Restricted Theses and Dissertations
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Item Embargo The RAD51C-XRCC3 Homologous Recombination Repair Complex: Structural Basis for its Interactions and Cancer Associated Mutations(2025-02-19) Pepper, Jordan Tan; Williams, Gareth; Schriemer, David C.; Lees-Miller, SusanThe RAD51 paralogs are crucial proteins involved in the repair of double-stranded DNA breaks (DSBs) via homologous recombination repair (HRR). There are six human RAD51 paralogs, RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and SWSAP1, and mutations in these genes are associated with cancer and other diseases. The RAD51 paralogs operate as discrete multi-protein complexes whose functional roles and structures are not fully understood. A key RAD51 paralog complex is the RAD51C-XRCC3 heterodimer (CX3), which is the focus of this thesis. I used biochemical, structural, and computational approaches to 1) profile disease and cancer-linked missense mutations found in RAD51C in the context of CX3, 2) determine the structural details of human CX3, and 3) identify and characterize potential CX3 protein interaction partners. I used the Alvinella pompejana ortholog of CX3 to investigate the impact of 5 different cancer associated missense mutations of human RAD51C on protein stability and biochemistry using heterologous expression and purification, mass photometry, fluorescence polarization assays, molecular dynamics simulations, and in silico mutation stability calculators. To investigate human CX3, I used a combination of small-angle X-ray scattering, cross-linking mass-spectrometry, structural prediction models and analysis to uncover features of how RAD51 family members interact with one another. Finally, I used affinity-purification and mass-spectrometry proteomics to detect possible CX3 protein-protein interaction partners, which I then attempted to verify using fluorescence-detection size-exclusion chromatography, with post-hoc analysis of candidate interaction partners using AlphaFold 3 and in silico calculation of interprotein energetics and affinity. From this work, I uncover insights in the structure of the CX3 complex, its possible roles in HRR, and a pathway towards characterizing it in association with interaction partners.Item Embargo Cellular Network Interactions Comprising the Pancreatic Ductal Adenocarcinoma (PDAC) Microenvironment(2025-02-05) Torabian, Pedram; Bathe, Oliver; Minoo, Parham; Wang, Edwin; Schaeffer, David; Bose, PinakiBackground: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, marked by complex interactions between tumor and stromal cells and significant resistance to treatment. Understanding the cellular and molecular heterogeneity within the PDAC tumor microenvironment is crucial for developing more targeted therapeutic strategies. Spatial transcriptomics offers a powerful approach to capture cell-to-cell interactions within the tumor microenvironment, revealing tissue architecture and providing insights into the spatial organization of cellular populations. Methods: Spatial transcriptomics was performed on three PDAC samples from a single patient to explore cellular and genetic complexities within the tumor microenvironment. Cells were manually annotated; however, some cells remained unclassified based on stringent criteria. To address this, an XGBoost machine learning classifier was developed, utilizing differentially expressed genes from tumor cells and fibroblasts as classification features. After sample integration, the number of clusters for tumor cells and fibroblasts was calculated, resulting in the identification of three tumor clusters (T1, T2, T3) and three fibroblast clusters (F1, F2, F3). The spatial organization of these clusters was further investigated using the BuildNicheAssay function, which applies a KNN algorithm to define the local neighborhood of each cell, followed by K-means clustering to categorize cells into three spatial niches based on prior knowledge. Results: Three distinct cell niches were identified: T1F2 (the proliferating hub), T2F3 (the metabolic battery), and T3F1 (the adaptive core). Each niche displayed unique functional properties. The T1F2 niche, containing proliferating tumor cells supported by fibroblasts, was associated with enhanced tumor growth and angiogenesis. The T2F3 niche demonstrated considerable metabolic plasticity, supporting energy demands. The T3F1 niche was characterized by epithelial-mesenchymal transition (EMT)-driven tumor cells interacting with fibroblasts, coupled with WNT/β-catenin and hedgehog signaling pathways, providing insights into PDAC invasion and metastasis mechanisms. Conclusion: Our study reveals a niche-based model of PDAC progression, where specialized microenvironments