VictorJuiz/thesis huggingface dataset:
Spatial Characterization of Rib Cortical Bone Microstructure and the Effect of Nutritional and Physiological Stresses

The dynamic relationship between bone tissue and life conditions (e.g. mechanical, nutritional and physiological stresses) is well known and makes bone histology appealing for reconstructing past life conditions. However, a comprehensive model for interpreting bone microstructure has not been established. Current studies are somewhat limited by population-centric approaches that do not enable us to gain an appreciation of the underlying etiologies for the observed differences. These approaches are in some ways inconsistent with recent bone biology research and often ignore the range of life conditions known to affect bone tissue. A growing appreciation for physiological differences between cortical bone envelopes and the spatial nature of bone biological processes further supports advancing histological methodologies. This research spatially characterized the effect of nutritional and physiological stresses on bone modeling and remodeling process in human rib cortical bone tissue. This study applied a novel histological, geographic information system based method to spatially map and analyze cortical bone microstructure from 138 rib cross-sections representing individuals aged 20 to 88 years (Nmale =75, Nfemale=63). Five distinct populations with different levels of nutritional and physiological stresses were included. This diversity enabled an in-depth examination of the effect nutritional and physiological stresses have on cortical bone tissue.This study demonstrates that nutritional and physiological stresses can alter bone microstructure, but this alteration is largely a result of growth and development perturbations prior to the observational window. Nutritional and physiological stresses minimally affect ongoing bone remodeling and modeling processes in adult rib cortical bone tissue. Histomorphological attributes and bone remodeling processes vary with respect to periosteal distance. This variation is not significantly related to nutritional and physiological stress, but appears to be mechanically constrained. This study demonstrates the resilience of adult human bone tissue to adverse life conditions; it enhances our ability to interpret human cortical bone microstructure.

Keywords: Bone Histology
Life Conditions
Spatial Characterization
Advisor: Pfeiffer, Susan
Investigation of Biopolyol Spray Foam Insulation Modified with Natural Fibers

Rigid spray foam insulation is widely used as wall insulation in construction industry. Replacing synthetic polyether and polyester polyols with bio-based polyol and using water as blowing agent, would provide eco-friendly spray foam which is good for the environment and make buildings a safer place to live. The objectives of this work were to produce sustainable spray polyurethane foam insulation from soy-based polyol, derived from agricultural product and enhance its properties by incorporation of wood and cellulose fibers, a consumer forest product. The composite foam systems and the neat foam prepared in this manner were evaluated in terms of their thermo-mechanical properties, morphological characterization, and also their resistance contribution to overall structural integrity of the buildings against natural shear forces. Wood fiber and cellulose fiber were incorporated as reinforcement in foaming in three stages, 13php, 26php, and 40php. The fiber size, dispersion and concentration within the matrix affected the reinforcing quality. The interactions and the effects of fiber in composite foams were observed at cellular level by Fourier transform infrared and scanning electron microscopy to evaluate their performances. The results indicated incorporation of fiber had an impact on the cell morphology of the composite foam system as compared to the non-fiber foam. The cell structure became more uniform while cell density was increased proportionate to the fiber concentration. Resin found to be compatible with fiber at interfaces but, the viscosity of matrix polymer increased with addition of fiber. The viscosity increase was 20% under 26php fiber concentration. The thermo-mechanical properties of the composite foam systems were improved to some extent at lower fiber concentration, under 26php, due to less impact of viscosity. Cellulose fiber performed better as reinforcement than that of wood fiber due to superior compatibility, higher strength and better fiber quality.

Keywords: Cellulose fiber
Isocyanate
Polyol
Polyurethane
Wood fiber
Advisor: Sain, Mohini
Deep Learning Approaches to Problems in Speech Recognition, Computational Chemistry, and Natural Language Text Processing

The deep learning approach to machine learning emphasizes high-capacity, scalable models that learn distributed representations of their input. This dissertation demonstrates the efficacy and generality of this approach in a series of diverse case studies in speech recognition, computational chemistry, and natural language processing. Throughout these studies, I extend and modify the neural network models as needed to be more effective for each task.In the area of speech recognition, I develop a more accurate acoustic model using a deep neural network. This model, which uses rectified linear units and dropout, improves word error rates on a 50 hour broadcast news task. A similar neural network results in a model for molecular activity prediction substantially more effective than production systems used in the pharmaceutical industry. Even though training assays in drug discovery are not typically very large, it is still possible to train very large models by leveraging data from multiple assays in the same model and by using effective regularization schemes. In the area of natural language processing, I first describe a new restricted Boltzmann machine training algorithm suitable for text data. Then, I introduce a new neural network generative model of parsed sentences capable of generating reasonable samples and demonstrate a performance advantage for deeper variants of the model.

