VictorJuiz/thesis huggingface dataset:
Investigations into the Targeting and Substrate Specificity of Activation-induced Deaminase
Keywords: activation induced cytidine deaminase
antibodies
somatic hypermutation
class switch recombination

The processes of secondary antibody diversification are initiated by the mutagenic, B cell specific enzyme, Activation-Induced Deaminase (AID). AID deaminates deoxycytosine (dC) that is located in single-stranded DNA (ssDNA) in actively transcribed DNA to initiate the processes of somatic hypermutation (SHM), gene conversion (GCV) and class switch recombination (CSR) at the antibody gene loci. These processes lead to high affinity antibodies and antibodies of various effector functions that are required to efficiently neutralize invading pathogens. It is currently unclear how the antibody genes are specifically targeted by AID over other genes. I found that AID is able to mutate a non-immunoglobulin (Ig) transgene independent of its chromosomal integration site at rates that were above background mutation rates, but were ~10-fold lower than at the antibody variable (V) region. This result suggests that AID can mutate non-Ig genes at low rates, which may explain AID’s role in oncogenesis, but nevertheless shows that AID preferentially mutates the Ig locus over other loci. While it is understood that AID specifically deaminates dC bases in ssDNA, the size, distribution and origin of these ssDNA substrates is unknown. By utilizing a unique in situ sodium bisulfite assay to detect regions of ssDNA in intact nuclei, I characterized ssDNA regions and found that they are accurate predictors of AID activity during the processes of SHM and CSR in mammalian B cells and E.coli. Importantly, with the use of E.coli models, I show that these ssDNA substrates are the product of transcription-induced negative-supercoiled DNA that correlates strongly with the mutagenic activity of AID. While several underlying mechanisms exist to prevent the mistargeting of AID, my findings suggest that by simply gaining access to ssDNA that is produced by transcription-induced negative supercoiling, AID has the potential to mutate non-Ig genes, albeit at lower rates than the antibody V-region.
Standing with Unfamiliar Company on Uncommon Ground: The Catholic Church and the Chicago Parliaments of Religions
Keywords: Religion
Religious History
Church History
Catholic History
American Religious History
American Catholic History
Chicago Religious History
Interfaith Movement
Parliament of Religions
Religious Pluralism
Interreligious Dialogue
Catholic Theology of Religions
Second Vatican Council
Assisi World Day of Prayer
Protestant perception of Catholics
Ecumenism

This study explores the struggle of the Catholic Church to be true to itself and its mission in the midst of other religions, in the context of the non-Catholic American culture, and in relation to the modern world and its discontents. As milestones of the global interfaith movement, American religious freedom and pluralism, and of the relation of religion to modernity, the Chicago Parliaments of Religions offer a unique window through which to view this Catholic struggle at work in the religious public square created by the Parliaments and the evolution of that struggle over the course of the century framed by the two Chicago events. In relation to other religions, the Catholic Church stretched itself from an exclusivist position of being the only true and good religion to an inclusivist position of recognizing that truth and good can be present in other religions. Uniquely, Catholic involvement in the centennial Parliament made the Church stretch itself even further, beyond the exclusivist-inclusivist spectrum into a pluralist framework in which the Church acted humbly as one religion among many. In relation to American culture, the Catholic Church stretched itself from a Eurocentric and monarchic worldview with claims of Catholic supremacy to the American alternative of democracy, religious freedom, and the separation of church and state. In relation to modernity, the Church stretched itself from viewing the modern world as an enemy to be fought and conquered to befriending modernity and designing some specific accommodations to it. In these three relationships, there was indeed a shift, but not at all a clean break. Instead a stretch occurred, acknowledging a lived intra-Catholic tension between religious exclusivism and inclusivism, between a universal Catholic identity and Catholic inculturation in America (and in other cultures), and between the immutability of Catholic eternal truths and their translatability into the new languages offered by the modern world. In all this the Second Vatican Council was the major catalyst. For all three cases the Chicago Parliaments of Religions serve as environments conducive to the raising of important questions about Catholic identity, the Catholic understanding of non-Catholics, and Catholic interfaith relations.
Inclusion in Peacebuilding Education: Discussion of Diversity and Conflict as Learning Opportunities for Immigrant Students
Keywords: peacebuilding
conflict
dialogue
discussion
democratic citizenship education
cultural diversity
immigrants
minority education
elementary classrooms
ethnocultural
multicultural education
critical multiculturalism

