VictorJuiz/thesis huggingface dataset:
Elucidating the Interaction between the Molecular Chaperone Hsp104 and the Yeast Prion Sup35

Hsp104 is a protein remodeling factor that is crucially important for induced thermotolerance and prion propagation in yeast. Recent work demonstrates that Hsp104 is able to directly recognize and interact with synthetic polypeptide substrates, and that this interaction is dependent on the amino acid composition or sequence (Lum et al., 2008). Here this concept is applied to the in vivo substrate Sup35. Sup35, a translation termination factor, also forms the yeast prion [PSI+]. The maintenance of the prion is critically dependent on the expression levels of Hsp104. Over-expression of Hsp104 leads to the loss of prions, as does inhibition of this protein remodeling factor. As part of this thesis, an in vitro assay was established in which spontaneous nucleation, the event preceding of fiber formation, was suppressed. Fibrilization itself then becomes strictly dependent on the chaperones Hsp104, huHsp70p and Ydj1. In line with in vivo observations, Hsp104 mutants that fail to propagate [PSI+] also fail to overcome nucleation inhibition in this assay. Following this, the next part of this work established that the middle (M) domain of Sup35 inhibited this process, while not affecting spontaneous fibrilization under non-inhibitory conditions. This finding was reproduced in vivo, as middle domain over-expression also led to curing of weak [PSI+]. This suggested that the M-domain contains an Hsp104 binding site. This hypothesis is supported by data presented in this thesis which show that a small segment 129-148 within the Middle domain has enhanced Hsp104 binding properties. Deletion of this 20-mer peptide also reduced the Hsp104 ability to interact with this prion substrate; it also results in the destabilization of the prion and enhanced curing by the prion curing agent guandidinium hydrochloride. This represents the first ever Hsp104 binding site identified within a natural substrate.

Keywords: Hsp104
Sup35
Advisor: Glover, John R.
Iterative, Interactive Analysis of Agent-goal Models for Early Requirements Engineering

Conceptual modeling allows abstraction, communication and consensus building in system development. It is challenging to expand and improve the accuracy of models in an iterative process, producing models able to facilitate analysis. Modeling and analysis can be especially challenging in early Requirements Engineering (RE), where high-level system requirements are discovered. In this stage, hard-to-measure non-functional requirements are critical; understanding the interactions between systems and stakeholders is a key to system success. Goal models have been introduced as a means to ensure stakeholder needs are met in early RE. Because of the high-level, social nature of early RE models, it is important to provide procedures which prompt stakeholder involvement (interaction) and model improvement (iteration). Most current approaches to goal model analysis require quantitative or formal information that is hard to gather in early RE, or produce analysis results automatically over models. Approaches are needed which balance automated analysis over complex models with the need for interaction and iteration. This work develops a framework for iterative, interactive analysis for early RE using agent-goal models. We survey existing approaches for goal model analysis, providing guidelines using domain characteristics to advise on procedure selection. We define requirements for an agent-goal model framework specific to early RE analysis, using these requirements to evaluate the appropriateness of existing work and to motivate and evaluate the components of our analysis framework. We provide a detailed review of forward satisfaction procedures, exploring how different model interpretations affect analysis results. A survey of agent-goal variations in practice is used to create a formal definition of the i* modeling framework which supports sensible syntax variations. This definition is used to precisely define analysis procedures and concepts throughout the work. The framework consists of analysis procedures, implemented in the OpenOME requirements modeling tool, which allow users to ask “What if?” and “Is this goal achievable, and how?” questions. Visualization techniques are introduced to aid analysis understanding. Consistency checks are defined over the interactive portion of the framework. Implementation, performance and potential optimizations are described. Group and individual case studies help to validate framework effectiveness in practice. Contributions are summarized in light of the requirements for early RE analysis. Finally, limitations and future work are described.