contribute distinct functionalities to tumor growth and adaptation. This model enhances our understanding of PDAC heterogeneity, offering insights that may guide the development of more targeted and effective therapies.Item Embargo A Feasibility Study of a Culinary Medicine Intervention for Bone Health in Adults Living with Age-Associated Low Bone Mass or Increased Fracture Risk(2025-01-23) MacLaren, Julia Marie; Campbell, David John Thomas; Billington, Emma Olive; Fenton, Tanis Rosemary; Chan, Catherine B.; McWhorter, John WesleyBackground: Dietary intervention is a valuable co-therapy in the primary and secondary prevention of fractures, and food and cooking skills protect against nutrition risk in older adults. Culinary Medicine (CM) interventions have potential to improve dietary quality and health outcomes, but there is a lack of randomized trials in this area. Objective: This pilot trial assessed the feasibility and acceptability of implementing and evaluating dietitian-led virtual CM intervention for bone health as an adjunct to usual care at our specialty osteoporosis center. Methods: Forty adults aged 45 years and older referred for fracture risk assessment were randomized to receive either usual care (group nutrition education) or usual care plus a CM program. The CM program included a 1.5-hour virtual group session with two dietitians, a recipe package, and an optional follow-up session. The usual care group could attend the CM program after study completion (wait-list control). At baseline and 3 months, participants completed surveys on home cooking and confidence in eating well for bone health and were asked to complete 2 dietary recalls. The CM group completed an acceptability survey post-session. Primary feasibility outcomes were recruitment (target: 100% in 6 months), adherence (target: ≥85%), and retention (target: ≥85%). Acceptability was measured using a questionnaire adapted from the Theoretical Framework of Acceptability. Findings: We recruited 40 participants in 6 months, meeting the recruitment target. The adherence target was also met. Most participants (80%, CI 64%-91%) were retained through the 3-month follow-up, indicating feasibility but suggesting this aspect of study design could be improved. Only 5 participants (25%, CI 9%-49%) completed all 4 dietary recalls. The intervention was generally acceptable, with the lowest scores in the ‘burden’ and ‘opportunity cost’ constructs. Conclusion: This pilot RCT suggests CM intervention is a feasible and acceptable adjunct to usual care at our osteoporosis center. However, dietary assessment measures were infeasible as delivered, and further refinement of the intervention may improve acceptability sub-constructs. In future studies, opportunities exist to increasingly tailor CM interventions for older adults, and test the optimal duration and intensity needed to achieve meaningful improvements in behavior change, nutrition status, and bone preservation.Item Embargo Quantifying Naturalistic Driving and Navigation Behaviours: Insights into Early Signs of Alzheimer’s Disease(2025-01-23) Long, Kelly; Bayat, Sayeh; Stefanakis, Emmanuel; Barber, Philip; Saidi, SaeidAlzheimer’s disease (AD) has been associated with changes in driving behaviours and navigational deficits, often emerging in early stages. The ATN framework defines AD pathology through beta-amyloid (A), tau (T), and neurodegeneration (N) biomarkers, which can manifest before clinical symptoms. In this study, we designed and calculated several metrics to quantify navigation and driving behaviours to understand how they relate to ATN biomarkers in individuals without cognitive impairment. Cerebral spinal fluid biomarker (CSF) concentrations and GPS driving data were collected from 125 cognitively normal participants between ages 65 and 85 enrolled in a longitudinal study at Washington University School of Medicine. Participants were categorized as biomarker-negative (-) or biomarker-positive (+) according to CSF concentrations of A, T, and N biomarkers. Several metrics were designed to capture temporal, spatial, and navigational aspects of driving. Temporal metrics included idle time at the start and end of trips to examine driver hesitation. Spatial metrics included distance travelled and life space (distance from home). Navigational metrics included turn counts, route straightness and route complexity, route diversity (proportion of unique routes), most common route concentration (frequency of most travelled route), and comparisons of actual versus time-optimized routes to evaluate navigational decision-making. Exploratory cross-sectional analyses over one and longitudinal analyses assessed trends over two years revealed notable relationships between the metrics and ATN