Ethnocultural minority immigrant students carry diverse histories, perspectives, and experiences, which can serve as resources for critical reflection and discussion about social conflicts. Inclusion of diverse students’ identities in the curriculum requires acknowledgement and open discussion of diversity and conflictual issues. In democratic peacebuilding education, diverse students are encouraged to express divergent points of view in open, inclusive dialogue. This ethnographic study with a critical perspective examined how three teachers in urban public elementary school classrooms with ethnocultural minority first- and second-generation immigrant students (aged 9 to 13) implemented different kinds of curriculum content and pedagogy, and how those pedagogies facilitated or impeded inclusive democratic experiences for various students. In these classrooms, peers and teachers shared similar and different cultural backgrounds and migration histories. Data included 110 classroom observations of three teachers and 75 ethnocultural minority students, six interviews with three teachers, 29 group interviews with 53 students, document analysis of ungraded student work and teachers’ planning materials, and a personal journal. Results showed how diverse students experienced and responded to implemented curriculum: when content was explicitly linked to students’ identities and experiences, opportunities for democratic peacebuilding inclusion increased. Dialogic pedagogical processes that encouraged cooperation among students strengthened the class community and invited constructive conflict education. The implicit and explicit curriculum implemented in these three diverse classrooms also shaped how students interpreted democracy in the context of multiculturalism in Canada. Teaching students as though they were all the same, and teaching curriculum content as if it were neutral and uncontestable, did not create equitable social relations. Explicit attention to conflict provided opportunities to uncover the hidden curriculum and to acknowledge structures of power and domination, creating space for development of critical consciousness. Thus culturally relevant curricula and democratic learning opportunities encouraged social and academic engagement and resulted in the inclusion of a wider range of diverse students’ voices.
Teacher Change in Bangladesh: A Study of Teachers Adapting and Implementing Active Learning into their Practice
Keywords: Teacher Development
Teacher Change
Bangladesh
Active Learning

The purpose of this study is to investigate the teacher change process and extend our understanding of how variability in the ways that primary school teachers in Bangladesh implement innovative pedagogical practices, such as active learning, reflects variations in their understanding, attitude, experience, and skill in the use of those pedagogical approaches. Multiple forms of data gathering were employed based on the concerns-based adoption model (CBAM) including an open-ended statement of concern, interviews, and class observations from a purposive sample of ten teachers working in ten different schools. Additional interviews were also conducted with staff responsible for the teachers' professional development. Five main findings emerged from the research. First, there was a split between novice teachers who were committed to following the prescriptive lesson plans and more experienced teachers who adapted their lessons to accommodate differences in student readiness and performance. Second, the majority of teachers appeared to be satisfied with their use active learning methods and the mandated lessons with little projected variation in how they will implement the innovation in the future. Third, the class observation findings indicate that the majority of teachers were rated as ideal users of active learning methods in the classroom. Fourth, findings indicate that professional development and a commitment to building networks among teachers and support staff helped facilitate teachers' confidence and competency. Fifth, among the most influential factors shaping teachers' use of active learning methods were the availability of supplementary learning and teaching resources. Implications for professional development and support for teachers, the applicability of CBAM-based research in low-income country contexts like Bangladesh, as well as future areas of comparative, international, and development education research are discussed in light of those findings.
Understanding of the Nature of Science: A Comparative Study of Canadian and Korean Students
Keywords: nature of science
perceptions of assessment formats
perceptions of assessment content
perceptions of learning science
comparative study

This study was designed to identify students’ perceptions of learning activities, assessment formats, and content on their understanding of the nature of science (NOS) by comparing and examining constructs created by Canadian and Korean students. Participants were 217 Canadian and 319 Korean Grade 8 students that filled out questionnaires; additionally, 9 students volunteered for semi-structured interviews. Descriptive statistics, multivariate analysis of variance and partial least squares were used to examine the quantitative data. A conceptually clustered matrix was used for the qualitative analyses. Results indicated that students from both countries perceived 1) their learning activities were teacher-directed, 2) class presentations and discussions occurred least frequently, 3) paper-and-pencil tests determined science scores, 4) science tests relied heavily on knowledge of science while knowledge about science was least likely to be assessed, and 5) generally students held relativistic views on science. The effect for country on NOS concepts was statistically significant across all of their perceptions except for the concepts of culturally embedded science and the perceptions of short-answer test formats. Specifically, Canadian students perceived that they had relatively more student-directed activities while Korean students perceived that they had more teacher-directed science lab activities. Further, Canadian students were inclined to hold more relativistic views across the NOS concepts. It was also noted that Korean students provided more political examples while Canadian students provided stem cell research or environmental issues. An examination of associations revealed that students’ learning activities, assessment formats, and content are good predictors of NOS understanding since these constructs explain variances from 19.7% for Empirical NOS to 63% for Scientific Methods. Results from students’ open-ended responses to the NOS concepts and the semi-structured interviews were consistent with the quantitative analyses. Most interviewees agreed that what, and how, they learned science-- and how their learning was assessed--affected their views of science since school science education was the important factor in developing their scientific knowledge. These results imply that diverse learning activities and assessments could prove to be a better approach to enhancing students’ understanding of NOS than teacher-directed learning activities and test formats requiring a single correct answer.
Rhodium and Palladium Catalysis in the Synthesis of Carbo- and Heterocycles
Keywords: heterocycles
transition metals
domino reactions
one-pot reactions
enantioselectivity
catalysis

