VictorJuiz/thesis huggingface dataset:
Investigation of Anthropogenic Processes on the Molecular Composition and Stability of Natural Organic Matter in Agroecosystems and Deep Geological Repository Conditions
Keywords: anthropogenic activities
dissolved organic matter
environmental conditions
molecular-level analysis
natural organic matter
organic carbon biogeochemical dynamics

Varied environmental conditions (e.g., soil physiochemical properties, temperature, precipitation, plant litter quality) and anthropogenic disturbance (i.e., land-use change to cultivation, agricultural land management) may alter natural organic matter (NOM) biogeochemical dynamics. Among these constraints, which environmental factors mainly regulate NOM composition and solubility and how human activities will change these relationships still needs to be studied. Moreover, how NOM composition and reactivity in Wyoming-type bentonite (MX-80) will change after being exposed to deep geological repository (DGR) conditions is still unknown, which is one of the key factors to evaluate the reliability of the long-term used nuclear fuel storage plan. To fill these gaps, molecular-level NOM characterization was performed in agroecosystems and DGR conditions. The quality and solubility of terrestrial-derived dissolved organic matter (DOM) were observed to be directly related to the chemistry of soil organic matter (SOM) and the soil physicochemical properties, and land-use change to cultivation altered these relationships considerably. The accumulation of relatively long-lived SOM components (i.e., long-chain aliphatic lipids) in mineral-associated soil carbon pools was observed by the molecular-level analysis of SOM in response to diversified crop rotations. Both quantity and quality analyses of SOM confirmed that the long-term crop rotational diversity enhanced soil carbon storage. The NOM composition and solubility in MX-80 bentonite after accumulated radiation and heat (100 kGy+80°C) exposure did not observe significant changes. Assessments of targeted NOM compound concentrations in MX-80 bentonite after relatively longer heat exposure periods (14 - 42 days at 90°C) detected nanogram-level differences in comparison to the control sample. The assessment also found minor DOM compositional differences after salinity and heat exposure. With broader assessments of NOM characteristics, the relatively short-term of (in comparison to the long lifetime of the DGR) heat, radiation and salinity exposure with the proposed DGR conditions were unlikely to alter NOM chemistry (including both chemical signature and organic carbon content) in MX-80 bentonite. Overall, this thesis investigated NOM stability and compositional differences in response to varied environmental factors in both agroecosystems and DGR conditions. Since the quantitative analysis may not always indicate variations, molecular-level analysis is crucial in assessing the biogeochemical dynamics of NOM under different environmental circumstances.
Teacher Professional Development in Rural Colombia and Honduras: An Accompaniment Approach for Everyday Teacher Agency
Keywords: agency
international comparative education
mentorship
reflection
rural schools
teacher professional development

This dissertation studies how an on-site mentoring approach to in-service teacher professional development called ‘accompaniment’ was used, in rural areas of Colombia and Honduras, to build teachers’ sense of agency, linked to a locally relevant knowledge base. In multiple local sites in each country, the case study organizations implemented an innovative alternative education system known as the Sistema de Aprendizaje Tutorial (Tutorial Learning System or SAT in Spanish) or the related Preparation for Social Action (PSA) program. This qualitative research looked at how these organizations conceptualized and practiced teacher accompaniment in each setting, emphasizing the relationships between mentors and teachers, to understand whether and how these rural teachers developed a sense of agency regarding their teaching decisions. The study is based on over 100 interviews with teachers, mentors, and support or leadership staff in the Colombian and Honduran organizations, complemented by analysis of program documentation provided by the organizations. These case studies, whose data collection took place during the height of the COVID-19 pandemic, also examine how the organizations’ approaches to accompaniment responded and endured in the face of the escalated risks and uncertainty of this pandemic situation. This research provides insights into the value of a supportive relationship between teacher and mentor as part of teachers’ professional development. It also shows the possibility of collective forms of teacher accompaniment mentorship. It also shows ways in which reflection, both individual and collective, can be encouraged through the use of accompaniment mentoring and tools (for example reflection notebooks) to assist teachers in thinking through ways to improve their teaching practices. The importance of supportive, teacher-centered and learning-driven environments, including elements of organizational culture, in fostering agency in rural teachers is also examined. Teacher accompaniment environments were explored in connection to the aims of the educational programs themselves, in particular their purpose of rural development and that students become “promoters of community well-being.” This research contributes to the understanding of reflective, formative mentoring (accompaniment) practices for paving the path of teacher professional development.
Mapping Nanoparticle Distribution Inside Solid Tumours
Keywords: Cancer
Heterogenity
Image Analysis
Nanomedicine
Tumour