biomarkers. N+ participants may have lower idle time at the start of a trip and lower route diversity than N- participants. Route diversity may also be reduced for T+ participants compared to T- participants. Complexity was higher for A+ participants after accounting for age, though it decreased with age. Idle time at the start of a trip increased with time for T- and N- participants but not T+ or N+ participants. Additionally, both straightness and the ratio of the actual route straightness to the optimized route straightness increased over time for N+ participants but not N- participants. These findings highlight the utility of the metrics in capturing subtle changes in driving and navigation behaviours and emphasize their potential as early markers of AD-related changes.Item Embargo Leveraging Solubility of Engineered Polysaccharides for Pickering and High Internal Phase Emulsions(2025-01-29) Firdous, Karim; Trifkovic, Milana; Bryant, Steven; Husein, Maen; Giovanni, NataleEmulsion design using sustainable materials remains a key area of interest in our efforts to move away from the use of inorganic molecules or surfactants that pose environmental risks. Polysaccharide-based stabilizers offer us a route towards sustainable emulsion design. However, their functional performance as emulsion stabilizers is limited and either surface modification or complexation with other molecules is required to enhance their interfacial affinity. In this thesis we demonstrate the use of enzymatically polymerized α-1,3-glucan (NG) and quaternized α-1,3-glucan (QG) for Pickering emulsion stabilization. Analyzing the microstructure and flow behaviour of generated emulsions and dispersions we investigate the network strength and the underlaying mechanisms governing the stability of emulsions. A new strategy to enhance emulsifying performance of polysaccharides that eliminates physiochemical modification and instead utilizes the solubility of polysaccharides with respect to pH to increase effective surface area is presented. The technique resulting in significant microstructural and rheological improvements over “as received” polysaccharide was successfully applied onto two physiochemically different polysaccharides i.e. α-1,3-glucan and β-1,4-chitosan demonstrating the versatility of the approach. Highly stable, gel-like high internal phase emulsions (HIPEs) using single stabilizer (QG) were generated using s single step homogenization approach. It was shown that QG had ability to reduce interfacial tension and provide electrostatic repulsion between droplets to provide stability owing to their permanent surface charge.Item Embargo Oil Sands Tailings Consolidation Employing Capillary Suction or Core-Shell Coagulant(2025-01-31) Lashkari, Reza; Husein, Maen; Salama, Amgad; Husein, Maen; Salama, AmgadThe Canadian oil sands bitumen extraction process produces a huge volume of tailings. Tailings are a mixture of water, fine particles, and residual hydrocarbons. Tailings gradually stratify into layers, with the middle layer being a stable gel-like suspension of fine clay particles, water, and bitumen known as mature fine tailings (MFT). MFT poses a considerable environmental concern, including air pollution, groundwater contamination, potential for tailings pond failure, as well as extensive land footprint. Additionally, the slow settling of MFT particles adversely affects dewatering and land reclamation, raising liability problems for operators. This work attempts to provide options to MFT reclamation using two approaches. The first approach uses the natural phenomenon of capillary action with porous surfaces to increase evaporation. The selective absorption of water into the porous substrate increases the surface area for evaporation. A filter paper substrate enhanced evaporation rates by ~ 35%, leading to a decrease in reclamation time by 33–55% relative to a non-porous surface. A mathematical model was developed to fit the evaporation rates coupling thermodynamic and mass transport principles. In the second approach, a novel core-shell coagulant (CSCC) consisting of 85 wt% Ca(OH)2 core and a 15 wt% CaCO3 shell, was assessed for its efficacy in enhancing the quality of recovered water and improving the geomechanical stability of the reclaimed MFT. At its optimum dose (4330 ppm) CSCC surpassed the performance of the optimum dose of the conventional Ca(OH)2 coagulant (3250 ppm). CSCC achieved 7% and 70% lower Na+ and Ca2+ concentrations, respectively, with 12% lower suspended solids. Therefore, the detrimental effects of these ions and suspended solids on the oil recovery and the processing equipment is reduced. At higher dose (5400 ppm), CSCC exhibited enhanced efficiency, decreasing Na+ and Ca2+ concentrations by 18% and 