VictorJuiz/thesis huggingface dataset:
The Fate of Organic Matter in Biochar-amended Soil
Keywords: biochar
biomarker
clay mineral
organic geochemistry
organic matter
soil

Biochar, an aromatic carbon-rich biomass pyrolysis product, has been proposed as a soil amendment to enhance soil properties and fertility. Biochar production also converts labile biomass carbon to a recalcitrant aromatic form, slowing CO2 emissions from biomass decomposition. However, biochar may stimulate soil microbial activity, potentially enhancing soil organic matter (OM) degradation. A laboratory incubation study was conducted to assess biochar-induced changes in microbial activity and soil OM molecular composition in a temperate forest soil using biomarker and nuclear magnetic resonance (NMR) techniques. Increased soil bacterial activity and enhanced degradation of plant waxes and polysaccharides were detected after 24 weeks, while lignin was more degraded after 32 weeks. NMR analysis of water- and base-extractable OM showed a reduction of labile components and an accumulation of recalcitrant soil OM constituents. The laboratory findings were tested at the field-scale via a three-year amendment study which examined changes in soil microbial activity and native OM composition following biochar, phosphorus (P) and biochar + P addition. P fertilization stimulated soil bacterial activity, whereas biochar and biochar + P addition increased both bacterial and fungal activity and shifted the soil microbial community toward fungi. P fertilization induced soil priming, resulting in an accumulation of primarily recalcitrant OM. Biochar and biochar + P shifted the soil OM composition toward a greater proportion of aliphatic lipids and lignin and a reduction in carbohydrates. The microbial community and native OM compositional shifts observed with biochar amendment may alter soil OM turnover and nutrient cycling rates in the long-term. Higher microbial activity following biochar addition may increase the production of dissolved organic matter (DOM) in soil. The role of OM-OM interactions in DOM sorption and layering on organo-clay complexes was examined through the repeated sorption of DOM onto three minerals with contrasting properties (kaolinite, montmorillonite and gibbsite). DOM sorption was initially controlled by mineral properties, but with increased DOM loading, OM-OM interactions also influenced the composition and concentration of DOM sorbed. Aliphatic-aliphatic and aromatic-aliphatic interactions were observed for organo-clay complexes containing all three minerals, and may represent important mechanisms by which DOM sorbs to minerals with diverse properties.
Jean-Luc Nancy and the Deconstruction of Christianity
Keywords: Christianity
Deconstruction
Derrida
Metaphysics
Nihilism
Religion

This dissertation is a study of the origins and development of the French philosopher Jean-Luc Nancy’s work on the “deconstruction of Christianity.” By situating Nancy's work in light of the broader Continental philosophical analysis of religion in the 20th Century, it argues that what Nancy calls the "deconstruction of Christianity" and the "exit from religion" is his unique intervention into the problem of metaphysical nihilism in Western thought. The author explains that Nancy’s work on religion does not provide a new “theory” for the study of religion or Christianity, but shows how Western metaphysical foundations are caught up in a process of decomposition that has been brought about by Christianity. For Nancy, the only way out of nihilism is to think of the world as an infinite opening unto itself, for this dis-encloses any transcendent principle of value or immanent notion of meaninglessness in the finite spacing of sense, and he finds the resources to think this opening within Christianity. By reading Christian notions like "God" and "creation ex nihilo" along deconstructive lines and connecting them with the rise and fall of this civilization that once called itself "Christendom," he attempts to expose "the sense of an absenting" that is both the condition of possibility for the West and what precedes, succeeds, and exceeds it.
Depression in People Living with HIV and Their Unmet Needs in Mental Health Care in Ontario: A Prospective Cohort Study
Keywords: Canada
Delivery of care
depressive disorder
HIV
Mental Health Services