Keywords: Boltzmann machines
connectionism
deep learning
machine learning
natural language processing
neural networks
Advisor: Hinton, Geoffrey E
The Politics of Knowledge Production in HIV/AIDS Research about Ontario's African, Caribbean, and Black Communities

HIV/AIDS science has long been a site of contestation by civil society actors. Early activists originating in the gay community affected the course of HIV/AIDS science by challenging the definition and treatment of the disease. However, little is known about the politicized efforts of other groups disproportionately affected by HIV/AIDS, particularly Black communities, to mobilize and shape research about their communities. This thesis interrogates social relations and power in research about HIV/AIDS in Ontario's African, Caribbean, and Black (ACB) population. Using Pierre Bourdieu's field theory, together with concepts from the sociology of science and race theory, I investigate tensions and struggles over the definition and production of ACB HIV/AIDS research. Through a review of research grants and 21 semi-structured interviews with actors engaged in research, I characterize the field of ACB HIV/AIDS research and explore the struggles therein. I also examine what is at stake in these struggles and their implications for the reproduction of, and resistance to, systems of domination. My findings indicate that the field of ACB HIV/AIDS research is composed of interlocking scientific disciplines and non-scientific domains. Struggles over the field's organizing principles are represented in the different stances that participants adopt concerning the legitimate definition of research. Some academic-based actors define HIV/AIDS research according to empiricist principles oriented toward technical control and prevention of disease. These serve to depoliticize science and defend scientific authority and the social order. Other actors, both academic- and community-based, depict HIV/AIDS research through a social justice lens focussed on the empowerment of the ACB population and improvement of its social position. Community-based ACB actors in particular resist the epistemic dominance of science and argue for the legitimacy of non-scientific actors as "knowers" of the ACB population, and research as a socio-political tool. These subversive strategies challenge scientific authority and threaten to disrupt the status quo. The findings suggest that ACB actors navigate between utilizing existing mechanisms of science and resisting the dominance of science in shaping knowledge about their lives. My research contributes to the sociology of science scholarship concerning the politics of knowledge, scientific boundary work, and health movements.

Keywords: boundary work
epistemology
field theory
HIV/AIDS
race
social movements
Advisor: McDonough, Peggy
The Examination of Changes in Dynamic Risk Factors and Recidivism Over Time in Youth Offenders

Risk assessments that include dynamic risk factors are increasingly being utilized within the youth justice system to predict a young person's likelihood to reoffend, to assist with case management, and to better inform intervention services. Based on the principles of the Risk-Need-Responsivity (RNR) framework, the Youth Level of Service/Case Management Inventory (YLS/CMI) is a widely used risk assessment tool that demonstrates strong psychometric properties among youth offenders. However, most studies to date have relied solely on single-wave, cross-sectional research designs that essentially treat dynamic risk factors as static. The purpose of the present study was to determine whether the RNR dynamic risk factors assessed by the YLS/CMI do in fact change over time and whether identifying these changes improved the prediction of recidivism. To answer these research questions, 200 12-18 year-old youth were tracked from the time of their first risk assessment conducted at probation to their transition out of the youth justice system. Information pertaining to post-assessment re-offences was collected from official conviction records. A series of generalized linear mixed modelling and latent class growth modeling analyses were used to assess change in dynamic factors over time and to examine the effect of youth-specific predictors on these changes. A hierarchical Cox regression with time-dependent covariates and Receiver Operator Characteristic (ROC) analyses were used to assess the predictive accuracy of the YLS/CMI on recidivism rates. Results indicated that most dynamic risk domain scores increased over time but that there was significant individual variation among youth at initial status and in the rate of change. Even when controlling for youth-specific factors, results showed that lower risk youth at the time of initial assessment increased in risk at a greater rate than higher risk youth; this finding was unlikely related to ceiling effects since most youth fell in the moderate risk range. The inclusion of dynamic risk scores improved the predictive accuracy of recidivism over and above static risk factors and risk scores obtained from the initial assessment. Findings from the current study have implications for enhancing the RNR framework, improving the accuracy of risk assessments, and informing treatment implementation.

