VictorJuiz/thesis huggingface dataset:
Developing a Proteomic Prognostic Signature for Breast Cancer Patients
Keywords: breast cancer
mass spectrometry

Breast cancer is a major health issue, affecting annually approximately 1.4 million women worldwide. It is a highly heterogeneous disease with the different subtypes having distinct clinical outcomes and different sensitivity to various treatment modalities. The focus of the present dissertation was the identification of novel proteomic prognostic markers for patients with early stage breast cancer. Three different approaches to identify potential prognostic markers were undertaken. First, we hypothesized that since different breast cancer subtypes have distinct clinical outcomes, breast cancer subtype-specific proteins may retain prognostic potential. Second, given the central role of estrogen signaling in breast epithelial cell biology, we hypothesized that estrogen-regulated proteins may be useful in predicting patient outcome. Finally, we hypothesized that genes related to survival based on meta-analyses of publicly available breast cancer tissue microarray data, may also demonstrate prognostic potential at the proteome level. As such, a variety of mass spectrometry-based approaches and biological samples were utilized for the discovery of these potential prognostic protein markers resulting in twenty-four candidates. Upon the identification of candidate biomarkers, a mass spectrometry-based assay for the simultaneous quantification of these proteins in breast cancer tissue samples was established. The developed assay was used for measuring the relative expression levels of the potential biomarkers in a cohort of 96 breast cancer tissue samples from untreated patients with early stage breast cancer. This exercise uncovered two proteins that showed the potential to discriminate between ER-positive patients at high and low risk of disease recurrence, namely KPNA2 and CDK1. In conclusion, the present dissertation describes the development of a preclinical exploratory study, from the discovery to the preliminary verification of potential prognostic biomarkers for breast cancer patients.
Physiological Regulation of Short-term Food Intake in Children During Puberty
Keywords: food intake regulation
puberty

Three studies were designed to investigate the hypothesis that physiological and environmental variables are both independent and interactive in determining food intake (FI) in children and adolescents during puberty (8 – 18 y old). Study 1 investigated the effect of obesity, sex and pubertal status on appetite hormones in response to a mixed glucose and whey protein (WP) drink in adolescents. Obese adolescents had higher insulin, PYY and lower ghrelin than normal weight (NW) controls, with a more pronounced effect in males. Puberty did not affect insulin, but the change in PYY in response to the drink was greater and ghrelin was lower in mid-late pubertal than pre-early pubertal obese males. To further describe the role of puberty, Study 2 examined the effect of pubertal status on FI following consumption of glucose and WP drinks in male and female children. In mid-late pubertal children, mealtime compensation for energy from glucose was less at 60 than at 30 min, but not for whey. However, compensation for either drink was not different at 30 and 60 min meals in pre-early pubertal children. Finally to demonstrate the interaction between puberty and environmental influences on FI, Study 3 examined the effect of distraction (television viewing, TVV) while eating and pubertal status on food intake after a pre-meal glucose drink in girls. In Study 3, TVV had no effect on FI, however, glucose suppressed FI more with no TVV compared with TVV (24% vs. 10%). In postpubertal girls, glucose reduced FI by ~27% in both the no TVV and TVV conditions, but in peripubertal girls, reduction in FI was 22% without TVV and only 1% while TVV. Thus, the results of this research support the hypothesis that physiological and environmental variables are both independent and interactive in determining FI in children and adolescents during puberty.
Microwave Assisted Extraction of Xylan
Keywords: Xylan
Microwave extraction
Hemicellulose
Characterization
Biopolymer