Nearly 50% of HIV-positive patients have a history of suffering from depression. Although the condition is treatable, depression in these patients is under-recognized and under-treated, resulting in poorer clinical and quality-of-life outcomes. There are also gaps and disparities in accessing mental health care among these patients, but current evidence is limited to U.S. studies. The primary objectives of this thesis work were to: (1) establish the validity and reliability of self-report measurement instruments in identifying depression against DSM-IV criteria; (2) examine the burden of current depression and the underlying factors driving the burden; (3) estimate the rate of publicly-funded mental health service use and unmet needs for mental health care among HIV-positive patients with depression; and (4) examine the impact of depression on costly and preventable acute health services use in the Canadian health care system. A prospective cohort study was conducted by following a cohort of HIV-positive patients from October 1, 2007 to March 31, 2013 in the province of Ontario, Canada. I adopted a novel longitudinal linked data approach. Various regression models were employed for the analysis. Three self-report instruments (CES-D20, K10, and PHQ9) performed equally well and accurately when compared against DSM-IV criteria. With regards to the burden of depression, one in four HIV-positive patients was depressed. Half of depressed HIV-positive patients had a recurrent episode. In addition, there were delivery gaps in mental health care for depressed HIV-positive patientsâ one-half used mental health services and of these, one-half received minimally adequate care. Furthermore, HIV-positive patients with depression and/or substance use issues were associated with a 19â 70% elevated rate of emergency department (ED) admissions and a 17-67% elevated rate of potentially preventable ED admissions compared to those without these conditions. In sum, depression is highly prevalent in HIV-positive patients and is likely to be chronic and recurrent over time. There are delivery gaps in mental health care for depressed HIV-positive patients. More effective mental health care policies and better access to mental health care services are required to address the unmet needs of HIV-positive patients and reduce the impact of depression on their lives.
Remembering Past(s), Imagining Futures: The Politics of Hope in Palestine
Keywords: Colonialism
Hope
Memory
Palestine
Urban

Using hope as a category of experience, this dissertation explores the ways Palestinians and their Israeli-Jewish allies undermine urban spatial expropriations under Israeli-settler-colonialism. Focusing on the city of Jaffa, I analyze the ways in which the Israeli state and the Tel Aviv municipality succeeded in ‘burying’ histories of mass expulsions, organized violence and appropriations of private and public spaces. I then follow the fortunes of Palestinians – those who remained in Jaffa and became a minority under regimes of neoliberalization and Judaicization, and those who were expelled, found themselves de-nationalized and precarious refugees, some confined to decrepit camps, while others pursued opportunities for meaningful political engagement and armed struggle. The dissertation ends with a powerful gesture towards a future that undermines the colonial present and its attendant sense of hopelessness: I explore how both Palestinians and Israeli-Jews engage with the ideas of reconciliation and “living together” in the “Jaffa of tomorrow.” My focus on hope as a category of experience hinges on two main intersecting axes: temporality and place. Just as political identities are rooted in the refugee camp experience and informed by the quotidian and the present, on the one hand, and memory and absence on the other, so, I argue, is Palestinians’ understanding of the local. Rather than accepting normative assertions that define the local as a bounded place that is both community-making and exclusive of those outside of it, I wish to suggest that locality, and attachment to it, is much more multi-directional, dispersed in time and space. This understanding brings to our line of sight those people who are geographically external to place, in this case Jaffa, but have nonetheless powerful attachment to it. In many ways, then, Palestinians are fighting for the right to belong against submerged histories of ethnic cleansing and entrenched colonial denial of their attachments to places they were expelled from.
The Role of Macrophages in Bone Development, Repair, and Aging
Keywords: Aging
Fracture repair
Macrophages

