VictorJuiz/thesis huggingface dataset:
Exploiting Problem Structure in QBF Solving

Deciding the truth of a Quantified Boolean Formula (QBF) is a canonical PSPACE-complete problem. It provides a powerful framework for encoding problems that lie in PSPACE. These include many problems in automatic verification, and problems with discrete uncertainty or non-determinism. Two person adversarial games are another type of problem that are naturally encoded in QBF. It is standard practice to use Conjunctive Normal Form (CNF) when representing QBFs. Any propositional formula can be efficiently translated to CNF via the addition of new variables, and solvers can be implemented more efficiently due to the structural simplicity of CNF. However, the translation to CNF involves a loss of some structural information. This thesis shows that this structural information is important for efficient QBF solving, and shows how this structural information can be utilized to improve state-of-the-art QBF solving. First, a non-CNF circuit-based solver is presented. It makes use of information not present in CNF to improve its performance. We present techniques that allow it to exploit the duality between solutions and conflicts that is lost when working with CNF. This duality can also be utilized in the production of certificates, allowing both true and false formulas to have easy-to-verify certificates of the same form. Then, it is shown that most modern CNF-based solvers can benefit from the additional information derived from duality using only minor modifications. Furthermore, even partial duality information can be helpful. We show that for standard methods for conversion to CNF, some of the required information can be reconstructed from the CNF and greatly benefit the solver.

Keywords: computer science
satisfiability
quantified boolean formula
solver
Advisor: Bacchus, Fahiem
Doing Homework, Doing Best? Homework as a Site of Gendered Neoliberal Governance

This thesis explores elementary schools’ homework practices on Prince Edward Island. I employ a feminist perspective that incorporates Foucault’s concept of governmentality (Foucault, 1991a) to examine homework as a ‘site’ where institutions (family and school) interact and power circulates. I focus on the ways in which the daily lives and subjectivities of mothers, and to a lesser extent teachers, are organized and regulated in the process of making homework work. I assembled and analyzed reports and policies related to education reform, parental involvement and homework. I draw on Foucault’s approach to genealogy (Foucault, 1984) to examine how homework has been established in these texts as a ‘good’ educational practice for young students, in spite of its dubious effects on educational achievement. Mothers and teachers are explicitly and implicitly addressed in education policy and practice as primary agents for the accomplishment of homework. Following qualitative research methodology, I conducted twenty in-depth interviews with mothers and teachers of elementary aged students. These mothers and teachers often have ambivalent feelings about homework, sharing frustrations about its effects on family time and relations and doubting its value for children. At the same time, ‘doing homework’ was closely linked to being a ‘good mother.’ Thus, my analysis draws attention to the complex ways that homework and parental involvement discourses work on and through people, to produce particular kinds of experiences and feelings. While homework may ‘fail’ to accomplish its professed educational aims for students, I argue that it serves to render women responsible for growing portions of educational labour. My study sheds light on the workings of power in the home/school relationship and more generally on the workings of neoliberal governance and educational reform. Modern government works through routine administration of our lives, in schools and families, and other institutions, often through persuasion, incitement and engagement rather than through explicit policy. I suggest the daily practice of homework is a concrete example of this and, extending Foucault’s analysis through feminist perspectives, I explore the unequal operation and effects of homework for those who are its main targets.

Keywords: homework
governmentality
Foucault
mothering
neoliberalism
Advisor: Dehli, Kari
Mechanisms of Yeast Gene Definition

The yeast Saccharomyces cerevisiae is a prevalent system for studying gene regulation because of the ease of experimental methods and the simplicity of its gene structure. Here, I describe my work that aims to identify the sequences and factors responsible for demarcating genes within the genome sequence. With comparative genomics and RNA-Seq, we are quite adept at identifying gene structure. However, the cell does not have access to this kind of information. Instead, it uses the specificities of DNA- and RNA-binding proteins to read and interpret the sequence of the genome; it is this process that I have studied in my thesis. In the first chapter, I describe my work collecting yeast transcription factor specificities. I evaluated these specificities using available confirmatory data to determine which one best represents the transcription factor; this gave me a high-confidence description of what DNA sequences yeast transcription factors recognize. Next, I look for over- and under-represented DNA words within and surrounding gene structures and attempt to explain these in terms of the specificities of known factors or other known biological phenomena. I found that the sequences in the 5' and 3' gene ends are very similar and can often be explained by similar phenomena. I also provide evidence that several factors may be involved in regulating transcription in non-canonical ways. In the final chapter, I describe my efforts to build a model that uses my collection of transcription factor specificities as well as DNA structural features to identify gene structure as we think the cell would. This model is comprised of two classifiers that identify mRNA initiation and termination sites, and these are used to provide evidence to a hidden Markov model that predicts gene structure. I test that the predicted determinants of promoter structure are sufficient to initiate transcription, and that the transcription arising from randomly-generated DNA is correctly predicted. Overall, my work demonstrates that the sequence elements demarcating yeast genes are relatively simple in nature, which has implications for how transcription is regulated and how genes evolve.