Nanoparticles have a promising future in cancer therapeutics as a drug delivery vehicle. However, the translation of nanoparticle therapeutics has been limited by a fundamental lack of understanding of how nanoparticles behave within the tumour. Recent advances have highlighted the barriers to nanoparticle delivery within the tumour but the impact of these barriers on the resultant nanoparticle delivery remains to be seen. In my thesis I develop tools that utilize tissue clearing, three-dimensional microscopy, image analysis and machine learning to study, map and predict nanoparticle distribution within solid tumours. First, I use these tools to study the heterogeneous tumour microenvironment and identify patterns in the 3D organization of tumour cells. I then use these patterns to predict the presence or absence of a model nanoparticle in specific regions of the tumour microenvironment. Second, I developed a chemical tag that enables me to map the distribution of clinically relevant nanoparticle formulations such as liposomes in cleared tissues. Prior to this tag it was not possible to study liposomes in cleared tissues because the processing required to render tissues transparent removes lipids. This tag provides a method to visualize liposome distribution in tissues, monitor their stability, and degradation rates in tissues. The knowledge established in this thesis has the potential to guide researchers in the study of nanoparticle behavior within tumours and help in the selection of nanoparticle formations with improved delivery to specific regions of the tumour microenvironment.
Targeting Carboxylesterase 2 Activity for Predicting and Improving Response to Pancreatic Cancer Treatment
Keywords: Activator
Carboxylesterase
Fluorescence chemosensor
High throughput screening
Pancreatic cancer
Photodynamic therapy

Pancreatic ductal adenocarcinoma is an aggressive form of cancer, with low patient survival rates. Irinotecan, a key chemotherapeutic drug, is activated by carboxylesterase 2, which has been established as a predictive and prognostic biomarker of patient response to irinotecan, whereby low activity of the enzyme confers resistance. In efforts to improve survival, clinicians have adopted personalized medicine approaches. Carboxylesterase 2 serves as a suitable biomarker for targeting given its indicated role and interindividual variability in activity. To this end, this thesis describes several applications towards predicting and improving resistance to irinotecan-based therapies. To measure carboxylesterase 2 activity, a fluorescent chemosensor, Benz-AP, was developed. Initially yellow-fluorescent, carboxylesterase 2-mediated hydrolysis of the benzoyl amide linkage releases a red-fluorescent amine fluorophore (40-fold increase), enabling ratiometric determination of carboxylesterase 2 activity, forming the premise of this thesis. Measurements in panels of commercially available and primary patient pancreatic cancer cell lines show significant non-linear correlations to irinotecan-based drug response, translating towards potential application of Benz-AP for clinical measurements of carboxylesterase 2 activity to guide clinical treatment decisions. Benz-AP further serves as a photosensitizer, in which two-photon photodynamic therapy may be used to cause death in low-activity carboxylesterase 2 environments, including pancreatic cancer tumour spheroids, for therapeutic alternatives to samples otherwise deemed resistant to irinotecan-based treatments. To improve irinotecan-based therapy, Benz-AP was engaged in a high-throughput screen against carboxylesterase 2 to find small molecule modulators capable of inhibition or activation, the latter of which provides the first record of allostery in carboxylesterase 2. Validation and characterization of the hits found 18 small molecule inhibitors that had inhibitory action against irinotecan conversion in vitro and in cellulo, several displaying tight-binding mechanism, indicating potential application towards control of pharmacokinetics. Characterization of the activator hits demonstrated ability to enhance conversion of Benz-AP with rate enhancement as high as 24-fold but did not translate to the same activity modulation for irinotecan conversion. In all, this thesis establishes a foundation and describes a diverse set of applications for targeting carboxylesterase 2 towards the goal of improving patient survival in pancreatic ductal adenocarcinoma.
Interpolative-Based Maximum-Entropy Moment Closures for Predicting Real-Gas Radiative Heat Transfer
Keywords: Combution simulation
Entropy maximization and optimization
Moment closures
Polynomial interpolation
Radiative heat transfer
Soot formation