With age, the risk of sustaining a fracture increases, yet bone repair becomes a slower and more fibrotic process. This fracture healing process recapitulates the process of bone development, except that fracture repair is initiated with an inflammatory response to injury resulting in the recruitment of various immune cells, including macrophages. Interestingly, macrophages are present during early bone development, yet their function during this process is not well understood. Hence, the purpose of this study was to determine the functions of macrophages during bone development, repair and aging. Using transgenic mice to constitutively ablate macrophages, we demonstrated that macrophage deficiency impaired bone marrow progenitor cell differentiation resulting in decreased bone mineral density. Constitutive or temporal depletion of macrophages during fracture repair led to decreased callus formation and bone deposition resulting in impaired bone union. When we compared fracture healing between young and old mice, we found that old animals developed a slower and more fibrotic response to healing. To determine whether the age-related delays in fracture repair are associated with changes in this macrophage population with age, we performed parabiosis and cell transplantation experiments. We found that young macrophages rejuvenated fracture repair in older animals by suppressing fibrosis and promoting bone mineralization. Furthermore, conditioned media from young, but not old, macrophages rescued osteoblast differentiation of old bone marrow progenitor cells, and analysis of these cells indicated that old cells polarized towards a pro-inflammatory phenotype. Mass spectrometry analysis of young and old macrophage secretomes identified 56 â youth factorsâ . One of these factors, LRP1, was found to promote osteoblast differentiation of old progenitor cells. Taken together, these findings demonstrate a functional role for macrophages in bone formation and fracture repair, and that substitution of old macrophages with young macrophages rejuvenates fracture healing in older mice.
Functional Dynamics of the β2-Adrenergic Receptor and Fluoroacetate Dehalogenase by 19F NMR
Keywords: Enzyme
GPCR
NMR
X-ray crystallography

Proteins represent 1/3 of the macromolecular constituents of cells and are responsible for key aspects of structural support, signal transduction, and catalysis. Protein function is controlled largely by dynamics. This is particularly true in the case of signal transduction and catalysis, where a protein is more aptly described in terms of an ensemble of key states associated with the signaling process or the reaction coordinate pathway. This thesis explores two proteins – namely, a G protein-coupled receptor, β2AR and a homodimeric enzyme, fluoroacetate dehalogenase (FAcD) - in terms of their functional ensembles and the dynamic processes which contribute to function. Chapter 2 of this thesis addresses aspects of GPCR dynamics in different detergents, as measured by 19F NMR. 19F NMR spectra of β2AR measured in dodecyl maltoside (DDM) and maltose-neopentyl glycol (MNG-3) detergent showed dramatic differences in receptor dynamics. The difference in detergent off-rates of the micelles was linked to the conformational exchange rates between functional states. Chapters 3 and 4 show that β2AR can be represented by four states (two inactive, an activation intermediate, and a fully active state). The two inactive states are in a fast exchange on an NMR time scale with lifetimes of hundreds of microseconds. The activation intermediate is found to be the most dynamic state and is entropically favored with a lifetime of ~660 milliseconds. Moreover, the full active state is only stabilized with G protein, or G protein mimetic nanobody (Nb80), and an agonist. The last part of this thesis details the role of asymmetric structure and dynamics along the reaction coordinate pathway of the bacterial dimeric enzyme, FAcD. NMR and time-resolved X-ray crystallography show that dynamic collective motions across the dimer drive its catalysis via allostery between protomers. The apo-enzyme is characterized by a subtle asymmetry, which is averaged by millisecond timescale conformational exchange between protomers. Asymmetric binding of substrate stabilizes an excited state in the apo-enzyme and increases the dynamics of protomer exchange. The stabilized excited state shows dramatic changes in local protein dynamics and the number of water molecules around the empty protomer which facilitates the catalysis in the bound protomer.
Mixed Reality Gaming for Older Powered Chair Users: A Human Factors Model of Well-being and Engagement
Keywords: engagement
game design
mixed reality
older adults
power mobility
well-being