Keywords: transcription
yeast
Advisor: Hughes, Timothy
Perceptual-cognitive Properties of Pictures, Diagrams, and Sentences: Toward a Science of Visual Information Design

Right now you are reading a sentence. Earlier, you might have been looking at a realistic picture, such as a photograph, or an outline drawing in a set of instructions. If you are a programmer, you work with sentence-like structures, such as code, or a system diagram. These are all graphic representations. To varying degrees, the effectiveness of every graphic representation relies on its ability to convey the designer’s intended meaning and elicit the intended reaction from its audience. However, the design of graphic representations, even in technical domains such as visual programming language design or interactive information visualization, currently relies heavily on general principles based solely on practice, intuition, and informal measures of effectiveness from the applied art and craft of design (as opposed to scientific analysis or theory). There is an increasing demand for a scientific understanding of design and its evaluation from stakeholders (who seek evidence for effectiveness) and designers (who seek to advance their field). Because both the creation of graphic displays and their perception are literally embodied experiences, a model was developed with an embodiment orientation, specifically based on how graphics are perceptually and cognitively processed. In my research, I found that graphic representations are constituted of two properties, pictorial and symbolic information, that emerge through two interrelated aspects of perception. In sighted individuals, for example, every graphic representation makes use of biological capabilities to process visual sensation (i.e., light hitting the retina), which are processed in relation to culturally-learned capabilities (i.e., writing). I observed how graphic representations – such as pictures, diagrams, and sentences – are “naturally selected” (i.e., during different phases of design or problem solving). From these observations, I developed a model that distinguishes and predicts the effectiveness of pictures, diagrams, and sentences, in terms of how object relations and attributes are pictorially or symbolically represented, relative to the functional roles of those representations, contexts, and in some cases, individual perceptual-cognitive differences among perceivers. This model is a step toward a science of graphics that could lead to evaluation techniques for information systems, theories for inclusive design, and ergonomically designed software programming tools.

Keywords: visual information design
diagrammatic reasoning
cognitive science of graphics
ecological psychology
theory of graphic representation
Knowledge Media Design
visual language
picture perception
Advisor: Smith, Brian Cantwell
Hockema, Stephen
The Role of p21-activated Protein Kinase 1 in Metabolic Homeostasis

Our laboratory has demonstrated previously that the proglucagon gene (gcg), which encodes the incretin hormone GLP-1, is among the downstream targets of the Wnt signaling pathway; and that Pak1 mediates the stimulatory effect of insulin on Wnt target gene expression in mouse gut non- endocrine cells. Here, I asked whether Pak1 controls gut gcg expression and GLP-1 production, and whether Pak1 deletion leads to impaired metabolic homeostasis in mice. I detected the expression of Pak1 and two other group I Paks in the gut endocrine L cell line GLUTag, and co-localized Pak1 and GLP-1 in the mouse gut. Insulin was shown to stimulate Pak1 Thr423 and β-cat Ser675 phosphorylation. The stimulation of insulin on β-cat Ser675 phosphorylation, gcg promoter activity and gcg mRNA expression could be attenuated by the Pak inhibitor IPA3. Male Pak1-/- mice showed significant reduction in both gut and brain gcg expression levels, and attenuated elevation of plasma GLP-1 levels in response to oral glucose challenge. Notably, the Pak1-/- mice were intolerant to both intraperitoneal and oral glucose administration. Aged Pak1-/- mice showed a severe defect in response to intraperitoneal pyruvate challenge (IPPTT). In primary hepatocytes, however, IPA3 reduced basal glucose production, attenuated glucagon-stimulated glucose production, and inhibited the expression of Pck1 and G6pc. This implicates that the direct effect of group I Paks in hepatocytes is the stimulation of gluconeogenesis, and that the impairment in IPPTT in aged Pak1-/- mice is due to the lack of Pak1 elsewhere. The defect in IPPTT in aged Pak1-/- mice could be rescued by stimulating gcg expression with forskolin injection or by enhancing the incretin effect via sitagliptin administration. In summary, my study demonstrates that: 1) Pak1 positively regulates GLP-1 production, 2) Pak1/β-cat signaling plays a role in gut/liver axis or gut/pancreas/liver axis governing glucose homeostasis, and 3) Pak1-/- mice can be utilized as a novel model for metabolic research.

