VictorJuiz/thesis huggingface dataset:
Sequence-selective DNA Binding by Basic Region/Leucine Zipper Proteins at Noncognate Gene Regulatory Sequences

This thesis explores how basic region/leucine zipper (bZIP) transcription factors target gene regulatory sequences. The GCN4 bZIP binds to more than one target site [CRE (TGACGTCA) and cognate AP-1 (TGACTCA)] and exhibits flexibility in -helical structure. These observations suggest that the GCN4 bZIP can establish sequence-selective DNA binding at noncognate target sites. Studies on such noncognate but sequence-selective binding can provide insights into how bZIP proteins search for and localize to their cognate target sites. This thesis investigates DNA binding by the GCN4 bZIP and its structural and functional mimic, the wild-type (wt) bZIP, at noncognate gene regulatory sequences C/EBP (TTGCGCAA), E-box (CACGTG), HRE (GCACGTAG), XRE1 (TTGCGTGA), and related DNA sequences. These DNA-binding activities are sequence-selective, as confirmed by DNase I footprinting and electrophoretic mobility shift assay (EMSA). Full- and half-site DNA-binding affinities, determined by EMSA titrations, decrease from cognate to noncognate binding. At noncognate target sites, the bZIP proteins form a dimer of -helices, as indicated by circular dichroism (CD) spectroscopy and EMSA. These results demonstrate that the bZIP proteins can establish noncognate but sequence-selective DNA binding, and suggest such DNA binding potentially contributes to structure preorganization and rapid translocation of the bZIP proteins when they search for their cognate target sites, to which they then bind with high affinity. This thesis also indicates a highly dynamic DNA-binding model for the bZIP proteins to establish strong and sequence-selective DNA binding. The C/EBP site includes two 5H-LR (TTGCG) half-sites, each of which comprises two 4-bp subsites. The in vitro and in silico results together demonstrate that the basic region at 5H-LR recognizes the 4-bp subsites alternately as distinct units, which requires it to translocate between the subsites, potentially by sliding or hopping. Taken as a whole, this thesis provides further insights into how bZIP transcription factors accomplish sequence-selective DNA binding.

Keywords: bZIP
DNA binding
GCN4
C/EBP
basic region
leucine zipper
transcription
gene regulatory
Advisor: Shin, Jumi A.
Holy Homophobia: Doctrinal Disciplining of Non-heterosexuals in Canadian Catholic Schools

In 2012 clashes between Catholic canonical law and Canadian common law regarding sexual minorities continue to be played out in Canadian Catholic schools. Although Section 15 of the Canadian Charter of Rights and Freedoms ensures same-sex equality in Canada, this study shows that some teachers in Alberta Catholic schools are fired for contravening Catholic doctrine about non-heterosexuality, while Ontario students’ requests to establish Gay/Straight Alliances are denied. This study seeks to uncover the causes and effects of the long-standing disconnect between Canadian Catholic schools and the Charter by comparing the treatment of and attitudes towards lesbian, gay, bisexual, transgender and queer (lgbtq) teachers and students in publicly-funded Catholic school systems in the provinces of Alberta and Ontario. I employ a multi-method qualitative research framework involving: 1) semi-structured interviews with 20 participants (7 current and former teachers and 13 former students), 18 of which are re-presented as condensed narratives; 2) media accounts that illustrate the Catholic schools’ homophobic environment; and 3) two key Alberta and Ontario Catholic policy and curriculum documents. The central question driving this study is: How does power operate in Canadian Catholic schools? Is it exercised from the top down solely, or are there instances of power rising up from the bottom as well? To answer this question, I draw upon the critical theories of Gramsci (1971), Althusser (1970/2008), Foucault (1975/1995), and Giroux (2001) in order to explain the phenomenon of “holy homophobia” in Canadian Catholic schools. The chief finding of this study is that contradictory Catholic doctrine on the topic of non-heterosexuality is directing school policy and practice regarding the management of sexual minority groups in Alberta and Ontario Catholic schools, positioning these schools as potential hotbeds for homophobia. Hopefully, this thesis can one day serve as a resource for anti-homophobia education researchers and practitioners, school administrators, educators and students who are interested in eliminating religiously-inspired homophobia in school settings.