Keywords: Requirements Engineering
Goal Modeling
Interactive Analysis
Model Analysis
Software Modeling
Iterative Analysis
Early Requirements Engineering
Advisor: Yu, Eric
Beyond Acculturation: Cultural Constructions of Immigrant Resilience and Belonging in the Canadian Context

The psychological literature on immigrants has identified numerous challenges of resettlement. Research on acculturation indicates that adaptive functioning is characterized as a bicultural prospect in which individuals balance their heritage and the dominant culture within the receiving society. This conceptualization of positive adaptation typically relegates culture to a broad-based and static property circumscribed within ethnicity, neglecting diverse cultural representations and the way specific mechanisms affect the process of adaptation. The current research sought immigrants’ subjective accounts of resilience. The aim of this study was to identify specific markers of significant adversity and corollary positive adaptation that intersect with diverse mechanisms of culture to develop a theory of cultural adaptation. A constructivist grounded theory approach was implemented in data collection and analysis. Eighteen first-generation immigrants, who represented a range of cultural backgrounds and geographic regions, each participated in one semi-structured interview. The overarching theme that emerged from data analysis, Belonging, was found to explicate the meaning of resilience for immigrants in terms of their cultural adaptation. Belonging indicated a process by which immigrants gained a sense of identification with and inclusion in Canadian society. Immigrants’ perception of Belonging was affected by two mid-level themes, Forming Attachments and Feeling Acceptance. Forming Attachments was contextually driven and highlighted a personal process of developing cultural attachments. The advancement of attachments, interpersonally, occupationally and to the larger sociocultural environment, was meaningful to recovery and had implications for Belonging. The second mid-level theme identified a reciprocal process of acceptance that revealed a struggle to accept cultural changes as well as the significance of feeling accepted as an equal member of society. Taken together, Forming Attachments and Feeling Acceptance had a significant effect on immigrants’ sense of Belonging and were contextualized within a range of cultural domains. This study highlights the dynamic role of culture in immigrant adaptation and contributes to both research and health care professionals by offering a framework of immigrant resilience that may promote healthy forms of functioning.

Keywords: immigrant
resilience
culture
belonging
adaptation
adversity
acceptance
attachment
Advisor: Moodley, Roy
Investigating a College Computer Course Delivered in Both Online and Face-to-face Classes

The purpose of this study is to investigate a college computer course delivered in both online and face-to-face classes. As more online courses and programs emerge, concerns about the quality and comparability of online instruction with face-to-face instruction have arisen. Questions about the relative effectiveness of each mode of instruction are important both at the stage of course development and at the stage of course delivery. Earlier comparative studies have shown that online courses were equal to face-to-face courses. These studies evaluated student services and technological infrastructure, student satisfaction, and learning outcomes. However, few studies have been conducted on computer applications at the community college level. This study seeks to fill in this gap by providing students’ perceptions of computer education for a business program at the three-year diploma level. This study has examined the learning environment and informed practice by presenting differentiation and diversity mainly due to different mode of delivery in a college computer course. This study aims to provide a detailed understanding of the similarities and differences of college students attending online class versus face-to-face class taught by the same professor. It examines students’ perceptions of course design and delivery, their attitudes and beliefs about acquisition of computer applications, and their academic achievement as measured by the test scores. Mixed methods are employed to investigate the research questions both in depth and in breadth. In the Fall of 2009, 60 out of 89 eligible participants filled out the online questionnaire resulting in the response rate of 67% and six students participated one-on-one in-person interviews. Results from both quantitative and qualitative studies show that there is no significant difference between the face-to-face and online students with respect to their perceptions, attitudes, motivation, and learning outcomes. The findings demonstrate that there was no evidence showing difference between online learning and face-to-face learning. The different learning modes provide students with positive learning experiences. This study provides stakeholders such as students, college administrators, and professors with a detailed and meaningful understanding of the important learning environments for the online and face-to-face classes. The implications from the findings will help to enhance, advance, and expand face-to-face and online education at both the theoretical and practical level.

Keywords: Distance education
Comparative studies
Advisor: McDougall, Douglas Emerson
Student Engagement: Views from Inside One Postsecondary Institution

