells. Interestingly, these clusters were lost in scRNA-seq of freshly isolated HUVEC recently exposed to laminar flow, suggesting that laminar flow suppresses tip EC gene expression. Through tip cell purification, we identified LINC02669, a VEGF-responsive lncRNA enriched in tip cells. Similar to tip-enriched protein-coding genes, this lncRNA was also suppressed by laminar flow. Thus, for the first time, we show that lncRNAs can be enriched in specific ECs. In our subsequent study, we identified GATA2-AS1, a hypoxia-responsive and abundant EC-enriched lncRNA. We found that GATA2-AS1 augments HIF1α induction to regulate the HIF switch. GATA2-AS1 regulates EC metabolism and coordinates tip-stalk signaling to regulate angiogenesis. GATA2-AS1 is not enriched in tip cells, suggesting it regulates tip cell biology in a paracrine manner. This may be another way in which metabolic and molecular coordination of sprouting can be controlled by lncRNAs. Taken together, our work establishes novel roles for lncRNAs in the transcriptional regulation of ECs during angiogenesis.
Synthesizing Divide-and-Conquer Programs
Keywords: automatic parallelization
divide-and-conquer
program synthesis

Multicore computers today are ubiquitous, from large distributed systems to desktops and mobile phones. Their complex memory architecture enables fast and efficient execution when used correctly. Many efforts have been invested in making the task of taking advantage of these architectures easier. Among them, the development of optimizing and parallelizing compilers as well as frameworks that provide skeletons for parallelism have abstracted the low-level details of the implementation and the optimization process. Techniques have been developed to optimize the efficiency of algorithms that fit particular skeletons, with one of the most commonly used of these being divide-and-conquer. However, the programmer still has to come up with the divide-and-conquer algorithm that fits such skeletons, often with an error-prone and tedious process. This research work aims at providing automated techniques to bridge the gap in the automated optimization process. Given an input program, our goal is to synthesize an equivalent divide-and-conquer implementation, which can then be optimized using the wealth of techniques available. The methods developed should be implementable in a practical tool leveraging the recent advances in program synthesis, but they should also act as a thinking tool for programmers when the solvers fail. This dissertation proposes methodologies to split the task of synthesizing a divide-and-conquer program into smaller but more tractable tasks. To solve these tasks, we propose both new deductive approaches to synthesize new functionality and an efficient use of existing synthesis methods. The combination of the methodologies and the synthesis techniques allows us to design a fully automated process, implemented in a tool Parsynt, which succeeds in synthesizing highly non-trivial divide-and-conquer algorithms from simple functions.
Community-based Research with Eastern Canadian Sex Workers on the use of Information and Communication Technology to Manage Occupational Health and Safety
Keywords: Co-design
Internet
Mobile phone
Occupational health and safety
Sex work
Structural determinants

In Canada, legal restrictions under Bill C-36 increase a sex worker’s occupational health and safety (OHS) risks by forcing the sex worker to work alone, placing the sex worker at risk for violence in the form of assault, robbery, non-negotiated sex acts, attempts to or removal of the condom, and clients trying to receive a sex act without paying for it. Other OHS risks experienced by sex workers are harassment, social isolation, and inadequate access to health services. To counteract these OHS risks, sex workers have begun using information and communication technologies (ICTs) to exchange tips and information. Through three interrelated studies, this dissertation seeks to understand how sex workers in Eastern Canada are currently using ICTs to access OHS information and manage OHS risks. Using a community-based research approach, and guided by the social ecological model, qualitative research methodologies were applied to gather insights as to whether the OHS information available via ICTs meets sex workers’ needs and explore sex workers’ suggestions for improvements in accessing OHS information. The first study in this dissertation, a scoping review, covers 12 countries, including Canada, and discusses the individual and institutional OHS risk mitigation strategies that sex workers access via ICTs. In the second study, 22 Eastern Canadian sex workers were interviewed. This study delivered a deeper understanding of the role ICTs play in a sex worker’s ability to find an online community where they can learn and exchange OHS strategies, and provided insights into the fragility of these communities, as the usage of ICTs for this purpose is prohibited by law. In the third study, a subset of sex workers from the previous study co-designed the digital prototype of a tool that could satisfy their needs for a central repository of OHS information. The overall vision for this digital OHS tool is a sex-worker friendly space, comprised of six core components: regional bad date resources, the work of sex work, supplies, STI information and education, sexual health, and harm reduction services. In designing their own OHS tool, sex workers apply their lived experience in mitigating the risks present in their profession.
Graduates of Ontario Secondary Schools' Experiences in High School and Intercultural Orientations
Keywords: Interculturalism
Intergroup contact
Recognition
Secondary schools
Sociocultural learning