Keywords: Diabetes
Pak1
GLP-1
Gcg
Advisor: Jin, Tianru
Heterophilic Cell Adhesion Molecule TgrC1 and its Binding Partners during Dictyostelium discoideum Development

During development, Dictyostelium discoideum cells assume muticellularity via their collective aggregation. Cell-cell adhesion is required for morphogenesis, cell differentiation, cell sorting and gene expression during development. TgrC1 is a heterophilic cell adhesion molecule which is indispendable for complete development. TgrC1 can be considered as the most important cell adhesion molecule for D. discoideum development because deletion of the tgrC1 gene completely arrests development at the loose aggregate stage and inhibits fruiting body formation. In order to investigate the biological role of TgrC1 during development, I have chosen to identify and charactize the extracellular heterophilic partner and the cytoplasmic binding partner(s) of TgrC1. Using different biochemical approaches, we identified TgrB1 as the heterophilic binding partner of TgrC1 and demonstrated that their association is mediated through IPT/TIG domains in the extracellular region of both proteins. Both tgrB1 and tgrC1 share the same transcriptional promoter and their spatiotemporal expression pattern is identical during development. We also examined the assembly of TgrC1-TgrB1 complexes via the split green fluorescence protein complementation assay and the fluorescence resonance energy transfer approach. Whereas TgrC1 is capable of forming cis-homodimers spontaneously, cis-homodimerization of TgrB1 depends on its trans-interaction with TgrC1. A model of the assembly process has been proposed. To investigate signalling events initiated by the interaction between TgrB1 and TgrC1, pull-down assays were employed and led to the identification of myosin heavy chain kinase C as the cytoplamic partner of TgrC1. Mutational analysis showed that the basic residues in the short cytoplasmic domain of TgrC1 are critical to the binding with MHCK-C. Disruption of the interation between MHCK-C and TgrC1 results in an alteration of cell motility at the aggregation stage and aberrant cell sorting in slugs. These studies have highlighted the role of TgrB1-TgrC1 complexes in the regulation of morphogenesis during Dictyostelium development.

Keywords: cell adhesion molecule
Dictyostelium discoideum
development
Advisor: Siu, Chi-Hung
Experiments on the Growth and Form of Icicles

Icicles are a ubiquitous and picturesque feature of cold winter weather. Their familiar form emerges from a subtle interplay between the solidification dynamics of ice and the gravity-driven flow of the thin water film flowing over their evolving surface. The latent heat released by freezing is advected by the water film and ultimately carried away by the surrounding sub-zero air, which is also flowing. Like many processes far from equilibrium, icicle growth can exhibit nonlinear pattern formation. While scaling theory predicts that icicles converge to `platonic', self-similar shapes, natural icicles often exhibit regular ripple patterns about their circumference, which are due to a morphological instability. This thesis presents a comprehensive experimental study of icicles that sheds new light on the dynamics of their growth and the origin of their form. A table-top apparatus was designed and built for the controlled growth of icicles, under different conditions of temperature, water supply rate, ambient air motion, and water purity. Image analysis and Fourier methods were used to examine their morphology. Contrary to theoretical expectations, ripples do not appear on icicles made from pure water. Instead, ripples grow and travel on icicles made from salt solutions, even at very low concentrations. The addition of non-ionic surfactant or dissolved gases does not produce ripples, unless ionic impurities are also present. The ripple wavelength is independent of time and growth conditions. The ripple amplification rate and traveling velocity vary weakly with the ionic concentration, as do the tip and radial growth speeds of the icicle. While the tip and radial growth also depend on the ambient temperature and input mass flux, the ripple dynamics is not correlated with extrinsic conditions. If the ambient temperature or input mass flux is sufficiently low, the tip growth only advances for a short period of time before it ceases. After cessation, the shape of the icicle deviates increasingly from self-similarity. The most self-similar icicles are made from pure water with the surrounding air gently stirred, whereas icicles made from impure water in still air tend to grow multiple tips.

Keywords: nonlinear dynamics
pattern formation
ice growth
heat transfer
fluid mechanics
thin film flow
non-equilibrium processes
morphological instability
natural phenomenon
table-top experiment
ionic impurities
surfactant effects
dissolved gases
icicles
stalactites
Advisor: Morris, Stephen W.
Efficacy and Impact of Key Performance Indicators as Perceived by Key Informants in Ontario Universities