56%, respectively, and lowering suspended solid content by 60%. Characterization methods, such as SEM, XRD, and TGA, validated the development of pozzolanic products in the solid phase separated from the MFT after 90 days of aging. The controlled release of Ca(OH)2 from the CaCO3 shell promoted prolonged pozzolanic reactions, hence enhancing long-term reclamation stability.Item Embargo A Glutamatergic Circuit Between the Medial Zona Incerta and Cuneiform Nucleus(2025-01-31) Belway, Cole R.; Whelan, Patrick; McGirr, Alexander; Trang, TuanMovement and locomotion are fundamental for goal-directed behaviours in diverse invertebrate and vertebrate organisms. Integrating higher brain centers with evolutionarily conserved descending brainstem locomotor command centers plays a key role in orchestrating context-specific behaviours. The mesencephalic locomotor region (MLR), primarily comprised of the cuneiform nucleus (CnF) and pedunculopontine nucleus (PPN) is one such conserved descending locomotor center in diverse vertebrate species shown to produce locomotion. Excitatory glutamatergic neurons of the CnF have been shown to set both speed and gait for high-speed locomotion implicated in defensive flight when activated. The medial zona incerta (mZI) is an important hub, allowing for rapid responses to sensory inputs. Projections from the mZI to CnF exist, forming a critical inhibitory circuit for the expression of exploratory behaviours. Less is known on the information however evolved around excitatory afferents to the CnF and their functional implications. Using both a retrograde and anterograde viral tracing approach, I identified a glutamatergic circuit between the mZI and CnF. Activation of the mZI-CnF glutamatergic circuit did not provoke an increase in locomotion within an open field. However, an increase in aversive behaviour with less time spent in a conditioned chamber as well as exhibited heightened levels of anxiety with increased grooming and immobility was observed. Mouse grimace scale (MGS) testing did not reveal any significant difference in pain-related facial expressions. Together, these results highlight that glutamatergic afferents from the mZI to CnF elicits aversive behaviour that is independent of locomotion. My thesis provides evidence that activation of this circuit is sex-specific, with females showing significant aversion compared to male mice.Item Embargo Enhancing remyelination through modulation of phagocytosis and lipid recycling(2025-01-30) Wuerch, Emily Claire; Yong, Voon Wee; Ousman, Shalina; Dufour, AntoineMultiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS), characterized by demyelination and neurodegeneration. MS pathology also includes the presence of inhibitory myelin debris. Current MS therapies primarily target inflammatory processes, such as immune cell infiltration, but fail to directly promote remyelination, representing a significant gap in treatment. Previous research has shown that niacin (vitamin B3) can promote remyelination in the lysolecithin-induced demyelination model by enhancing the phagocytic clearance of inhibitory myelin debris by macrophages and microglia. However, its therapeutic potential in experimental autoimmune encephalomyelitis (EAE), an inflammatory MS model, was previously unexplored. In the first part of my thesis, I tested the hypothesis that niacin administration could ameliorate EAE-induced clinical disability and neuropathology through immune modulation and enhanced remyelination. We found that niacin inconsistently ameliorated EAE clinical disease scores, and failed to promote remyelination. We propose that these outcomes may stem from the inability of niacin to modulate lymphocyte activity, a key driver of EAE pathology. Building on this work, I began investigating lipid recycling from foamy macrophages, as evidence suggests that microglia may be a source of cholesterol for oligodendrocytes during remyelination. Following demyelination, macrophages engulf myelin debris, including lipids, and develop a foamy, lipid-laden phenotype, characterized by increased inflammation and diminished capacity to clear additional toxic debris. We investigated strategies to improve phagocytosis and lipid recycling, hypothesizing that promoting lipid export from foamy macrophages could enhance neuronal and oligodendrocyte survival and facilitate remyelination. To test this hypothesis, we first characterized myelin phagocytosis by human and murine microglia and macrophages, and generated foamy macrophages through chronic exposure to myelin and inflammatory cytokines. To enhance lipid export, we treated foamy macrophages with cyclodextrins, compounds known to promote lipid clearance in other disease models. In collaboration with our chemistry