Keywords: Homophobia
Canadian Catholilc Schools
Non-heterosexual
lesbian, gay, bisexual, transgender, and queer
Qualitative Research
Narrative Inquiry
Critical Theory
Canadian Law
Anti-Oppressive Research
Anti-Homophobia Education
Advisor: Sykes, Heather
Predictor Virtualization: Teaching Old Caches New Tricks

To improve application performance, current processors rely on prediction-based hardware optimizations, such as data prefetching and branch prediction. These hardware optimizations store application metadata in on-chip predictor tables and use the metadata to anticipate and optimize for future application behavior. As application footprints grow, the predictor tables need to scale for predictors to remain effective. One important challenge in processor design is to decide which hardware optimizations to implement and how much resources to dedicate to a specific optimization. Traditionally, processor architects employ a one-size-fits-all approach when designing predictor-based hardware optimizations: for each optimization, a fixed portion of the on-chip resources is allocated to the predictor storage. This approach often leads to sub-optimal designs where: 1) resources are wasted for applications that do not benefit from a particular predictor or require only small predictor tables, or 2) predictors under-perform for applications that need larger predictor tables that can not be built due to area-latency-power constraints. This thesis introduces Predictor Virtualization (PV), a framework that uses the traditional processor memory hierarchy to store application metadata used in speculative hardware optimizations. This allows to emulate large, more accurate predictor tables, which, in return, leads to higher application performance. PV exploits the current trend of unprecedentedly large on- chip secondary caches and allocates on demand a small portion of the cache capacity to store application metadata used in hardware optimizations, adjusting to the application’s need for predictor resources. As a consequence, PV is a pay-as-you-go technique that emulates large predictor tables without increasing the dedicated storage overhead. To demonstrate the benefits of virtualizing hardware predictors, we present virtualized designs for three different hardware optimizations: a state-of-the-art data prefetcher, conventional branch target buffers and an object-pointer prefetcher. While each of these hardware predictors exhibit different characteristics that lead to different virtualized designs, virtualization improves the cost-performance trade-off for all these optimizations. PV increases the utility of traditional processor caches: in addition to being accelerators for slow off-chip memories, on-chip caches are leveraged for increasing the effectiveness of predictor-based hardware optimizations.

Keywords: predictor virtualization
hardware optimizations
processor caches
Advisor: Moshovos, Andreas
Transitioning To High School: Parent Involvement And School Choice

Abstract The disquiet around parent-school relationships is the focus of this study. During transitioning to high school, the boundaries around this relationship changes. Few studies have addressed these changes, particularly from parents’ perspectives. It is parents’ voices which are central to this study. This dissertation uses the standpoint of parents, which is often absent or silent in educational literature and research. Within a critical and constructivist paradigm, and influenced by Institutional Ethnography, two elementary schools (divergent in race, social class, ethnicity and immigrant status) and one high school are the sites for interviews with 14 parents and 13 educators. 11 parents were re-interviewed after their children entered high school. Four questions were addresses: How has parent involvement come to be understood? How is the parent-school relationship experienced by parents and educators? How and why are decisions made around the transition and school choice process? Do parents’ perceptions align/vary from those of educators? Based on historically constructed notions and assumptions, parent involvement is usually understood as a visible and public demonstration of appropriate and caring parenting ignoring interactions outside of the public’s gaze. Illustrated through Parent Council membership, parent involvement is gendered, classed, culturally related and race, ethnic and immigrant status specific. Some parents had more social, cultural, economic and emotional capital to bring to the transition process, while others were marginalized and had to rely on/trust the education system. School and Board policies and procedures were examined and their varied affects on parents’ experiences and choices analysed. Educators assisted in disseminating assumptions around parent-school relationships and contributed to inequitable parent knowledge, partially as a result of too little training. By examining social, economic and cultural positioning of parents within local school communities, positive parent-school relationships can be nurtured, which political pundits and educationalists have failed to accomplish. During transitioning, organization and social discontinuities contributed to parent and school disconnects and constructed borderlands in the parent-child-school relationship. This study evidenced the fragility of the parent-school relationship, especially during this vulnerable time for parents and thus, reflective questions are presented in hope of initiating a crucial conversation in local school communities.