This thesis explores the complex and multidimensional topic of student engagement in one Ontario postsecondary setting. This study was designed to discover if faculty and students agree or differ in their understanding and perceptions of student engagement and, if so, how. Using a qualitative approach, full-time faculty and students from one school in one college were observed and interviewed about their understandings and perceptions regarding student engagement in the classroom. Faculty volunteers had at least two years of full-time teaching experience and students were past their first year of study. Study participants confirm that student engagement differs in definition and understanding among and between individuals, shifts over time, and can be experienced in isolation or with others. There are cognitive, behavioural and emotional aspects of engagement that participants described as having a clear impact on their learning. In addition, various demographic factors were deemed to influence experienced and perceived variances in levels of engagement. Discussions of demographic factors reveal a great deal of work needed in order to understand and work with these areas to foster engagement. Interviews revealed a narrow iii interpretation of concepts, such as gender interpreted as sexual designation and socio-economic status as financial income. To support engagement a deeper understanding of, and appreciation for, these factors is needed. Added understandings of culture, race and ethnicity are needed to truly honour students in the classroom. Faculty need to take the time to look past surface behaviours, invite student collaboration and truly attend to individual needs to facilitate a deeper level of engagement in the classroom. This study confirms that our perceptions and experiences with engagement are highly personal and complex. There was no common definition found; student engagement is as diverse as the student population. It is an elusive, evolving, complex phenomenon. To understand and promote engagement in the field of postsecondary education, it is imperative that student engagement remain a focus of ongoing dialogue and reflection. Implications for practice and consideration for future areas of research are suggested.

Keywords: Student
Engagement
Advisor: Ryan, James
Essays in Internationsl Political Economy

This dissertation studies three important questions in international political economy: The long run consequences of social divisions created by historical colonialism, the importance of trade shocks in shifting political power balances and shaping institutional development and the influence that major political powers have over the decisions of smaller nations. I study these three questions empirically in four papers that span three distinct regions and time periods. The first paper asks whether the large differences in economic development across Native American reservations today can be explained by social divisions that were created more than 150 years ago when the US government forcibly integrated distinct Native American bands into shared reservations, condemning them to a system of shared governance that was not consistent with their political traditions and tribal identities. The second and third papers study the effect of the first globalization on the political and economic equilibrium in seventeen 19th century British Caribbean plantation colonies. I use this set of highly comparable but in precise ways distinct islands as a laboratory to study the effect of globalization on the long run development of representative institutions and on the coerciveness of labour markets at the time. The first of two papers provides insights into the working of colonial institutions and traces the mechanisms through which the planter elite managed to maintain a monopoly over policy making and retard long run development. The second paper highlights the importance that exogenous output price changes had for the willingness of planter elites to engage in costly coercion that distorted labour markets in their favour. In the final paper I test whether major aid donors use foreign aid to buy the votes of developing countries. Taking advantage of a unique long-running dispute between major donors in the International Whaling Commission, I am able to address the three major empirical challenges in answering this question: that aid moves much slower than voting behaviour, that alliances constantly change with issues and that most international organizations vote frequently and on a range of issues while data on aid disbursals is available only in yearly aggregates.

Keywords: Political Economy
Development
Advisor: Trefler, Daniel
Genomic Context, Sequence Evolution, and Evolutionary Ecology of Major Histocompatibility Complex (MHC) Genes in the Red-billed Gull (Larus scopulinus)

Genomic organization of the major histocompatibility complex (MHC) can profoundly influence gene function and multigene family evolution. Situated at the interface of individual genetic variation and the adaptive immune response, MHC class I and II loci are intensively studied for disease associations and used as markers of adaptive genetic variation in evolutionary ecology research. Genomic sequence of MHC-containing cosmid clones from the red-billed gull (Larus scopulinus, Charadriiformes: shorebirds, gulls, and allies) was obtained for comparative analysis of avian MHC evolution. MHCI polymorphism was further investigated using cDNA library screening and locus-specific genotyping protocols. This first information regarding MHC organization and MHCI variation in charadriiforms suggests a complex evolutionary history to MHC architecture in birds. Duplication of MHCIIα loci in tandem MHCIIα/β pairs and their proximity to MHC-region gene COL11A2 are similar to arrangements in nonavian vertebrates, and contrast with the “minimal essential” MHC of the chicken (Gallus gallus, Galliformes: gamebirds). MHCI–TAP2 organization is shared with Galloanserae (gamebirds + waterfowl), as is a proposed major classical function for this MHCI gene. In contrast, the placement of MHCI genes adjacent to sequence from chromosomes 3, 5, and 22 of the chicken and zebra finch (Taeniopygia guttata, Passeriformes: perching birds) indicates interchromosomal rearrangements in birds and the possible genomic dispersal of nonclassical MHCI genes in the red-billed gull. Screening for avian malaria, genetic parentage tests, and field data from red-billed gulls at Kaikoura Peninsula, New Zealand were combined with MHCI genotypes to investigate relationships with disease and reproduction. Plasmodium infection was confirmed in red-billed gulls, and breeding condition was negatively associated with malarial infection and positively related to variation at the putative major MHCI locus. A low rate of extrapair paternity was identified across thirteen breeding seasons. Partners without extrapair young (EPY) had greater MHCI dissimilarity than was expected by chance, whereas lower individual MHCI variation and elevated hatching failure existed for pairs with EPY. In addition to contributing to studies of MHC evolution, sexual selection, and disease dynamics in the New Zealand avifauna, this research will facilitate studies of MHC genes in related charadriiforms, many of which are of conservation concern.