How do secondary school experiences influence student intercultural orientations and how do students’ identities influence student intercultural orientations? This study uses Allport’s (1954) intergroup contact theory (the idea that sustained contact with others can reduce prejudice), Vygotsky’s (1933/1967) sociocultural theory (that we learn with and from others in specific sociocultural contexts), Charles Taylor’s (1994) theory of recognition (that human dignity demands equal recognition), John Dewey’s views on education and democracy, and a critical lens to understand the potential connections. The study accepts that students come to school with perceptions of themselves and others based on the specific sociocultural environments in which they are raised (as suggested by Vygotsky). These perceptions are influenced by such social constructions as race, Indigeneity, ethnicity, class, gender, and ability, and the embedded, internalized and often unexamined power relationships attached to these constructions of identity. The study explores how schools may affect student intercultural orientations by whether or not they bring students with different backgrounds, experiences, and cultural identities together under the conditions specified by Allport, (sustained contact, enhanced equality, institutional support, and common purpose), and whether they provide adequate recognition (following Taylor) for students’ complex, interactive and developing identities. Based on a survey of 390 recent graduates of Ontario secondary schools and fourteen individual interviews, the study finds that inequitable structures and mechanisms for school programming as well as school environments that fail to support individual student identities hinder intergroup contact in Ontario schools. Learning settings often do not allow for open discussion of local and global issues through a human rights framework, and limit students’ experience of and participation in democratic activity. The implications for Ontario education may include: a re-examination of individualism and competition in teaching and learning; contextualizing of academic merit; an examination of discriminatory school structures including state funding of denominational schooling; culturally responsive and de-colonizing pedagogy; broader and more equitable access to extra-curricular activity; greater emphasis on teacher-student relationships; and more school-based student democratic participation.
Aural Readings: Performative Monologues as Oppositional Narratives
Keywords: Monologue
Narratology
Oppositional narratives
Orality
Performance
Speech-act theory

My dissertation aims to classify and elucidate a group of unembedded monologues in prose whose narrative voice adopts a spoken or pseudo-spoken mode. In each of the works I study—Samuel Beckett’s The Unnamable (1953), António Lobo Antunes’s The Land at the End of the World (1979), Thomas Bernhard’s Wittgenstein’s Nephew (1982) and Roberto Bolaño’s Amulet (1999)—a first-person narrator adopts a mode of speech/narration that is stylistically crafted to simulate differing degrees of spoken discourse. I look to speech-act theory and a variety of narratological concepts to show how the unembedded monologue form manifests a performative function. In this vein, I show that the unframed/unembedded aspect of these monologues is performative in its omission of a descriptive (constative), third-person framework that might suggest a narrative situation in readers’ imaginations. In the last two chapters, I also examine how this performative function is present in the narrators’ tendency to address a fictional listener or group of listeners. In addition, the narrators of these texts all occupy their respective sociopolitical spheres as outsiders or subjects of alterity and position themselves in opposition to cultural and political institutions, adopting critical/nonconformist attitudes towards power structures. I am interested in showing how performative language becomes a tool for endowing these works, and their narrators, with a political edge and a sense of agency; my selection of texts by post-WWII authors, stemming from vastly different literary traditions, aims to explore the performative monologue’s genesis and stages of development. The scope of primary texts establishes a traceable chronology and a cohesive means of grouping together previously isolated examples of this unorthodox narrative mode.
The Role of Extrinsic Connections and Stimulus Identity in Ventral Hippocampus Mediated Approach-Avoidance Conflict Resolution
Keywords: Anxiety
Approach-Avoidance Conflict
DREADDs
Hippocampus
Lateral Septum
rs-fMRI

