VictorJuiz/thesis huggingface dataset:
Modelling the Effects of Seston Food Quality on Zooplankton Growth: Implications for Broader food Web Dynamics

An increasing number of contemporary studies in aquatic ecology emphasize the im- portance of highly unsaturated fatty acids (HUFAs) at the plant-animal interface. Studies have demonstrated a wide range of fatty acid profiles in primary producers, forcing her- bivorous zooplankton to differentially retain fatty acids to meet somatic requirements. Herbivores also vary in their somatic fatty acid profiles; cladocerans collect Eicosapen- taenoic Acid (EPA), copepods prefer Docosahexaenoic Acid (DHA). Fatty acid internal reserves can be broken down to meet structural needs (i.e. phospholipid synthesis), fuel reproduction and may play a role in cold weather adaptation. Several authors have noted increases in HUFA concentration with lowering ambient temperatures. Cladoceran membranes form a gel at lower temperatures, while copepod membranes remain fluid and allow active overwintering. Both fish and crustaceans accumulate high concentrations of HUFAs during periods of rapid growth, but colimitation with elemental resources may exist. Recent modeling results suggest food webs with high quality (nutritional and biochemical) primary producers can attain inverted biomass distributions with efficient energy transfer between trophic levels. The adoption rate for this material into man- agement studies remains low, and while other sectors of the scientific community thrive on the potential of HUFAs, planktonic food-web studies are choosing traditional view points over forward thinking. Bearing in mind the emerging hypotheses on the critical factors that drive the energy flow in the plant-animal interface, my dissertation will at- tempt to address the following general questions: What are the distinct signatures of food quality and food quantity on planktonic food web dynamics? How do nutritional and biochemical factors affect the flow of energy at the plant-animal interface? What is our current understanding of the role of highly unsaturated fatty acids (HUFAs) in aquatic food webs? To what extent can the current generation of plankton models reproduce the lower food web patterns when explicitly accounting for HUFAs? Is the integration of the HUFA role into water quality management models feasible? Explicitly accounting for HUFAs requires integrating factors of animal physiology with macro-ecology: what are the ramifications? Finally, what are the evolutionary aspects of animals coping with food quality?

Keywords: Phytoplankton
Zooplankton
food web ecology
food quality
highly unsaturated fatty acids
stoichiometry
mathematical modelling
bifurcation analysis
Advisor: Arhonditsis, George
Iron Particle Attachment onto Model Geological Substrates

Fresh and aged iron particle attachment onto model mineral surfaces was studied using atomic force microscopy based – force spectroscopy (AFM) in different water chemistries as well as in the presence of surface modifiers for the particles (carboxymethyl cellulose polymer). The forces of interactions measured with AFM were explained in terms of classical DLVO forces (electrostatic, Born and van der Waals forces) as well as hydration, steric and magnetic forces, which are not accounted for by classical models. Theoretical interpretation of the results was thus performed using extended models, in which such interactions were considered. In the absence of surface modifiers, iron particle attachment onto silicates and iron oxides appeared favorable in pure water and salt solutions at pH 4 and 5.5, but was hindered in water amended with humic acids. Attachment of bare CIP was also unfavourable at pH 8, except in the presence of CaCl2 salt at 100 mM concentrations. Attachment between iron particles and iron oxides was favorable even in the presence of polymeric coatings. Conversely, in all solutions such coatings contributed to electro-steric repulsion between particles and silicates, which dominated over attractive van der Waals forces, albeit to a lesser extent in the presence of salts. To best assess the role of polymeric coatings in particle attachment, polymer sorption onto the model mineral surfaces considered was investigated using a Quartz Crystal Microbalance with Dissipation Monitoring. The results obtained confirmed the AFM findings, and furnished insights regarding the role of salts on polymer sorption onto substrates. Finally, the effect of aging on attachment was probed both by AFM and by analyzing cementation phenomena of iron aggregates using scanning electron microscopy, as well as by probing changes in particle compositional properties with various spectroscopy tools. The major effect of aging was to promote the formation of large cemented aggregates, which did not appear prone to disruption or remobilization.