The issue of performance indicators for colleges and universities in Ontario was first raised in the early 1990s by the Ministry of Education and Training’s Task Force on University Accountability. The decision to develop and use Key Performance Indicators (KPIs) was made in the 1990s (Ministry of Education and Training, 1998). The three KPIs for Ontario universities are Graduation Rates, Employments Rates, and OSAP Loan Default Rates. The declared purposes of the publication of the KPIs evolved over time. Initially, they were to enable parents and students with data to inform post-secondary education choice. The purposes then became benchmarks without any clear indication of what constituted satisfactory or unsatisfactory performance. Performance funding based on KPIs introduced a third phase. Finally, they were to influence the universities' programming behaviour without government’s direct intervention. The overall intent was to help universities improve their performance (MTCU, 2012). My study focused on the impact of KPIs on Ontario universities 10 years after they were instituted. This exploratory and descriptive study examined the history of why and how KPIs were introduced in Ontario and the perception of 12 key informants of 11 participating universities regarding the efficacy and effectiveness of the existing KPIs. The study sought to identify areas of concern of the participants and their suggestions on how the KPIs can be altered to improve their effectiveness. The findings provide an understanding of the impact of the KPIs and suggested alternatives, and provide valuable information and a potential source for evidence-based MTCU policy decisions that impact Ontario’s universities and their stakeholders. The findings suggest that a review and redefinition of the theory of accountability as applied in Ontario universities are required as the initial interpretation of accountability defined by the three KPIs is too narrow to be pragmatically useful. Most university participants perceived that the current KPIs are not having the intended impact. I recommend that both parties work together and be clear on each other’s goals and expectations to develop effective measures on institutional performance and accountability, and to satisfy the needs of the government, the universities and the public.

Keywords: key performance indicators
post-secondary education
Advisor: Janzen, Katharine
Asymmetric Division of Damaged Proteins in Proliferating Cells

This thesis explores the unequal partitioning of damaged proteins during mitosis and its implications for cell fate. Initially described in unicellular organisms, it was unclear if this method was used in vivo in multicellular organisms and had functional consequences in mammalian cells. To determine if this asymmetry was conserved in multicellular organisms, I studied three stem/progenitor populations in Drosophila: the larval neuroblast, adult female germline stem cell, and adult intestinal stem cell. Each cell type was found to asymmetrically segregate damaged proteins identified by the 2,4-hydroxynonenal (HNE) modification, which are associated with oxidative stress and age. Both the larval neuroblast and female germline stem cell were found to retain damaged proteins during division, whereas the intestinal stem cell segregated damaged proteins to differentiating progeny. I suggest that functional lifespan, and not cell type, determines the cell that receives the majority of damaged proteins during division. In each cell type, damaged proteins were associated with DE-Cadherin, a common component of the stem cell niche and removal from the niche was associated with reduced damaged protein polarization. Interestingly, when larval neuroblasts were mechanically dissociated from their niche and placed in culture, the internal polarization of damaged proteins was found to increase with progression through the cell-cycle. Therefore, I suggest that both the niche and intrinsic factors play a role in the asymmetric division of damaged proteins. To determine if an asymmetric division of damaged proteins influenced cell fate, I used a mammalian cell line with inducible expression of misfolded Huntingtin, which shares similar properties to damaged proteins. This study also revealed that the conformation of damaged proteins impacts cell fate: cells with diffuse Huntingtin displayed greater proliferation and reduced resistance to stress. Tracking cells containing an aggregate with live-imaging revealed that the cell that inherits the aggregate has a longer cell-cycle and an enhanced capacity to differentiate. Therefore, the asymmetric inheritance of damaged proteins impacts cell fate. In the final chapter of this thesis, I discuss the implications of an asymmetric division of damaged proteins on cell fate and how this information can be applied to cancer treatments.

Keywords: Stem cell
Mitosis
Advisor: Kooy, Derek van der
The Flutist as Co-creator: Composer-performer Collaborations in the Flute Music of Hungary

The objective of this dissertation is to explore how collaborative partnerships between composers and performers can shape musical repertoire. Since composers do not work in isolation and they often compose with specific players in mind, the person they write for can influence their approach to a given piece. If they consult the performer, a working relationship might ensue in which the performer’s contribution to the music can range from the interpretation of the piece to its co-creation. Numerous flute compositions in Hungary since the 1950s were created for specific performers and have therefore greatly benefited from this type of music-making. This study proposes a theoretical model of composer-performer collaborations that classifies these artistic partnerships into six types, according to the amount and kind of influence the performer has on the music. Based on score analysis and interviews conducted with Hungarian performers and composers, the creative contributions made by flutists István Matuz, Zoltán Gyöngyössy, Gergely Ittzés, Gyula Csetényi, Bea Berényi, Ákos Dratsay and János Bálint are examined in the music of Miklós Kocsár, Iván Madarász, László Dubrovay, József Sári, Miklós Sugár, István Láng, László Tihanyi, István Szigeti, Máté Hollós and Péter Eötvös. In addition, pieces by flutist-composers István Matuz, Zoltán Gyöngyössy and Gergely Ittzés are also studied. The focus is directed to music for one to four flutes, flute with orchestra and flute with piano, as these are the types of pieces in which composer-performer partnerships are most apparent.

Keywords: Hungarian music, Flute Music, Hungarian flute music, Composer-Performer Collaborations, István Matuz, Zoltán Gyöngyössy, Gergely Ittzés, Theory of artistic collaborations, Performers' effect on repertoire
Advisor: McKay, Gillian