Keywords: transitioning, parent involvement, school choice, high school, high school, parent-school relationships, parenting, capital, Parent Councils, specialized schools/programs, critical analysis, constructivism, institutional ethnography
Advisor: Eichler, Margrit
Two Orchestral Songs

The song cycle, Two Orchestral Songs, is a setting of two texts by Canadian poet Gwendolyn MacEwen (1941–1987) from her 1969 collection, The Shadow-Maker. The texts are symbolic in nature and discuss the question of personal sacrifice. In “The Sacrifice,” the narrator observes leaves falling in autumn and compares this “necessary death” against the “unnecessary” sacrifices that we make when we lay down our most beautiful aspects, our “golden selves,” at the “altars of the world” in order to please some external arbiter (the “shapeless ghost”). However, much like a man raking leaves in autumn, these dropped aspects get gathered up by “the Gardener” (a metaphor for Time), and we are left questioning whether our deliberate sacrifices enabled us to achieve the divine end to which we were intended. “How Weeps the Hangman,” employs similar imagery of leaves representing the “season’s sacrifice” of “pain, love, glory, blood.” The titular metaphor of the Hangman, however, draws on tarot imagery, specifically the twelfth Major Arcana card known as The Hanged Man, which depicts a man hanging upside-down by one foot from a cross or living tree; the man’s facial expression is usually neutral, not an expression of suffering. The card is interpreted in various ways as meaning sacrifice, letting go, surrender, and acceptance. In MacEwen’s poem, the narrator places herself (and us) on the way to the scaffold to offer up our seasonal sacrifices, but the lingering question focuses not on the object (us, The Hanged Man), but on the agent of change, the hooded Hangman who “does his duty to you and me.” She wonders what pain our own whimpering in the sacrificial process causes to him, whether he and the “embarrassed tree” weep at our losses. The musical language of this composition employs extended tonal key areas based on synthetic scales, in particular the four transpositionally related enneatonic scales. The harmonies are largely tertian in structure, with added tones and superimposed sonorities creating an effect of bitonality. The imagery of dropping leaves is recreated musically by the prominent use of descending seconds and descending thirds in the melodic and accompanying parts.

Keywords: orchestral song
contralto voice
song cycle
Gwendolyn MacEwen
music composition
enneatonic scale
Advisor: Kulesha, Gary
Reason, Evolution, and the Possibility of Cooperation

“Cooperation” has distinct meanings in biological and moral contexts. In nature, “cooperation” is commonly equated with “altruism,” and involves an apparent fitness cost to the actor. In the moral context, it is often employed to describe the behaviour required by a particular subset of morality, namely that of distributive justice. The existence of cooperation in nature poses a difficulty for those who seek explain it in evolutionary terms. There is an analogous problem in normative moral theory of reconciling cooperative behaviour with rationality. The constraints imposed by natural selection in the former context and by rationality in the latter make explaining or justifying cooperation difficult. Insofar as the social contract tradition is concerned with articulating or justifying the terms of social cooperation, these two problems are united through the contract metaphor. I examine these two structurally similar problems through the lens of the social contract tradition. In the descriptive arena, I argue that cultural group selection provides the most plausible explanation of the emergence of altruistic behaviours in nature. In the normative context, I argue that David Gauthier’s argument for the rationality of adopting the disposition of constrained maximization provides a defensible route to reconciling morality with rationality. I draw two conclusions with respect to how these two enterprises are connected. First, I argue, contrary to many critics of an empirically informed ethics, that the descriptive and normative projects are very much dependent upon one another. Insofar as culture is required for a descriptive account of the emergence of cooperation, and to the extent that reasoning about which norms ought to govern our interactions plays a role in their transmission, our descriptive account not only leaves room for normative considerations, but in fact requires them. Second, I argue that there is a convergence in the outcomes of both the descriptive and normative projects. I show that the explanation of the existence of cooperation that I favor also provides us with an explanation of the emergence of dispositions that structurally resemble those that Gauthier defends as rational. And thus we arrive at an account that brings together rationality, evolution, and morality.

Keywords: Rationality
Morality
Evolution
Cooperation
Advisor: Thompson, Paul
Synthesis and Mechanical Properties of Bulk Quantities of Electrodeposited Nanocrystalline Materials