The ventral hippocampus (HPC) has is a key mediator of approach-avoidance conflict, which occurs when organisms are confronted with a stimulus associated with opposing valences. Surprising findings have emerged regarding how different ventral HPC subregions mediate conflict resolution, and additionally suggest that only certain conflict conditions elicit ventral HPC activity. This thesis set out to investigate the role of the ventral HPC subregions and their extrinsic connections in approach-avoidance conflict, the conditions in which they are necessary for conflict mediation, and the extent to which established pathways that mediate conflict in rodents generalize to humans.The first experiment utilized established mixed valence Y-maze and metric pattern discrimination paradigms to investigate the extent to which the ventral and dorsal dentate gyrus (vDG and dDG) mediate approach-avoidance conflict and spatial pattern separation, respectively. These experiments revealed a double dissociation, with pharmacological inhibition of the vDG leading to conflict approach responses, while inhibition of the dDG impaired metric pattern discrimination. The second study investigated the extent to which conflict scenarios with simple light/sound cue signaled outcomes are mediated by the ventral HPC. Chemogenetic inhibition of the ventral HPC led to no alterations in response to conflict in either reinforced or non-reinforced conditions, suggesting that sufficiently simple conflict conditions do not require ventral HPC activity. The third investigation examined the role extrinsic connections from the ventral CA3 and CA1 (vCA3 and vCA1) to the lateral septum (LS) play in approach-avoidance conflict. It was found that chemogenetic inhibition of the vCA3 to caudodorsal LS pathway released approach responses to conflict stimuli, while inhibition of vCA1 to rostroventral LS pathway led to non-specific behavioural disinhibition. The fourth investigation used human functional magnetic resonance imaging data to examine the correlations between the human HPC, LS, and hypothalamus at rest. This found that activity between these 3 regions are correlated, and the details of these connections suggest a continuity of pathways responsible for conflict mediation between species. Together, these results reveal that the ventral HPC subfields contain multiple pathways that mediate approach-avoidance conflict elicited under complex conditions and suggest that these pathways are preserved in humans.
Development of a Mathematical Model for Monitoring Recovery Boiler Dissolving Tank Sounds
Keywords: Acoustic Monitoring
Chemical Recovery
Industrial Application
Pulp and paper
Smelt-water Interaction
Stochastic Model

In the chemical recovery process of kraft pulp mills, molten smelt falls into the dissolving tank where it interacts violently with hot water. These smelt-water interactions allow for fast smelt dissolution, however too many violent interactions can also cause equipment damage. In severe cases, violent smelt-water interactions may result in dissolving tank explosions, costing millions of dollars to pulp mills. One way to monitor smelt-water interactions within the dissolving tank is through the sound they generate. In this work, an acoustic model of smelt-water interaction was developed to examine dissolving tank sound characteristics and operating factors affecting the sound intensity. Field studies were conducted to obtain acoustic data at several mill sites. Laboratory experiments were then conducted to study each part of the smelt-water interaction process. The results of field measurements and laboratory experiments allowed for better understanding of the physical mechanisms involved in smelt-water interactions in the dissolving tank. This model is stochastic in nature and describes the physical processes from the moment molten smelt droplets enter water to the acoustic signals produced by numerous vapour bubble expansions and collapses. Each component of the model was verified through empirical data. The simulation results of the integrated model were then compared against acoustic measurements taken from mill visits. The model predictions were in good agreement with the sounds recorded from pulp mills under various operating conditions. The model could also accurately predict other mill variables such as the temperature of green liquor in the dissolving tank based on acoustic signals. In addition, the model provides predictions of changes within the dissolving tank when parameters such as smelt droplet size distributions and smelt flow rate are varied. The results obtained through these simulations show trends that are in agreement with findings from other studies. The results also suggest that dissolving tank water temperature, smelt flow rate, and smelt droplet size are amongst the most important factors in the intensity of explosion events. The model and algorithmic procedures developed in this thesis work may be used to develop an acoustic monitoring system for recovery boiler dissolving tanks.
Performing Migrant Identity: Canadian Yiddish Personal Narratives
Keywords: Eastern Europe
Ethnography
Migration
Minority Culture
Personal Narratives
Yiddish

This dissertation explores the multiple ways migrants use their personal narratives to create, express, and transmit new hybrid transnational cultures and identities. Between 1900 and 1930, over half a million Eastern European Jews settled in Canada, increasing Canada’s Jewish population by more than 800%. These migrants established new Jewish communities in cities, towns, and farming colonies and changed the face of Canadian Jewish society. This dissertation undertakes an analytical reading of Yiddish personal narratives, published and unpublished, written by 21 of these migrants. A range of approaches to stories of self, including folkloristic, literary, and psychological combined with ethnopoetic analysis provide insight into the multiple functions and meanings integrated into these migrant personal narratives. Contact approaches and postcolonial theory are utilized to understand the relationships between the individuals, space, and group identities. This work uncovers what migrant personal narratives reveal about individual and communal creative adaptation and the connections between individuals, their previous home(s) and culture(s), and their new ones. דיסרטציה זו בוחנת את מגוון הדרכים שבהן מהגרים משתמשים בסיפורים אישיים כדי לכונן ולבטא זהויות בינלאומיות היברידיות. בין השנים 1900 ו-1930, יותר מחצי מיליון יהודים ממזרח אירופה התיישבו בקנדה, ובכך הגדילו את אוכלוסיית היהודים בקנדה ביותר מ-800%. מהגרים אלו הקימו קהילות בערים, כפרים, ומושבות חקלאיות ושינו את האופי של החברה היהודית בקנדה. מחקר זה מנתח סיפורים אישיים ביידיש, שנכתבו על ידי עשרים ואחד מהגרים, חלקם ראו אור וחלקם נותרו בכתב יד. מספר שיטות ניתוח של סיפורים אישיים – מחקר הפולקלור, חקר הספרות, פסיכולוגיה, ואתנו-פואטיקה – שופכות אור על הפונקציות והמשמעויות שגלומות בסיפורים אישיים של מהגרים. המחקר עוסק ביחסים בין אנשים, מרחב, וזהות הקבוצה, תוך שילוב בין תיאוריות מגע (contact approaches) ותאוריה פוסט-קולוניאלית (post-colonial theory).
Atomic Structure of Thin Films in the Cesium-lead-bromine System
Keywords: CsBr
PbBr2
Perovskite
Physical Vapor Deposition
STM
Thin Films