Keywords: iron
attachment
Advisor: Sleep, Brent E.
Surviving War: The Congolese Refugee Experience

A qualitative approach was taken to explore Canadian Congolese refugees’ experience of war trauma recovery. Six volunteers (three men and three women), who self-identified as traumatized by their experience of war in Congo and had lived in Canada for less than ten years, participated in in-depth interviews. Using a constructivist grounded theory approach to analysis, a core construct of Surviving War was identified. A hierarchical model of surviving war was developed that subsumed all other categories. By extrapolating principles from this model, a theory of Surviving War was developed which identifies factors that contribute to surviving war. Limitations of the current research are presented along with suggestions for further research. Recommendations for professionals working with a refugee population are also presented.

Keywords: trauma
war trauma
war trauma recovery
surviving war
PTSD
DRC
Constructivist Grounded Theory
refugees
staged model of surviving war
psychological toll of war
war survivors
agency
fortitude
serendipity
dissociation
using interpreters in research
theoretical model of surviving war
Advisor: Watson, Jeanne
Continuity and Renewal in English Homiletic Eschatology, ca. 1150–1200

This study examines English eschatological homilies of the later twelfth century and their adaptation of both Anglo-Saxon traditions and sources introduced after the Norman Conquest. Later and non-homiletic texts are also discussed when these give clues to the continued prevalence of Anglo-Saxon and twelfth-century eschatological traditions in the later Middle Ages. Chapter 1 introduces the eschatology of the Anglo-Saxon homilists, describes English homily manuscripts written ca. 1150–1200, summarizes scholarly opinions on these texts, and details the author’s approach to the texts’ eschatological ideas. Chapter 2 examines the ‘Visit to the Tomb’ motif, which deeply influenced Anglo-Saxon depictions of individual mortality. Two early Middle English texts––Lambeth III and a treatise on the vices and virtues––contain versions of the motif that indicate a familiarity with the earlier homilies, though they also adapt the ‘Visit to the Tomb’ in new ways. The Old English texts in British Library, Cotton Vespasian D. xiv are the focus of Chapter 3. These include a description of the coming of Antichrist, the first English text of the ‘Fifteen Signs before Doomsday,’ and a typological interpretation of the Babylonian captivity. These pieces draw on both the Old English homilists and works unknown in England until ca. 1100, suggesting that twelfth-century English homilists did not sense any tension in combining ideas from pre- and post-Conquest traditions. Chapter 4 describes the Middle English reflexes of two Doomsday motifs common in the Old English homilies––the ‘Three Hosts of Doomsday’ and the ‘Four Angels of Judgment.’ The persistence of such motifs in later medieval England raises the possibility of a significant influence of Old English works on Middle English homiletic eschatology. The Conclusions section addresses this issue in further detail and suggests avenues of future research, while restating the importance of the twelfth-century homilies for the study of medieval English religious literature.

Keywords: Old English
homilies
Middle English
sermons
Advisor: Orchard, Andy
Working Together across Primary Care, Mental Health & Addictions: Exploring the Association between the Formalization of Organizational Partnerships & Collaboration among Staff Members

The purpose of this study was to explore the relationship between the formalization of inter-organizational partnerships and collaboration among staff members working together across primary care, mental health and addition organizations to provide services to adults with complex mental health and addiction needs. Phase I of the study provided an environmental scan of existing partnerships among Family Health Teams (FHTs) and Community Health Centres (CHCs), and the Mental Health and/or Addiction (MHA) organizations they partner with, in the province of Ontario (Canada). Phase II explored the relationship between formalization and a) administrative collaboration and b) and service delivery collaboration. The hypotheses proposed that staff members who are part of formalized partnerships would report higher levels of collaboration. Phase III explored how formal and informal partnerships and collaboration are experienced by the administrative and service provider staff members who work across FHTs, CHCs and MHAs organizations. Using a mixed methods approach, data were collected using electronic surveys and telephone interviews. The results of Phase I indicated that FHTs and CHCs in Ontario have between 1-3 partnerships with MHA organizations. Most are informal partnerships, have existed for less than 5 years, and most staff members (partners) interact on a monthly basis. The quantitative results of Phase II showed no significant relationship between formalization and either form of collaboration. The qualitative findings from Phase III provide two key contributions. First, the results of the interviews may help explain why collaboration was not higher in formalized partnerships, as demonstrated by the range of advantages and disadvantages experienced by administrators and service providers in both formal and informal partnerships. Second, the findings illuminate factors related to the process of creating and/or formalizing partnerships, suggesting that there may be other factors that mediate or have a direct impact on the relationship between formalization and collaboration. By bringing together the study findings, the study addresses a gap in the literature by proposing a pathway through which formalization may be associated with collaboration. The results of the study provide opportunities for future research to help improve the quality and accessibility of services to adults with complex mental health and addiction needs.