Nanocrystalline materials have generated immense scientific interest, primarily due to observations of significantly enhanced strength and hardness resulting from Hall-Petch grain size strengthening into the nano-regime. Unfortunately, however, most previous studies have been unable to present material strength measurements using established tensile tests because the most commonly accepted tensile test protocols call for specimen geometries that exceeded the capabilities of most nanocrystalline material synthesis processes. This has led to the development of non-standard mechanical test methodologies for the evaluation of miniature specimens, and/or the persistent use of hardness indentation as a proxy for tensile testing. This study explored why such alternative approaches can be misleading and revealed how reliable tensile ductility measurements and material strength information from hardness indentation may be obtained. To do so, an electrodeposition-based synthesis method to produce artifact-reduced specimens large enough for testing in accordance with ASTM E8 was developed. A large number of 161 samples were produced, tested, and the resultant data evaluated using Weibull statistical analysis. It was found that the impact of electroforming process control on both the absolute value and variability of achievable tensile elongation was strong. Tensile necking was found to obey similar processing quality and geometrical dependencies as in conventional engineering metals. However, unlike conventional engineering metals, intrinsic ductility (as measured by maximum uniform plastic strain) was unexpectedly observed to be independent of microstructure over the grain size range 10-80nm. This indicated that the underlying physical processes of grain boundary-mediated damage development are strain-oriented phenomena that can be best defined by a critical plastic strain regardless of the strength of the material as a whole. It was further shown that the HV = 3•σUTS expression is a reliable predictor of the relationship between hardness and strength for electrodeposited nanocrystalline materials, provided the material is ductile enough to sustain tensile deformation until the onset of necking instability. The widely used relationship HV = 3•σY was found to be inapplicable to this class of materials owing to the fact that they do not deform in an “ideally plastic” manner and instead exhibit plastic deformation that is characteristic of strain hardening behaviour.

Keywords: nanocrystalline materials
electrodeposition
ductility
tension test
hardness test
Weibull
Advisor: Erb, Uwe
Decision-theoretic Elicitation of Generalized Additive Utilities

In this thesis, we present a decision-theoretic framework for building decision support systems that incrementally elicit preferences of individual users over multiattribute outcomes and then provide recommendations based on the acquired preference information. By combining decision-theoretically sound modeling with effective computational techniques and certain user-centric considerations, we demonstrate the feasibility and potential of practical autonomous preference elicitation and recommendation systems. More concretely, we focus on decision scenarios in which a user can obtain any outcome from a finite set of available outcomes. The outcome is space is multiattribute; each outcome can be viewed as an instantiation of a set of attributes with finite domains. The user has preferences over outcomes that can be represented by a utility function. We assume that user preferences are generalized additively independent (GAI), and, therefore, can be represented by a GAI utility function. GAI utilities provide a flexible representation framework for structured preferences over multiattribute outcomes; they are less restrictive and, therefore, more widely applicable than additive utilities. In many decision scenarios with large and complex decision spaces (such as making travel plans or choosing an apartment to rent from thousands of available options), selecting the optimal decision can require a lot of time and effort on the part of the user. Since obtaining the user's complete utility function is generally infeasible, the decision support system has to support recommendation with partial preference information. We provide solutions for effective elicitation of GAI utilities in situations where a probabilistic prior about the user's utility function is available, and in situations where the system's uncertainty about user utilities is represented by maintaining a set of feasible user utilities. In the first case, we use Bayesian criteria for decision making and query selection. In the second case, recommendations (and query strategies) are based on the robust minimax regret criterion which recommends the outcome with the smallest maximum regret (with respect to all adversarial instantiations of feasible utility functions). Our proposed framework is implemented in the UTPref recommendation system that searches multiattribute product databases using the minimax regret criterion. UTPref is tested with a study involving 40 users interacting with the system. The study measures the effectiveness of regret-based elicitation, evaluates user comprehension and acceptance of minimax regret, and assesses the relative difficulty of different query types.

Keywords: Utility elicitation
Decision theory
Advisor: Boutilier, Craig
When Social and Physical Pain Intersect in Humans

Prior research has shown that the distress associated with social exclusion (i.e., social pain) and physical pain share biological and neural substrates. This social-physical pain overlap has spawned a number of hypotheses regarding how both types of pain might interact. The dissertation research reported here employed diverse methodologies to investigate two questions stemming from these hypotheses: 1) what is the effect of social pain on physical pain sensitivity and 2) what is the effect of physical pain on social pain sensitivity? Pertaining to the first question, Study 1 showed that a socially disconnecting live interaction with a partner led to a decrease in physical pain sensitivity. This result, however, was not replicated in Study 2 using an imagination paradigm to conjure two different types of social exclusion experiences, nor did low levels of social connectedness predict subsequent physical pain levels in a sample of chronic pain patients in Study 3. Pertaining to the second question, pain levels did not predict subsequent reports of social disconnection in the diaries of chronic pain patients in Study 3, nor did participants experiencing capsaicin-induced physical pain report social judgments any different from their pain-free counterparts in Study 4. The reasons for, and meaning of, these findings are discussed in detail. Crucial questions that must be confronted to continue advancement in this area of research and recommendations for future studies are also explored.

Keywords: Pain
Relationships
Social Exclusion
Advisor: MacDonald, Geoff