Cesium lead bromide (CsPbBr3) perovskite nanocrystals have a promising future in the field of optoelectronics. Their potential applications are primarily in improving the efficiency of solar cells and light emitting diodes (LEDs). However, it remains a great challenge to fabricate halide perovskite nanodevices using traditional methods as they dissolve in polar solvents used in the fabrication of the devices. The available research regarding CsPbBr3 crystals is insufficient, particularly in the area of growth by solid phase evaporation. Therefore, the growing interest in perovskite crystals motivated us as to study the growth of the two binary constituents, Cesium bromide (CsBr) and Lead bromide (PbBr2) on a metallic substrate, as well as the results of co-deposition. In this study, ultra-thin films have been grown using thermal evaporation, studied using low energy electron diffraction (LEED), scanning tunneling microscopy (STM) and density functional theory (DFT). The growth of CsBr on Ag (111) has been observed in the coverage range 2.5 to 5 ML. Analysis of atomically resolved images show that the thin films have the NaCl structure. At higher coverages, significant mobility is seen in the films imaged at room temperature. The growth of PbBr2 epitaxial layers in the coverage of ~ 0.05 to ~ 1 ML results in the decomposition of PbBr2 to Pb and mobile Br atoms and later their recombination to form PbBr2. Co-deposition of these binary components shows the evidence of formation of the cubic and the orthorhombic phases of CsPbBr3 perovskites thin films. Finally, a study on the phase control as a function of molar deposition ratio has been performed which will lead to better control of the quality of perovskite thin films.
Mitochondrial Genome Dynamics in Yeast: How Mutation and Selection Inform the Fate of a Dispensable Genome
Keywords: mitochondrial DNA
multilevel selection
population genetics

The accumulation of mutant mitochondrial DNA (mtDNA) results in cellular pathologies in single-celled organisms and is implicated in disease and aging in multicellular organisms like humans. However, much remains to be understood about the dynamics of the generation of mutant mtDNAs that lead to their propagation in cell populations. In particular, it is unclear what characteristics of mutant mtDNA enable the out-competition of wild-type mtDNA and what mechanisms are involved in this displacement of healthy genomes. The interplay between intracellular and intercellular selection in shaping the fate of mtDNA is also poorly understood. To investigate the generation of mutant mtDNAs and why they propagate, first I present an experiment where I use long-read sequencing to track the mutational trajectories of mtDNA in Saccharomyces cerevisiae. This experiment reveals a previously unseen pattern that constrains the mutational trajectories of mtDNA in yeast. This study also shows that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Next, I introduce a computer-vision tool to increase the throughput of a laborious experimental assay used to infer the integrity of mtDNA in yeast. This automated tool detects colonies with wild-type and mutated mtDNA and computes their frequencies from scanned images of Petri dishes. It addresses issues in scalability and reproducibility of existing mtDNA mutation assays which currently rely on laborious manual colony counting methods. Finally, I explore the interplay between the multiple levels of selection acting on mtDNA in cell populations through mathematical models that highlight important features of systems with multi-level selection. I also propose a collection of new experiments to test these model predictions in yeast. Altogether, this work provides further insight into the dynamics of mtDNA in yeast which helps to answer some long-standing questions in mitochondrial genetics. It also provides new tools to experimentalists in the form of a bioinformatics approach that enables the reconstruction of complex mtDNA structures through long-read sequencing and a computer-vision tool to speed up assays that measure mtDNA integrity within cells. Lastly, it lays out a theoretical foundation for future multi-level selection studies in yeast.