Keywords: Changes in Risk
Dynamic Risk Factors
Dynamic Risk Prediction
Risk Assessment
YLS/CMI
Youth Offenders
Advisor: Peterson-Badali, Michele
A Highly Perfused Tissue-engineered Construct for Gingival Tissue Regeneration using Degradable/Polar/Hydrophobic/Ionic Polyurethanes and A Dynamic Co-culture System

Gingival tissue engineering represents a promising method for regenerating the gingival lamina propria. In this thesis, a degradable polyurethane (degradable/polar/hydrophobic/ionic polyurethane (D-PHI)) scaffold was shown to support the proliferation and collagen production by human gingival fibroblasts (HGFs). As the gingival lamina propria is highly vascular, a perfusion bioreactor was designed to facilitate medium perfusion through HGF-seeded scaffolds. In the perfused (dynamic) culture, HGFs showed enhanced proliferation, metabolic activity and collagen production when compared with static cultures. These data suggest that the metabolic, phenotypic and differentiation state of HGFs were altered in dynamic cultures. Hence, the influence of the D-PHI material and perfusion on myofibroblast differentiation was explored. This study demonstrated that D-PHI does not enable myofibroblast differentiation over the 28-day culture. Moreover, it was shown that the perfused D-PHI scaffold modulated the fibroblast phenotype through complex mechanisms involving transforming growth factor (TGF)-beta1, basic fibroblast growth factor (FGF-2), beta1-integrin, and focal adhesion kinase, all of which were upregulated at the early time point (1 day) of the dynamic culture. These data provided new insights into the signalling pathways that are associated with the regulation of myofibroblast differentiation in a perfused system with elastomeric polymers such as D-PHI. Furthermore, using the bioreactor system developed in this thesis, a dynamic co-culture system with human umbilical vein endothelial cells (HUVECs) and HGFs was established. With the perfusion of medium, the production of vascular endothelial growth factor, an angiogenic factor, was induced in the HGFs. This study also investigated different co-culturing conditions (e.g. cell density, type of culture medium, cell seeding ratio) that can optimize cell growth, HUVEC cluster formation, angiogenic factor production, inhibition of myofibroblast differentiation, and collagen expression. It was found that at 80,000 cells/scaffold (12.95 mg, 80% porosity), a greater proportion of HGFs in the co-culture (i.e. 1:2 (HUVEC:HGF)) cultured in a 50/50 mixture of the HUVEC medium and HGF medium (by volume) can potentially induce HUVEC cluster formation, augment cell proliferation, and increase angiogenic factor production. The knowledge from this thesis could enable rational developments of the co-culture systems for building a functional, highly vascularized tissue-engineered construct for gingival tissue regeneration.

Keywords: Endothelial Cells
Fibroblasts
Gingival Tissues
Myofibroblast Differentiation
Polyurethane
Tissue Engineering
Advisor: Santerre, Paul
Pedagogical Stylistics and Concept-based Instruction: An Investigation into the Development of Voice in the Academic Writing of Japanese University Students of English

This thesis study examines, through the lens of Vygotsky's sociocultural theory of mind, the influence and relationship of pedagogical stylistics (an analytic technique for examining text-based discourse features) and concept-based instruction (CBI) on academic writing performance and authorial voice construction in a high-stakes, essay writing context. Guided by CBI, 7 Japanese university-aged ESL students engaged in stylistics-based analyses of literary texts during a 3-week intensive course designed to prepare participants for the independent writing task of the TOEFL iBT. Participants were asked to consider how authors' lexical choices inform the semantic and pragmatic features of English literary texts associated with 5 target voice features: hedges, boosters, attitude markers, authorial self-mention, and direct reader references. Writing development was traced across 9 writing samples collected prior to, during, and after the intervention. The written compositions were analyzed and then compared, using non-parametric statistics, over time and with the writing of 3 students in a control group (that did not receive the intervention). Post-intervention stimulated recall and semi-structured interviews complemented the dataset. The analyses revealed: (a) statistically significant differences and large effect sizes across the written compositions, indicating improvements in learners' overall quality of writing (p = .002; W = .5) and in learners' overall quality of authorial voice (p = .002; W = .51); (b) authorial voice development involved a nonlinear, iterative process of cognitive uptake derived from classroom-based affordances focused on stylistics; and (c) CBI-informed pedagogy mediated authorial voice development despite limitations in the teaching method. Based on these findings, instructors may consider employing stylistics by using CBI for improving students' overall writing and authorial voice in high-stakes writing contexts, implementing iterative learning environments for developing overall writing and authorial voice, focusing on writers' authorial voices in high-stakes writing contexts, and ensuring learners have sufficient opportunities to develop metalanguage in stylistics-informed contexts; researchers should examine the microgenetic development of authorial voice through the lens of a complex dynamic systems theory of SLA, expand the purview of L2 stylistics using empirically-based studies, and analyze how learners develop and use metalanguage in stylistic contexts.