New, efficient, realizable and hyperbolic interpolative-based first- and second-order maximum entropy, M1 and M2, respectively, moment closures for providing approximate numerical solutions to the radiative transfer equation (RTE) in both gray (for M2) and non-gray (for M1 and M2) participating media are proposed and described. These newly-developed interpolative closures allow to accurately reproduce maximum entropy solutions at a fraction of the computational costs associated with the expensive direct numerical solution of the entropy optimization problem. New boundary conditions, based on the method of characteristics, are also proposed for use with the hyperbolic systems of moment equations arising from the M1 and M2 closures. The predictive capabilities of the M1 and M2 closures are then assessed by comparing their solutions to those of the more commonly adopted first-order, P1, and third-order, P3, spherical harmonic moment closures, as well as the popular discrete ordinates method (DOM). The assessments involve both gray and non-gray radiative heat transfer within one- and two-dimensional enclosures, with prescribed thermochemical quantities, as well as reactive flows simulations of high-pressure sooting laminar co-flow diffusion flames. The numerical results for most of the test cases involving non-reactive flows show that the M1 closure provides solutions of at least comparable accuracy to those of the P3 closure while incurring only a rather modest or minor increase in computational costs relative to the P1 closure. In situations involving crossing streams of photons emanating from different directions, the M2 closure represents a better alternative to the M1 closure which cannot properly capture such phenomena and may yield unphysical solutions, though the computational costs of the former are observed to be more involved than those associated with the latter. For the high-pressure reactive flow simulations, the predictive capabilities of the M1 and M2 closures were observed to be superior to those of the P1 closure for all the pressures studied. On the other hand, the P3 closure was observed to be of comparable accuracy to the M2 closure at low pressures. However, at higher pressures, both the M1 and M2 closures displayed a trend of increasingly improved accuracy compared to the P3 closure.
Growing Our Roots: Exploring the Home Language and Literacy Environment within the Context of Indigenous Ways of Knowing and Being
Keywords: Emergent Literacy
Indigenous Culture
Indigenous Knowledge
Language
Reconciliation