Keywords: Inter-organizational partnerships
Formalization
Interprofessional
Collaboration
Service integration
Mental health
Addictions
Primary care
Advisor: Barnsley, Janet
Nanoscale Chemical Imaging of Synthetic and Biological Materials using Apertureless Near-field Scanning Infrared Microscopy

Apertureless near-field scanning infrared microscopy is a technique in which an impinging infrared beam is scattered by a sharp atomic force microscopy (AFM) tip oscillating at the resonant frequency of the cantilever in close proximity to a sample. Several advantages offered by near-field imaging include nanoscale imaging with high spatial resolution (near-field imaging is not restricted by the diffraction limit of light) and the ability to differentiate between chemical properties of distinct compounds present in the sample under study due to differences in the scattered field. An overview of the assembly, tuning, and implementation of the near-field instrumentation is provided, as well as detailed descriptions about the samples probed and other instrumentation used. A description of the near-field phenomena, a comparison between aperture and apertureless-type near-field microscopy, and the coupled dipoles model explaining the origin of the chemical contrast present in near-field infrared imaging was discussed. Simultaneous topographic and chemical contrast images were collected at different wavelengths for the block copolymer thin film, polystyrene-b-poly(methyl ethacrylate) (PS-b-PMMA) and for amyloid fibrils synthesized from the #21-31 peptide of β2-microglobulin. In both cases it was observed that the experimental scattered field spectrum correlates strongly with that calculated using the far-field absorption spectrum, and using near-field microscopy, nanoscale structural and/or compositional variations were observed, which would not have been possible using ensemble FTIR measurements. Lastly, tip-enhanced Raman spectra of the #21-31 and #16-22 peptide fragments from the β2-microglobulin and Aβ(1-40) peptide were collected, examined, and an outline of the optimization conditions described.

Keywords: near-field microscopy
polymer
amyloid fibril
nano
Advisor: Walker, Gilbert C.
Asymptotic Analysis of Some Stochastic Models from Population Dynamics and Population Genetics

Near the beginning of the last century, R. A. Fisher and Sewall Wright devised an elegant, mathematically tractable model of gene reproduction and replacement that laid the foundation for contemporary population genetics. The Wright-Fisher model and its extensions have given biologists powerful tools of statistical inference that enabled the quantification of genetic drift and selection. Given the utility of these tools, we often forget that their model - for reasons of mathematical tractability - makes assumptions that are violated in many real-world populations. In particular, the classical models assume fixed population sizes, held constant by (unspecified) sampling mechanisms. Here, we consider an alternative framework that merges Moran’s continuous time Markov chain model of allele frequencies in haploid populations of fixed size with the density dependent models of ecological competition of Lotka, Volterra, Gause, and Kolmogorov. This allows for haploid populations of stochastically varying – but bounded – size. Populations are kept finite by resource limitation. We show the existence of limits that naturally generalize the weak and strong selection regimes of classical population genetics, which allow the calculation of fixation times and probabilities, as well as the long-term stationary allele frequency distribution.

Keywords: Stochastic processes
Population genetics
Population dynamics
Applied probability
Advisor: Abrams, Peter
Repka, Joseph
Investigations into the Targeting and Substrate Specificity of Activation-induced Deaminase

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.

Keywords: activation induced cytidine deaminase
antibodies
somatic hypermutation
class switch recombination
Advisor: Martin, Alberto
Standing with Unfamiliar Company on Uncommon Ground: The Catholic Church and the Chicago Parliaments of Religions

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.

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
Advisor: Troper, Harold M.
Inclusion in Peacebuilding Education: Discussion of Diversity and Conflict as Learning Opportunities for Immigrant Students

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.

Keywords: peacebuilding
conflict
dialogue
discussion
democratic citizenship education
cultural diversity
immigrants
minority education
elementary classrooms
ethnocultural
multicultural education
critical multiculturalism
Advisor: Bickmore, Kathy