Keywords: molecular evolution
major histocompatibility complex
red-billed gull
Larus scopulinus
extrapair copulations
avian malaria
Advisor: Baker, Allan J.
An Investigation of the Possible Mechanisms of Change in Supportive-expressive Therapy for Depressed/Anxious Adolsecents

The present research explores a promising therapy – Supportive Expressive Therapy (SET; Luborsky, 1984) – for adolescents with mood and/or anxiety disorders. It has been proposed that therapist expressive techniques (e.g., challenges and interpretations) and client interpersonal mastery (i.e., self-understanding and self-control in relationships) are two elements central to the success of SET (Luborsky, 1984; Grenyer & Luborsky, 1996). The current thesis employs a microprocess approach to examine expressive techniques and interpersonal mastery as potential mechanisms of change in SET. The study first provides preliminary evidence that SET is effective in helping adolescents suffering from internalizing disorders. Clients (N = 10) reported significantly fewer symptoms of depression and anxiety post-therapy. The body of the study then focuses on two research questions pertaining to the microprocesses occurring during SET. First, employing graphical and statistical analyses, the study investigates the notion that SET helps clients develop greater interpersonal mastery. Ten clients’ levels of interpersonal mastery were assessed at four points throughout therapy to determine whether clients demonstrated higher levels of interpersonal mastery over time. Secondly, this dissertation explores the impact of therapist expressive statements on clients' narratives, using a lag sequential analysis. Clients' statements were examined to determine whether higher levels of interpersonal mastery were exhibited following higher-level expressive techniques versus other therapist statements (i.e., supportive statements). Statistical analyses pertaining to the first research question did not reveal significant changes in interpersonal mastery over the course of therapy. However, graphical analyses suggested specific patterns of gains in interpersonal mastery during SET. With respect to the second research question, results demonstrated therapists employed significantly more higher-level expressive techniques in the later stages of SET, in accordance with the guidelines provided in SET manuals. Lag sequential analyses did not, however, provide substantial evidence of gains in interpersonal mastery following higher-level therapist techniques. Despite a lack of evidence supporting a general link between higher-level techniques and increased client mastery, exploratory analyses suggested change-focused expressive statements were linked to fewer client statements reflecting low interpersonal mastery. Future research should examine (1) change-focused statements as potentially important variables fostering improvement, and (2) moderators of client responses to higher-level techniques.

Keywords: supportive expressive psychotherapy
supportive
expressive
brief psychodynamic psychotherapy
mastery
therapist techniques
interpretations
adolescents
supportive expressive therapy
psychotherapy process
Advisor: Manassis, Katharina
The Structure of Cultural Orientations to the Good Life and their Expression in Personal Narratives

Understanding the rational and ethical sense that people make of their actions and experiences requires understanding the lives they are trying to live. The narrative visions of a good life that are dominant in a society thus represent an important aspect of cultural orientation. To gain insight into the form and function of these visions, two studies were conducted. In Study 1, the various criteria by which people judge their lives as good or worthy were examined using multidimensional scaling of responses from four different cultural groups of students: Chinese, East Asian Canadian, South Asian Canadian, and Western European Canadian. The results revealed two underlying structural dimensions on which both criteria and cultural groups could be differentiated. One reflected the locus of criterial goods and the other their morality. The clearest cultural contrast was between Chinese participants, who tended toward the prudential, materialistic, and hedonistic pole of the morality dimension, and South Asians, who tended more toward the spirituality and beneficence pole. In Study 2, the content of personal narratives produced by Chinese and South Asian students was analyzed to examine whether their contrasting orientations to the good life would be reflected in the kinds of life experiences they recounted. Some evidence of correspondence in this regard was found.

Keywords: Culture
Narrative
Good Life
Life Satisfaction
China
South Asia
Identity
Self
Advisor: Tafarodi, Romin