Older adults who develop mobility impairments and begin to use powered chairs, such as mobility scooters and electric wheelchairs, are at risk of experiencing parallel declines in well- being. Yet, most interventions focus on training, chair function, and environmental factors. To address this gap, a cooperative dyadic mixed reality platform was developed to improve the well-being of older powered chair users along two lines: internal, in terms of performance mastery; and external, in terms of empathy training of an able-bodied other. Four studies were conducted: (1) a needs and requirements analysis study using human factors focus group methodology; (2) a usability evaluation of the game prototype, which also captured baseline well-being data; (3) a usability evaluation of the facilitating display for mixed reality during powered chair use; and (4) a semi-longitudinal, exploratory evaluation of the mixed reality gaming platform. Psychological measures of well-being, particularly eudaimonia (personal growth, self-determination and self-expression) and hedonia (pleasure, enjoyment) were captured and analyzed in combination with measures of game engagement and usability. The main contribution is a theoretically- and empirically-supported human factors model of well-being, game engagement, and usability based on established measures and validated with older powered chair users within a human- computer interaction context.
Capital-nation-state: A Genealogy of Yasukuni Shrine
Keywords: Conscription
Land Reforms
Political Economy
Tokyo
Urban History
Yasukuni

Japanâ s militaristic past continues to haunt the present and often at the center of these debates is the site that commemorates the war dead, Yasukuni Shrine. This dissertation seeks to address the political economy of the shrine and argues that this issue cannot be transcended if the history of the development of capitalism in Japan continues to be bracketed off in favor of narrating the shrine strictly through the discourse of the nation and the state. This claim derives from the observation that Yasukuni Shrine and the development of capitalism in Japan emerge at the same historical moment and thus they must also share an underlying logic. By adding capital to the equation, it becomes evident that the shrine is at the nexus of the operation of Capital-Nation-State and thus played a role in producing the very idea of modern Japan. Using a variety of primary sources, from state documents to personal diaries and newspaper reports, the archival research reveals how the shrine, as a state institution, was shaped by economic interactions just as much as it was by state ideology. In each chapter a different aspect of how the history of capitalism intersects with the space of the shrine is examined through the themes of everyday life, commodity exchange, urban planning, and universal conscription. Key to all of these themes is the relation of political economy to space. Whether it was facilitating commodity exchange on the shrine grounds or making land transactions, Yasukuni Shrine was an active agent in shaping not only the immediate space around it, but also in forming a national space. By examining the political economy of Yasukuni, it becomes evident that the shrine played an important role in propagating various types of exchanges (whether economic, religious or political) that were essential to forming this space. Thus, the results of this project show that Yasukuni was more than just a state institution that fostered the creation of national subjects; it was a space that brought together the three social forms, Capital-Nation-State, which characterizes and dominates our current socio-political landscape.
HELB Is a Feedback Inhibitor of DNA End Resection
Keywords: DNA repair
HELB
Homologous recombination
Resection
RPA

DNA double-strand breaks are toxic lesions, which jeopardize the genomic integrity and survival of all cells and organisms. Repair of these lesions by homologous recombination requires the formation of 3′ single-stranded DNA (ssDNA) overhangs by a nucleolytic process known as DNA end resection. Recent studies have significantly expanded our understanding of the initiation of resection, the molecular machinery involved in its execution, and its regulation throughout the cell cycle. However, the mechanisms that control and limit DNA end resection once the process has begun are unknown. I hypothesized that such activities may be coordinated by the ssDNA-binding complex Replication Protein A (RPA), which rapidly coats the 3′ ssDNA overhangs produced by resection. A proteomic analysis of RPA interactions following DNA damage identified the superfamily 1B translocase, DNA helicase B (HELB). Using cellular and biochemical approaches, I found that following RPA-dependent recruitment of HELB to the sites of DNA double-strand breaks, HELB inhibits EXO1 and BLM-DNA2 nucleases, which catalyze long-range resection. This function requires HELB’s catalytic activity and ssDNA binding, suggesting a mechanism where HELB translocates along ssDNA to displace the nucleases. HELB acts independently of 53BP1 and is exported from the nucleus as cells approach S phase, concomitant with the upregulation of resection. I conclude that mammalian DNA end resection triggers its own inhibition via the recruitment of HELB.
Economies of Flesh: Event-led Urbanism and the Impact on Sex Work in Rio de Janeiro, Brazil
Keywords: affective-performative labour
event-led urbanism
physical cultural studies
sex work
sport mega-event