team, we tested both a standard commonly-used commercial cyclodextrin and novel formulations. We also used the lysolecithin demyelination model to assess the therapeutic potential of cyclodextrins in an animal model of multiple sclerosis. Cyclodextrins facilitated lipid export from foamy macrophages in culture, and promoted a beneficial macrophage phenotype in lysolecithin lesions. Cyclodextrins also preserved axons and increased the presence of oligodendrocyte lineage cells in lesions. In conclusion, cyclodextrins offer a promising therapeutic strategy for people with MS by enhancing oligodendrocyte cell number and reducing neurodegeneration, addressing limitations of current therapies. Overall, this thesis explores several novel therapeutic approaches to modulate lipid metabolism and myelin debris clearance in MS, with the overarching goal of advancing remyelination therapies.Item Embargo The Role of the Pumilio Protein Puf4 and P-Bodies in DNA Replication Stress in Schizosaccharomyces pombe.(2025-01-31) Chow, Jeffrey William Dat Ho; Chua, Gordon; Ayyaz, Arshad; Lees-Miller, Susan; Shemanko, Carrie Simone; Hansen, David DonaldReplication stress is caused by the delay or compromise of DNA synthesis in S-phase. The ability for cells to properly respond to this stress determines viability or lethality and is implicated in many human diseases such as cancer. Post-transcriptional regulation plays an important role in the replication stress response to properly modulate RNA levels. Puf4 is a pumilio family RNA-binding protein that facilitates mRNA degradation through binding the pumilio response element in 3’ untranslated regions. Cytoplasmic RNA granules such as stress granules and p-bodies also show critical roles in the stress response through mRNA triage, storage, and decay. Puf proteins, stress granules, and p-bodies are all highly conserved throughout eukaryotic organisms from single-cell yeasts to humans. However, biological function and mRNA targets of Puf4 and these RNA granules during replication stress remains relatively uncharacterized. In this study, we investigated the role of Puf4, stress granules, and p-bodies in response to hydroxyurea-induced replication stress in the fission yeast Schizosaccharomycess pombe. We determined that p-bodies, but not stress granules, form in response to replication stress and that Puf4 plays a role in regulating p-body formation. Moreover, we suggest Puf4 may play a role in regulating the DNA replication checkpoint as misregulation of puf4+ leads to an increase in cut cells, an abnormal septation phenotype where the septum overlays the nucleus, as seen in several checkpoint mutants. Transcriptome profiling of puf4+ mutants identified four novel putative mRNA targets that are degraded by Puf4 during replication stress. Three of the Puf4 mRNA targets, hhf1+, hht1+, and hta2+, encode for histone proteins while dut1+ encodes a deoxyuridine triphosphate nucleotidohydrolase. The deletion of hhf1+ and hht1+ both suppressed the HU sensitivity of puf4Δ, further supporting the relevance of these genes as Puf4 target mRNAs during replication stress. Lastly, we provided evidence that the 14-3-3 protein Rad24 is an activator of Puf4 by potentially causing cytoplasmic retention of Puf4. Overall, this study provides a foundation for Puf4 function in replication stress through identification of novel target mRNAs and characterizing regulatory interactions with Rad24.Item Embargo Design, Development, and Usability Testing of Robin’s Nest Platform Supporting the SENSE Program for Addressing Moral Injury in Nurses and Social Workers(2025-01-29) Savalanpour, Majid; Moshirpour, Mohammad; Duffett-Leger, Linda; Drew, Steve; Pauchard, YvesThe COVID-19 pandemic has exacerbated mental health challenges for nurses and social workers, exposing them to increased risks of stress, moral injury, and psychological disorders such as anxiety and Post-Traumatic Stress Disorder (PTSD). To address this critical need, with the generous funding support from the Government of Alberta, our interdisciplinary team of researchers in Nursing, Social Work, Electrical and Software Engineering, and Kinesiology initiated the design, development, and usability evaluation of the Robin’s Nest telehealth platform. This platform hosts the Supporting Emotional wellness in Nurses and Social workers E-mental health (SENSE) program and was developed using a User-Centered Design (UCD) approach, co-designed with participants. This innovative e-health intervention integrates virtual Cognitive Behavioral Therapy (CBT), stress monitoring using wearable technology, and real-time feedback to provide personalized mental health support. Usability evaluation, as a key element of the UCD approach, plays a pivotal role in