Xylan is one of the major hemicelluloses present in plant cell wall matrix, where it is closely associated with other cell wall components, cellulose and lignin. Xylan has enormous potential as a renewable biopolymer and recently, research in the direction of isolation and utilization of xylan is gaining lot of research attention. Extraction of xylan from the plant cell walls involves the hydrolysis of xylan and its transfer from the plant cell wall matrix to the hydrolyzing media. Current process of extraction involves prolonged heating of the biomass with the hydrolysis media at high temperature and/or pressure that leads to molecular degradation of xylan and limits its high potential polymeric applications. In this research, microwave assisted alkaline extraction of polymeric xylan from birch wood is investigated as an alternative to the time intensive conventional extraction. The hypothesis to be tested is that the microwave’s selective heating ability leads to the generation of hot spots through its interaction with the alkali present in the fibers and the resulting "explosion effect" loosen the recalcitrant fiber structure network thereby facilitating the hydrolysis of xylan and its dissolution before undergoing significant degradation. Effect of microwave extraction on the yield of xylan and wood solubilization, physico-chemical properties of wood fibers and of isolated xylan were investigated in comparison with conventional extraction. Low power input microwave (110 W) alkaline extraction was found to be an efficient alternative to the conventional extraction. FTIR and chemical composition of wood fibers after extraction demonstrated an increased removal of xylan from the wood fibre using microwave extraction. SEM, X-ray microtomography, and X-ray crystallinity studies of wood fibers demonstrated a porous and loosened fibre structure after microwave extraction confirming the hypothesis. Molecular weight of the isolated xylan using microwave extraction was found to be higher compared to the xylan isolated using conventional extraction indicating less molecular degradation. About 75% of xylan present in birch wood could be extracted using a low power input microwave heating under optimized extraction conditions of 8wt% NaOH solution, 1:8 (g:mL) solid to liquid ratio, and 25 minutes of extraction time.
Recognition of Diversity: Charles Taylor's Educational Thought
Keywords: recognition
diversity
Charles Taylor
philosophy
education
Canada
Descartes
Kant
Herder
Hegel
Scientific Rationality
Exclusive Humanism
Ethics of Authenticity
Politics of Recognition

This study focuses on Charles Taylor’s educational thought with a view to understanding his contributions to the discipline of Philosophy of Education. No comprehensive study of Charles Taylor’s educational thought has been attempted. There is a single dissertation and a dozen or so published periodical articles that do take Taylor’s educational views into consideration, to be sure. Yet these studies, which limit themselves to Taylor’s account of the recognition and/or non-recognition of identity in multicultural societies, are insufficient on five accounts: i) they are indifferent to the historical nature of Taylor’s scholarly work; ii) they neglect the philosophical sources of his educational thought; iii) they fail to highlight the interconnections between the key educational themes he takes up; iv) they disregard his major critics and the dialectical tensions raised by these critics; and v) they are somewhat dated in that they do not consider his more recent scholarship. My dissertation seeks to fill these scholarly gaps. My thesis is that an inner logic is implicit in Charles Taylor’s educational thought. I argue that Taylor’s views on the modern condition, (i.e. in his readings of Descartes, Kant, Herder, and Hegel), are closely interwoven with his views on modern education, and that interconnected currents in the modern history of ideas elucidated by Taylor, (i.e. scientific rationality, exclusive humanism, and the ethics of authenticity), have contributed to the rise of, and the sensitivity toward, both the theory and the practice of the politics of recognition in contemporary educational institutions. I conclude that an education for culturally diverse minds and hearts, anchored in human, historical, and epistemological recognition, and democratically open to both immanence and transcendence, is the true calling of Taylor’s educational thought.
The Art of Remembering: Iranian Political Prisoners, Resistance and Community
Keywords: learning
violence
memory
resistance
Iran
Middle East
political prisoners
art
public testimony
role of the witness

Over the last three decades, many women and men who were political prisoners in the Middle East have come to Canada as immigrants and refugees. In their countries of origin, they resisted oppressive social policies, ideologies, and various forms of state violence. Their journeys of forced migration/exile took them away from their country, families, and friends, but they arrived in Canada with memories of violence, resistance and survival. These former political prisoners did not want the sacrifices that they and their colleagues had made to be forgotten. They needed to find effective ways to communicate these stories. This research was conducted from a critical feminist‒anti-racist perspective, and used life history research to trace the journey of one such group of women and men. This group of former political prisoners has been meeting together, using art as a mode of expression to share their experiences, inviting others to join their resistance against state violence. Interviews were conducted with former political prisoners and their supporters and artist facilitators who were part of the art workshops, performances, and exhibits held in Toronto, Canada from January 2010 through December 2011. This dissertation examines the importance of memory projects and of remembering in acts of public testimony and the significance of providing spaces for others to bear witness to those stories. This research also contributes to the body of knowledge about the role that remembering, consciousness, and praxis play in individual and community recovery, rebuilding community, and continued resistance.
A Parallel Implicit Adaptive Mesh Refinement Algorithm for Predicting Unsteady Fully-compressible Reactive Flows
Keywords: CFD
Newton-Krylov-Schwarz
Laminar Flames