This thesis describes the development of transition metal catalyzed transformations towards the synthesis of stereochemically rich motifs and heterocycles. The main themes present throughout this thesis are rhodium-catalysis in reactions of boronic acids with alkenes and alkynes, the use of alkynes as a key motif in the synthesis of heterocycles, and the use of domino and one-pot processes to effect high efficiency in multistep transformations. In Chapter 1, a rhodium-catalyzed desymmetrization of diazabicyclic alkenes with boronic acids is discussed. In this work a chemodivergent and enantioselective process for the synthesis of substituted cyclopentenes and cyclopentanes is developed. Both the chemo- and the enantioselectivity of the reaction are shown to be highly dependent on the phosphine ligand structure. The observed reactivity of rhodium is further applied to a domino reaction to synthesize highly substituted benzofuranones. In Chapter 2, the reactivity of boronic acids and alkynes under rhodium catalysis is exploited as a key step to access polycyclic motifs. In the first part of this chapter the development of a domino process using both rhodium and palladium catalysis is described. Detailed mechanistic investigations allow some insight into the interactions between two catalysts. In the last part of this chapter, preliminary experiments in the application of multimetallic catalysis in the synthesis of azadibenzoxepines are discussed. Chapter 3 summarizes work on the arylation of propargylic alcohols with boronic acids under rhodium catalysis. This reaction is shown to proceed with high regioselectivity and can be conducted under mild conditions. The resulting allylic alcohols are shown to be versatile motifs and are applied in a synthesis of indenes and quinolines. In the final chapter of this thesis, iodotriazoles are explored as key intermediates in the synthesis of fused triazole-containing heterocycles. Palladium-catalyzed cyclization, either through C-H functionalization or through Heck coupling, is achieved. Furthermore, it is shown that the copper-catalyzed azide-alkyne cycloaddition and palladium-catalyzed C-H arylation can be combined into a one-pot process.
The Healing Journey: What Are the Lived Experiences of Suicide Survivors Who Become Peer Counsellors?
Keywords: suicide bereavement
peer counselling

The suicide of a loved one is a traumatic life event that brings considerable emotional suffering. In the present study, the term suicide survivor refers to an individual bereaved though suicide. In the aftermath of their loss, some suicide survivors become peer counsellors and thereby draw on their painful experiences to provide assistance to others bereaved in this manner. Although these individuals play an important supportive role, little is known about their experiences with doing this kind of volunteer work. This study sought to explore the phenomenon of peer counselling in suicide bereavement by addressing the question, what are the lived experiences of suicide survivors who become peer counsellors? The purpose of the study was to understand how these individuals conceptualize their volunteer work and how their volunteerism may affect their own ongoing healing from the loss to suicide. Participants were 15 individuals bereaved through suicide who had been volunteering with others bereaved in the same manner for at least two years. This research employed a qualitative phenomenological methodology to provide a detailed description of participants’ journeys that went from experiencing the suicide of a loved one, to the decision to become a peer counsellor, to, finally, providing support to other survivors. The findings suggest that participants understand the provision of peer counselling as a transformative process. As a result of their volunteering, they undergo personal growth and acquire new skills. They conceptualize providing peer counselling as reaching out to other survivors of suicide and thereby countering the loneliness and isolation of suicide bereavement. For the participants, being a peer counsellor means actively challenging the silence around suicide by speaking out about suicide-related issues and offering other survivors a safe space to share their stories. The broader implications of these findings for suicide postvention research and clinical practice are addressed.
The Effect of Docosahexaenoic Acid in a Mouse Model of Neuroinflammation
Keywords: docosahexaenoic acid
neuroinflammation