assessing the platform's effectiveness. This research employs a multi-method usability evaluation approach, combining quantitative assessments using the mHealth App Usability Questionnaire (MAUQ), qualitative insights from focus group interviews, and Heuristic Testing. The findings demonstrate that the platform successfully meets users’ needs, achieving high usability scores and user satisfaction (median responses: 4 out of 5). Thematic analysis conducted during the usability evaluation highlights the platform’s effectiveness and high usability. Recommendations for improving usability, identified through this analysis, include enhancing communication features, resolving learning management system login issues, and refining the video conferencing interface design. This research underscores the importance of usability in e-health interventions and offers actionable insights for future advancements in digital mental health solutions.Item Embargo A New Permutation-based Digital Signature and its Application to Verifiable Random Function from Symmetric Key Primitives(2025-01-31) Bodaghi, Omid; Safavi-Naeini, Reyhaneh; Reardon, Joel; Yanushkevich, SvetlanaVerifiable Random Functions (VRFs) are public-key primitives that enable the key owner to generate a pseudorandom output for any given input, along with a proof that allows others to verify the correctness of the output. VRFs are closely related to signature schemes with uniqueness property, meaning that for any given message and public key—even if the key is maliciously generated—there is only one valid signature. There are known approaches for turning unique-signature schemes into VRFs. With the advent of quantum computers, problems such as prime factorization can be solved efficiently. Consequently, it is critical to move toward post-quantum VRF constructions that remain secure. In this thesis, we discuss a novel symmetric-key primitive based one-time signature scheme, named POTS, whose security relies solely on pseudorandom functions (PRFs), a primitive that is secure against quantum adversaries. We prove that POTS is a secure one-time signature scheme and can be extended to a many-time signature scheme with provable security. Compared to other one-time signature schemes, POTS offers faster verification at the cost of a larger public key. Then we construct PVRF, a one-time VRF scheme based on POTS. We introduce a new assumption on the underlying PRF needed by POTS and, based on this assumption, prove PVRF’s security. Finally, we implement POTS and compare our performance results to WOTS+, a standardized one-time signature scheme. This comparison highlights the practical advantages of our approach in terms of verification efficiency.Item Embargo Personalizing Reminiscence Therapy Experiences Through the Use of Generative AI in Dementia Care(2025-01-30) Ranjbar, Payam; Moshirpour, Mohammad; Duffett-Leger, Linda; Drew, Steve; Kim, KangsooDementia is a global health challenge affecting millions, significantly diminishing the quality of life for people living with dementia (PLWD) and their caregivers. Reminiscence Therapy (RT) is a non-pharmacological intervention that enhances the well-being of PLWD by prompting them to recall and share past experiences through photographs, and artifacts. Although effective when personalized, scaling RT interventions remains challenging due to their labor and time-intensive design. To address this, we developed the Autobiography Gallery, an AI-powered system that uses Generative AI and Large Language Models to transform narrated memories into personalized photo albums. This thesis evaluates the effectiveness of AI-generated images in RT through feedback from dementia care stakeholders, identifying refinement needs, and proposing features like user-driven customization. We also provide design recommendations for scalable, AI-based RT interventions. Our findings highlight the potential of AI to enhance personalization and scalability in RT, advancing the development of accessible, user-centered solutions for dementia care.Item Embargo Sodium Dodecyl Sulfate-combined Cellulose Nanocrystals for Enhanced Heavy Oil Recovery from Berea Sandstone Reservoirs(2025-01-29) Ullah, Aqrab; Nassar, Nashaat N.; Hassanzadeh, Hassan; Sumon, KaziFor heavy oil recovery, thermal and gas injection techniques have recently shown substantial difficulties associated with heat loss, inefficient oil recovery, and large greenhouse gas footprints. Alternatively, chemical assisted heavy oil recovery techniques can enhance the micro- (displacement) and/or macroscopic (sweeping) efficiencies with employment of long-chained polymers or surfactants. However, most of recently implemented polymers tend to be structurally changed or degraded at the steam