A new parallel implicit adaptive mesh refinement (AMR) algorithm is developed for the prediction of unsteady behaviour of laminar flames. The scheme is applied to the solution of the system of partial-differential equations governing time-dependent, two- and three-dimensional, compressible laminar flows for reactive thermally perfect gaseous mixtures. A high-resolution finite-volume spatial discretization procedure is used to solve the conservation form of these equations on body-fitted multi-block hexahedral meshes. A local preconditioning technique is used to remove numerical stiffness and maintain solution accuracy for low-Mach-number, nearly incompressible flows. A flexible block-based octree data structure has been developed and is used to facilitate automatic solution-directed mesh adaptation according to physics-based refinement criteria. The data structure also enables an efficient and scalable parallel implementation via domain decomposition. The parallel implicit formulation makes use of a dual-time-stepping like approach with an implicit second-order backward discretization of the physical time, in which a Jacobian-free inexact Newton method with a preconditioned generalized minimal residual (GMRES) algorithm is used to solve the system of nonlinear algebraic equations arising from the temporal and spatial discretization procedures. An additive Schwarz global preconditioner is used in conjunction with block incomplete LU type local preconditioners for each sub-domain. The Schwarz preconditioning and block-based data structure readily allow efficient and scalable parallel implementations of the implicit AMR approach on distributed-memory multi-processor architectures. The scheme was applied to solutions of steady and unsteady laminar diffusion and premixed methane-air combustion and was found to accurately predict key flame characteristics. For a premixed flame under terrestrial gravity, the scheme accurately predicted the frequency of the natural buoyancy induced oscillations. The performance of the proposed parallel implicit algorithm was assessed by comparisons to more conventional solution procedures and was found to significantly reduce the computational time required to achieve a solution in all cases investigated.
In Situ Technologies for Structure Determination in the Liquid Phase
Keywords: Transmission Electron Microscopy
X-Ray Diffraction
Liquid
In Situ
Protein Crystallography
In Liquid
Solution Phase
Structural Dynamics
Diffraction
Molecular
High Resolution
Nanoscale
Nanofabrication
Microfabrication

One of the oldest goals across the science is to watch atoms undergo reactions in real time. However, such observations are only meaningful if the object of interest is looked at in its natural environment. For most biological and materials sciences samples, this means in solution phase or dispersed in a liquid. Unfortunately, this restriction normally prohibits either reaching atomic spatial (10-10m) or ultrafast time (10-15sec) resolution. Here, two sample preparation techniques are shown providing a natural environment for experiments with high spatial and temporal resolution: a nanofluidic cell for electron microscopy, and a chip for serial time resolved x-ray crystallography. The nanofluidic cell was implemented into different transmission electron microscopes, and in initial experiments, the key features of the sample cell are shown, namely the ability to create stable ultrathin liquid layers of tuneable thickness within the harsh electron microscope vacuum. The option to directionally flow liquid through the sample cell opens the door to high throughput electron microscopy and on-the-fly sample exchanges with the option of triggering and influencing chemical reactions with external sample control. First applications highlight the impact of the nanocell: structural disintegration of gold nanorods exemplary for materials science, and amyloid fibrils, exemplary for biomedical applications. In future applications diffractive imaging with high time resolution is planned, and will complement the range of experiments within the fields of traditional transmission electron microscopy. The second half of this thesis presents a solid target for x-ray crystallography. The chip enables the arrangement of thousands of micrometer sized protein crystals in a regular array. The ability to prepare protein crystals in such a fashion is unique and permits serial in situ crystallography. Real time crystallography requires samples to be mounted in a saturated natural environment, i.e. under ambient pressure and temperature conditions. The crystallography chip fills this need while being easily integrated into a synchrotron beam line. In a first set of experiments, the chip design was refined and could prove functionality for static in situ structure analysis of protein systems. Based on this success, future time resolved experiments are under way and will show the full capability of this device.
Socially Cohesive Nations: Evidence from the Individual, Community, and National Levels
Keywords: Social cohesion
inequality

Written as three publishable papers, this dissertation examines the individual, community and national level factors related to social cohesion with emphasis placed on the role of economic inequalities. The core of dissertation revolves around two main arguments: The first argues that there is a direct negative association between economic inequality and social cohesion. The second states that this connection is influenced by other factors that include the individuals’ position in the stratification system. The contextual effects are of particular importance because they influence both the relationship between individual economic realities and economic inequality and the link between social cohesion and economic inequality. Focusing on two aspects of social cohesion—civic engagement and social tolerance—I present evidence that (a) high levels of inequality are related to low levels of social cohesion and inclusion; (b) high levels of inequality are associated with lower commitment to democratic principles; and (c) low levels of inclusion are associated with lower commitment to democratic principles such as social tolerance. This dissertation provides links between these topics by exploring the comparative role of inequality in varying social, economic, political, and religious contexts. It examines contextual effects at both the community-level and at the cross-national level to illustrate the patterns and results of social cohesion.
The Influence of Body Size on Adult Skeletal Age Estimation Methods
Keywords: age estimation
body size