Physical Cultural Studies has examined the extent to which a (sport) mega-event, like an environmental disaster, can facilitate the implementation of a “shock doctrine” (Klein, 2007) in which controversial policies, used to impose particular ideological ends, are pushed through in the wake of a cultural spectacle (Boykoff, 2013; Hayes Horne, 2011), and the urban environment is created as a series of spectacularized spaces of leisure consumption, the ultramodern sanctuaries for bourgeois bodies (Belanger, 2000; Friedman Andrews, 2011; Silk, 2013). The sentiment of shock or enthusiasm is used to distract from, and rationalize, the political-economic restructuring observed in a moment of crisis or celebration. At the heart of disaster (or event) capitalism is the need to facilitate accelerated capitalist expansion by reconfiguring the existent sociopolitical agenda. Celebration capitalism has been characterized by the emergence of a state of exception, unfettered commercialism, repression of dissent, questionable sustainability claims, and the complicity of the mainstream media (Boykoff, 2013). The manifestation of narrow, market-driven ideologies, coupled with the aggressive pursuit of growth-inducing resource material, has continued to foster resistance across host cities. In the current moment, FIFA (Fédération Internationale de Football Association) and the IOC (International Olympic Committee) have generated an increasing scale of dissent (Davidson, 2013; van Luijk Frisby, 2012). Yet the overemphasis on resistance has detracted from the everyday realities of those stuck in the pseudoshadow of the mega-event spotlight. In my work I ask: How does the everyday react to the intervention of a mega-event? This dissertation focuses on the “lived experience(s)” of local women who embodied market-oriented ideologies to react entrepreneurially to a FIFA-crisis/celebration, in order to create and enhance their “survival circuits” (Sassen, 2009) within contested urban terrain. Through the collection and analysis of ethnographic data, I document stories of everyday life from women involved in sexual commerce in Rio de Janeiro, Brazil, during the 2014 FIFA World Cup to connect their “everyday” with larger social processes of global capitalist expansion, and demonstrate the manner in which these local women produce (un)intended/under-examined embodied physical cultural legacies associated with the sport mega-event.
Clinical Reasoning by Expert Bobath Instructors
Keywords: Bobath
Clinical Framework
Clinical Reasoning
Conceptualization of Movement

Background: Clinical reasoning, a complex clinical skill, is central to professional accountability but currently invisible in the rehabilitation sciences evidence base with an associated under-development of underpinning theory. Understanding and minimizing movement problems is a focus of rehabilitation. Movement performance is a key aspect of Bobath clinical practice, the most widely used neuro-rehabilitation approach. To date there are no publications addressing the clinical reasoning process or the conceptualization of movement by Bobath therapists despite considerable investigation of the effectiveness of this rehabilitation approach. Purpose: To address this research gap, this dissertation aimed to develop an interpretive understanding of the clinical reasoning process of expert Bobath therapists. Methods: To accomplish this aim, a modified e-Delphi method was used to define a Bobath Clinical Framework. A qualitative research approach was adopted for the second study using Interpretive Description methodology to explicate a conceptual understanding of movement and the clinical reasoning process of expert Bobath therapists. Results: Eight statements representative of the conceptual framework, and three assumptions and eight principles representing key aspects of clinical practice reached consensus in the modified e-Delphi successfully identifying a Bobath Clinical Framework. Twenty-two IBITA instructors participated in the Interpretive Description study identifying three key elements integral to the instructorsâ conceptualization of movement specifically the integration of postural control and selective movement, and the unique role of visuo-spatial kinesthetic perception, an aspect of practical wisdom, in the clinical reasoning process. Conclusions: The development of a Bobath clinical framework and explication of the Bobath therapistsâ conceptualization of movement formed a practice epistemology exposing and illustrating the critical role of phronesis (practical wisdom), in the clinical reasoning process. This thesis highlights the need for a multi-dimensional knowledge base, procedural and conditional knowledge, in addition to declarative knowledge, necessary for clinicians to make wise judgments with respect to individual clients, the clinical reasoning process.