Several studies have shown that dietary omega-3 polyunsaturated fatty acids (n-3 PUFA) are beneficial in neurodegenerative diseases, although the mechanism of action is not agreed upon. Because most neurodegenerative diseases have an inflammatory component, it is possible that docosahexaenoic acid (DHA) is anti-inflammatory in the brain as it is known to be in several non-neural tissues. Specialized pro-resolving mediators (SPM) are metabolized from DHA and are leading candidates to explain the anti-inflammatory effects of DHA. The goal of this work was to investigate the role and potential mechanisms of action of DHA in neuroinflammation. In our first approach, fat-1 transgenic mice had higher phospholipid and unesterified DHA levels in their hippocampi, and attenuated lipopolysaccharide (LPS)-induced neuroinflammation, compared to wildtype littermates. Feeding wildtype littermates n-3 PUFA mimicked hippocampal DHA levels and LPS-induced neuroinflammatory responses of fat-1 mice, indicating DHA is anti-neuroinflammatory whether derived from the diet or the activity of the fat-1 protein. In an attempt to further augment hippocampal DHA levels, feeding n-3 PUFA adequate mice an n-3 PUFA diet increased phospholipid but not unesterified DHA levels, and did not attenuate LPS-induced neuroinflammation, highlighting the potential importance of unesterified DHA. Directly infusing unesterified DHA into a cerebral ventricle throughout LPS-induced neuroinflammation mimicked several aspects of the attenuated neuroinflammatory response seen with our chronic dietary and transgenic models, as did infusing its 17S-hydroperoxy-DHA (17S-HpDHA) derivative, a precursor to SPM. The metabolism of DHA to SPM in the brain was found to be distinct from non-neural tissues, characterized by the presence of protectin D1 and maresin 1, and the absence of resolvin D1 or D2. Further, infusing 17S-HpDHA increased protectin D1 concurrent to attenuating neuroinflammation, suggesting protectin D1 is responsible for some of the anti-neuroinflammatory effects of DHA. In conclusion, DHA is anti-neuroinflammatory in a mouse model of neuroinflammation, in part, via its metabolism to SPM.
Issues in the Left Periphery of Modern Irish
Keywords: Modern Irish
Syntax
Relative Clause
Linguistics
Morphology
Semantics

Although the syntax of the left periphery of the Irish clausal architecture has been the subject of considerable research within the generative paradigm, many questions remain unresolved. The general goal of this thesis is to explore some of these understudied territories. Specifically, I consider two distinct, but ultimately related phenomena: headless relative clauses and dependent verbal morphology. I will make four major claims: The first two concern the syntax (and semantics) of the headless relative clause. First, despite the fact that the particles that appear in resumptive relative clauses and in headless relative clauses are morpho-phonologically identical as aN, headless relative clauses are derived by movement, not by means of resumption, and thus the particles in these two constructions are not the same. Second, headless relative clauses are amount relative clauses, in the sense of Carlson (1977); and thus I claim, adopting Grosu and Landman's (1998) notion of complex degree, that the element that undergoes A$'$-movement in a headless relative clause is a complex degree, causing degree-abstraction in the semantics. The maximalization operator then applies to the degree-abstracted relative CP. I argue that it is this operator that triggers the appearance of the particle aN in the headless relative construction. The latter two claims concern the morphosyntax of the left periphery of Irish syntax: First, I claim that there are two tense features in a single finite clause domain of Irish, and that the so-called dependent forms of irregular verbs are the surface realization of the two tense features. This account provides a stepping stone to my final claim that a feature agreeing with the maximalization operator, but not the operator itself, is realized in the headless relative particle aN and that the particles found in resumptive relative clauses and in headless relative clauses are in fact distinct Vocabulary Items and thus they are homophonous. This thesis thus fills a gap in the descriptive account of Irish syntax, and provides new insights to the theory of relativization.
Examining Sport-for-development Using a Critical Occupational Approach to Research
Keywords: sport-for-development
occupational science
Zambia
critical social science

Operating under the rubric of sport-for-development, nongovernmental organizations have mobilized sport activities as a tool for international development. Along with these initiatives, a scholarly analysis of the phenomenon has emerged. However, this body of research has not included analysis from a critical occupational perspective. This is a conspicuous shortcoming since, in the language of occupational science, sport-for-development initiatives are occupation-based programs. This study explored sport-for-development using a critical occupational approach to research I constructed, wherein the central site of knowledge production was occupations used in sport-for-development programs. Through five case studies with sport-for-development organizations in Lusaka, Zambia, I describe how staff and youth participants spoke about and understood the use of sport occupations in sport-for-development programs and the sport-for-development ideologies and practices in Zambia and how these shaped the participation of youth. Data generation included observing program activities, interviewing participants, and analyzing organization documents. The findings drew attention to the form, function, and meaning of the sport occupations used in sport-for-development, and illuminate that football, which is a heavily gendered and segregated sport, was constructed as the preferential activity for programs. This prioritization of football, in conjunction with a hierarchical, authoritative approach to decision making, and focus on the development of youths’ sports skills, led to athletic, non-disabled boys living in urban areas being the primary beneficiaries of the programs. I argue that the ideological beliefs that re/produced these understandings contributed to occupational injustices by (1) contributing to the practice of sport being used uncritically as an activity for all youth, (2) perpetuating what were considered acceptable activities for boys and girls in the local context to do, and (3) defining boys in opposition to girls, rural youth, poor youth, and youth with disabilities from both genders. Finally, I propose directions for institutionally-orientated actions to address occupational injustices and consideration of the wider uses and implications of a critical occupational approach within health and social research.