Learning to read and write sets children up for success in school and in life. The development of these early skills is highly dependent upon children’s home language and literacy environments and experiences before formal schooling begins. However, Indigenous children experience a disproportional exposure to risk factors related to language and literacy which are strongly associated with lower levels of school achievement. A mismatch between Indigenous home experiences compared to mainstream perceptions of early skills may contribute to this disproportion. There is a dearth of research on unique Indigenous perspectives about early language and literacy development as well as a lack of culturally sensitive tools to measure and interpret these constructs. The present study explored Indigenous perspectives, beliefs, and practices around early language and literacy in the home and community as well as unique challenges that Indigenous parents face when supporting their child’s development. These Indigenous perspectives were mapped onto mainstream perspectives to elucidate culturally dissonant aspects that may contribute to misinterpretations and mismeasurement of unique knowledge and abilities of Indigenous children. The study followed an Indigenous methodological approach by engaging 22 participants from an Indigenous preschool through an open-ended questionnaire and in-depth interviews. Four inter-related themes were identified: 1) embrace culturally sensitive practices/assessments and Indigenous oral traditions when supporting language and literacy development in both English and heritage language; 2) language and literacy can be further leveraged through support of foundational development such as relational skills, as well as self-esteem, self-regulation, and resiliency which incorporates modeling and acknowledgement of child agency; 3) practice, celebrate, and preserve cultural traditions, heritage language, and kinship ties which also promotes belonging and pride in heritage/roots; and 4) acknowledge that intergenerational trauma contributes to challenges in supporting early learning and language development such as disruption of family relationships, disconnection from culture and language as well as mistrust in the school system related to bullying, stereotyping, culturally dissonant language and literacy assessments, and lack of teacher understanding about Indigenous history, language, and ways of knowing. Building equitable relationships through mutual understanding and acceptance is a way forward on our journey to reconciliation. This research brings long overdue acknowledgement of and value to Indigenous perspectives as well as recommendations for supporting Indigenous language, literacy and cultural learning in the home, school, and community.
Identification and Assessment of Adverse Occupational Health Risks Among Public Safety Personnel: A Biopsychosocial Investigation of Stress Biomarkers in Naturalistic Settings
Keywords: Allostatic Load
Cortisol
Heart Rate Fragmentation
Mental Health
Public Safety Personnel
Stress

Chronic occupational stress is one of the most significant contributors to adverse health and performance outcomes among public safety personnel (PSP). This dissertation builds upon prior research on the allostatic load (AL) model of stress and health, investigating PSP’s occupational stress, health, and performance in naturalistic settings from a biopsychosocial perspective across three components: a) AL from occupational stressors and adverse health outcomes (study 1–2), b) the impact of subclinical health outcomes on occupational performance (study 3), and c) the exploration of an emerging cardiac metric to address current biomarker literature gaps and confounds (study 4). Study 1 examined occupational stress subcomponents and their association with mental health; findings revealed that organizational in contrast to operational stress was the strongest occupational subcomponent associated with adverse mental health risk. Building upon prior research, study 2 added an objective stress biomarker (i.e., diurnal cortisol) to investigate occupational factors related to physical health; findings indicated that as operational risk increased, dysregulated neuroendocrine function was more pronounced. Study 3 combined biopsychosocial variables of stress and AL (e.g., occupational stress, mental health symptoms, cortisol) to investigate potential associations with a timely and urgent behavioural outcome among PSP — lethal force decision-making; findings revealed that dysregulated neuroendocrine function (when including outlier data) increased the odds of lethal force decision-making errors. Together, study 2 and 3’s findings demonstrated the strengths and weaknesses of AL neuroendocrine biomarkers among PSP in naturalistic settings. Building on that knowledge, study 4 investigated an emerging cardiac biomarker (heart rate fragmentation — HRF) that may better capture AL. Study 4 found that HRF can detect acute psychological stress in both healthy individuals and those with probable mental health (pMH) symptoms; while pMH and healthy individuals did not differ in baseline HRF, exploratory analyses revealed that pMH individuals had significantly blunted HRF stress reactivity. Overall, this dissertation demonstrates significantly prevalent health and performance risks associated with acute and occupational stress in otherwise healthy, nonclinical adults. A further novel contribution, is the introduction of an emerging cardiac biomarker with promise for detecting AL risk among PSP; knowledge may inform future occupational interventions and policy for adverse health prevention.
Multiscale Mechanical Behaviours of a Near-alpha Titanium Alloy Made by Additive Manufacturing
Keywords: Additive manufacturing
Fatigue property
Microstructure
Nanoindentation
Tensile property
Titanium alloys