Keywords: authorial voice
concept-based instruction
L2 writing
microgenesis
sociocultural theory
stylistics
Advisor: Cumming, Alister
Reconstructing Social Housing: The Socio-spatial Effects of Welfare State Transformation in Toronto's Regent Park

This dissertation charts the socio-spatial impacts of welfare state reform on the landscape of public housing, and the transformation in modes of governance that mark the shift from a welfare state to a more neoliberal regime. Specifically, it explores the processes and implications of socially-mixed public housing redevelopment, and the ways in which urban planning is used as a social fix. Its focus is Toronto's Regent Park, Canada's first and largest government housing project, which is currently undergoing a $1.75 billion overhaul in which the entire 69-acre site will be razed and rebuilt. Regent Park is widely considered to be a mid-century planning project that failed. Its redevelopment, premised upon the planning philosophy of social mix - diversity of income groups and housing tenure - is intended to be a reversal of poor design and residential segregation. The redevelopment is also financially motivated, unrolling against a backdrop of encroaching neoliberal reform.The appeal to a "healthy" community is central to the re-imagined Regent Park. I explore Regent Park's redevelopment as an exercise in community building and as a political-economic project, with a focus on the rhetoric that underlies these motivations, and on the ways in which these interventions have material effects on the built environment, and on the people who live there. This dissertation, then, is an exploration of attempts to ensure physical and social well-being through an engineering of urban space, and the forms of governance made manifest in these attempts. As such, it is also an exploration of the intersection of two political rationalities. In the current moment, private entities are increasingly called upon to provide public services, in tandem with or in lieu of the state. In Regent Park, the ideals of neoliberal city-building sometimes clash with transforming, but still-existing, bureaucratic welfarist institutions. This thesis examines the ways in which discourses of redevelopment are in tension with the operating of the bureaucratic welfare state, and the ways in which social housing residents experience these competing rationalities and contradictions in political agency.

Keywords: Canada
poverty
social housing
social mix
urban revitalization
welfare state transformation
Advisor: Barker, Joshua
McElhinny, Bonnie
Desert Storm

Desert Storm (Asifat Al Sahra) for orchestra is a contrapuntal composition in which the melody and counter melody are based on an Arabic mode called the nahawand. The nahawand mode is similar to the Western natural minor scale ascending, and to the harmonic minor descending. The unique characteristic of this scale is the final descending sequence of seconds. The opening of the piece introduces three intervals which become the basis of the non-contrapuntal sections, as well as the 10-beat rhythm called wazn aqsaq sama'i which is omnipresent throughout the entire composition, resulting in a sense of relentlessness. Following the opening section, the piece moves into a non-contrapuntal, bi-tonal section dominated by pizzicato strings, before transitioning back into the contrapuntal material. Following this, the next section creates a wash of sound, before pulling the other instruments into the storm and arriving at the piece's first climax. The climax itself uses the major 3rd, the 2nd interval introduced in the opening. In the calm after the storm, the harp is first introduced, carrying both melody and counter melody, before being unsettled by a "ticking" sensation created in the rest of the orchestra and using the tritone, the 3rd interval introduced in the opening, as if counting down towards the next storm to come. The piece ends in a dramatic and sudden climax, recalling the same chords as the previous climax, but slower and with more foreboding than fury. The meaning behind Desert Storm can be seen in layers, the outermost of which is how the music depicts the sensation of being trapped in a sand storm. Sand storms begin with the wind picking up, then escalate into a suffocating and relentless force. Using bi-tonality, the layering of many parts on top of one another, and the relentless underlying rhythm gives the sensation of a lack of clarity, and also of the uncontrollable and unstoppable violence that is wielded by nature. Aside from this, I feel Desert Storm to be a reflection on life in the Middle East - every situation is complex, unclear, and constantly on the verge of explosion, where one storm ends with the clock already ticking towards the next one. It was my desire that through this piece I would explore some musical elements of my own culture, but approach them from a classical standpoint, working with them not in the way that an Arabic musician would, but as a Western classical composer.

Keywords: Arabic Scale
Nahawand
Orchestral Work
Advisor: Rapoport, Alexander