When human skeletal remains are found in prehistoric, historic, or forensic contexts, establishing age at death is an important step in reconstructing life histories, building demographic profiles, and identifying victims. Reliability for adult skeletal age estimations is generally lower than ideal, especially for individuals over the age of 40 years. A factor rarely considered in age estimation is that of body size; namely, how individuals of varying body sizes experience skeletal aging. This thesis explores the variables of BMI, stature, and body mass to quantify the influence of error from body size on adult skeletal age estimates. Eight age estimation methods were tested on 764 adult skeletons from the Hamann-Todd and William Bass Collections. These individuals were documented to have ranged in stature from 1.30m to 1.93m and body mass from 24.0kg to 99.8kg. Each age estimation method was evaluated separately. Analyses show that underweight individuals have the most error associated with their age estimations for all methods. All methods under-age underweight individuals by 5 to 15 years compared to average and obese individuals. The Kunos et al. method is the most reliable rib method, and the Lovejoy et al. and Suchey-Brooks methods are the most reliable pelvic methods. The İşcan et al. fourth rib method under-ages individuals by the highest degree compared to all other methods. The DiGangi et al. method is the most unreliable method with low accuracy (over twenty years) and high bias scores (under-aging individuals by almost 20 years). Body mass has a stronger influence on age estimation than stature. Studies have shown that body mass has a strong impact on bone resorption and remodelling rates, regardless of nutrition, and that tissue type (i.e. fat vs. muscle), physical activity, and mechanical loading influence bone remodelling. Skeletal remains of underweight individuals have fewer age markers while obese individuals show an increase in surface texture degeneration and osteophytic lipping. This is the first study to show that body size influences skeletal age estimation, and that age estimations are significantly different between weight-bearing and non-weight-bearing joints.
Dancing-bodies-moving-Spaces: An Ethnography of Disabled and Non-disabled Children's Movement in a Kindergarten Classroom
Keywords: Nursing
Rehabilitation
Philosophy
Ecological Psychology
Early Childhood Education
Classroom Design
Neuroscience
Dance

Contemporary neuroscientific evidence indicates that unrestricted movement and gesture enhance children’s physical, social and cognitive development by engaging them with the external properties of their environments. Current understanding of children’s engagement with indoor environments is limited. This knowledge gap matters because children’s health, social abilities and cognitive development may be compromised in physical environments that inhibit rather than enhance their movement capacities. This gap is especially problematic for physically disabled children because their motor impairments, exclusionary societal attitudes, safety concerns and environmental barriers curtail their movement. In this study, I describe and interpret the relationship between disabled and non-disabled children’s movement and a kindergarten classroom. Their bodies were conceptualized according to Deleuze’s premise that nothing can be known about bodies until they demonstrate what they can do (1988). The classroom was conceptualized according to Gibson’s theory of affordances, which posits that people and environments are inextricably related (1979). I used a choreographic perspective underpinned by Manning’s philosophy of relational movement (2009) to accentuate the dynamic reciprocity between children’s bodies and the classroom. Eight disabled and 12 non-disabled children participated in this interdisciplinary, ethnographic study. Data were elicited through observations, video recordings and semi-structured interviews. I developed a taxonomy of indoor affordances or ‘compositional elements’ to categorize classroom objects/features that children discovered and actualized through their movement interactions. Subsequently, I observed a dance-in-the-making that led to deeper understandings of the relational and emergent properties of these interactions. Findings suggest that assemblages of bodies, objects and features trigger dynamic movement, and indicate that disabled and non-disabled children alike discover and creatively assemble affordances to facilitate their movement. Overall, my findings recast children’s body-environment interactions and contribute to understandings about environmental features that enhance or inhibit movement capacities. This knowledge could be used to design i) learning environments that are redolent of movement possibilities, ii) interventions to enhance children’s physical, social and cognitive capacities, and iii) education and rehabilitation strategies that encourage them to explore, navigate and shape their environments.