Laser-based directed energy deposition (LDED), one of the additive manufacturing (AM) techniques, offers the advantage of fabricating titanium components with reduced manufacturing time and material waste compared to conventional manufacturing methods. However, LDED-produced titanium alloys often suffer from low ductility and limited resistance to fatigue crack growth, which hinders their widespread use in aerospace and biomedical industries. These undesirable mechanical properties have been linked to their microstructural characteristics, such as lamellar morphology and small grain size, as well as the mechanical properties of the constituent phases, namely α and β phases. Nonetheless, there have been limited studies exploring the phase/grain level mechanical properties and microstructural characteristics of LDED-produced titanium alloys. Consequently, the influences of these microscale properties on the unsatisfactory mechanical properties of the bulk LDED-produced titanium alloys are not clear. This thesis aims to investigate the microstructure and multiscale mechanical behaviours of a LDED-produced Ti-6Al-2Zr-Mo-V alloy, employing high-throughput nanoindentation mapping, in situ microscale tension, and macroscale fatigue tests. Firstly, the hardness (H) and modulus (E) of the α and β phases in both as-deposited and heat-treated titanium samples are measured, and the strong dependencies of the measured H and E values on factors such as chemical composition,crystal orientation, and nanoindentation depth are discussed. Secondly, the tensile deformation behaviours of the as-deposited and heat-treated samples are characterized, revealing two types of deformation behaviours: slip banding in soft α grains and microscale shear banding in hard α grains. The observation of microscale shear banding, for the first time, demonstrates its beneficial effect on enhancing the tensile ductility of LDED-produced titanium alloys. Lastly, the fatigue crack growth behaviours of the as-deposited and heat-treated samples are also studied. The grain size, crystal orientation, and spatial distribution of the α lamellae play crucial roles in determining both intergranular and transgranular crack growth, as well as the local plastic deformation behaviours along the cracks. In the thesis, a new model is proposed to predict secondary crack initiation in the α lamellae based on their spatial and crystallographic orientations. This research will significantly contribute to the understanding of multiscale mechanical beheaviours of LDED-produced titanium alloys.
Regulation of the Actin Cytoskeleton by Palmitate: Implications for Lymphatic Endothelial Barrier Function and Skeletal Muscle GLUT4 Translocation
Keywords: actin cytoskeleton
GLUT4
insulin
lymphatic endothelium
palmitate
skeletal muscle

The actin cytoskeleton is a critical component of cells that regulates core cellular processes in diverse cell types. It provides structural and mechanical support, regulates intracellular trafficking, mediates contacts between cells and more. During the development of obesity, cells are exposed to increasing levels of saturated fatty acids (SFAs). SFAs have been implicated in the development of two obesity-associated disorders that I was interested in investigating: lymphatic dysfunction and skeletal muscle insulin resistance, but their precise impact on the actin cytoskeleton in the lymphatic endothelium and skeletal muscle and how it alters their canonical functions (fluid homeostasis and glucose disposal) is incompletely understood. In this dissertation, I identify the actin cytoskeleton as a target of the SFA palmitate (PA) that confers cell type-specific dysfunction in both lymphatic endothelial cells and skeletal muscle cells. In Chapter 3, I describe how PA, but not its unsaturated counterpart palmitoleate (PO), alters the lymphatic endothelial junction by remodelling the actin cytoskeleton. I detail how PA caused the accumulation of actin stress fibres that disrupted cell-cell contacts and compromised wound healing. In Chapter 4, I outline how PA impaired GLUT4 translocation in skeletal muscle cells by abrogating insulin-stimulated actin remodelling and by disrupting the intracellular trafficking of GLUT4. Moreover, I determined that the failure of actin remodelling and GLUT4 mis-localization in these cells are governed by distinct mechanisms, endoplasmic reticulum stress and protein palmitoylation, respectively. In Chapter 5, I uncovered a previously unappreciated role for complexin-2 in insulin-stimulated GLUT4 vesicle fusion with the plasma membrane in skeletal muscle cells that requires actin remodelling. This work establishes PA as a regulator of the actin cytoskeleton in two cell types with unique functional implications for each. My work advances our understanding of how SFAs regulate the cellular actin architecture and how these alterations confer cell type-specific dysfunction. While my work focused on only two cell types, it provides compelling initial evidence that SFAmediated dysregulation of the actin cytoskeleton may represent a common mechanism underlying cellular dysfunction during nutritional excess in additional cell types.