chamber temperature or under saline conditions, which significantly limits their oil recovery effectiveness. Thus, the surfactant injection has been successfully remained as the most effective chemical enhancing the oil recovery technique, which typically work through a combination of mechanisms, including interfacial tension (IFT) reduction, wettability alteration, foam generation and emulsification. Through these mechanisms, the use of vast groups of anionic, cationic, and amphoteric surfactants have been widely investigated to enhance the volume of the recovered oil. Compared with cationic and amphoteric surfactants, the anionic surfactants, such as sodium dodecyl sulfate (SDS), has been extensively utilized at high dosages in sandstone reservoirs, due to less chances of SDS adsorption on the rock surface. Herein, a stable nanofluid is produced using biodegradable and organic-based nanomaterials that consists of cellulose nanocrystals combined with SDS at room conditions to enhance the residual oil recovery in the sandstone reservoirs. This production method for the nanofluid systems was done by directly dispersing diverse concentrations of SDS (0.01-0.5%) with certain amount of CNC (0.01-0.5%) under acidic conditions at room temperature. After that, the generated systems were examined in reducing the IFT with spinning drop tensiometer (SDT), and the optimized one was well characterized using fourier transform infrared spectroscopy (FTIR) to confirm the surface functionality change after combining the CNC with the dissociated and acid treated SDS. Then, the combined SDS-CNC systems were used to generate diverse nanofluids that their stabilities were indicated by conducting zeta potential measurements and dynamic light scattering (DLS). At last, the capability of the combined CNC-SDS nanofluids to enhance the residual oil recovery performance were examined, compared with the surfactant and low salinity fluids, by spontaneous imbibition experiments and oil displacement tests under confining pressure of 1500 psi. The results revealed that the interfacial tension (IFT) between aqueous phase and crude oil was reduced considerably by 91.2%, using 0.1 wt. % SDS and 0.05 wt.% CNC as the organic based nanomaterials can mitigate the desorption of surfactant at the interface. Besides, the SDS-CNC nanofluids were able to displace 11% more oil during imbibition as compared to SDS alone, indicating that the nanofluids generated with our nanofluids had strong capabilities to alter wettability of the cores from oil wet to water wet due to arise of structural disjoining pressure. From the core flood testing, it was also confirmed that the oil recovery was increased from 57.5% (by 0.1 wt. % SDS) to 74.4% (0.1 wt. % SDS and 0.05 wt. % CNC) which unveils the competency of SDS-CNC nanofluids for cEOR applications.Item Open Access Blind Source Separation in Dynamic Networks(2025-01-29) Maneshkarimi, Shirin; Dankers, Arne; Westwick, David; Dankers, Arne; Westwick, DavidBlind source separation (BSS) is a mathematical technique that addresses the challenge of separating a mixture of signals into its original, independent sources without prior knowledge of the mixing process. The main objective of this research is to propose a BSS algorithm focused on identifying mutually uncorrelated sources that drive the network, which consists of discrete-time linear time-invariant (LTI) interconnected modules. This study first improves an existing BSS method, which uses a finite impulse response (FIR) model in the prediction error method (PEM) framework to model the input-output transfer function matrix and make it applicable in real-time scenarios. Implemented on field data from Hifi Engineering Inc., this algorithm has demonstrated reliability in online estimating sources over several commercial deployments. However, this method, refined by choosing an automatic regularization factor, still reveals certain limitations: the optimal order of the FIR model remains indeterminate, affecting accuracy and computational efficiency. Moreover, precisely predicting delays between measurement locations and adjusting various parameters requires significant manual intervention, posing barriers to scalability and automation. Next, we propose a novel method within a subspace framework to address these constraints, using the known network topology while minimizing prediction error. Given the network's structure, this approach first integrates elements of PEM with subspace identification techniques, allowing us to identify parameterized state-space matrices through sequential optimization processes aimed at reducing prediction error, which is defined as the difference between the estimated and parameterized Kalman filter predictor. This technique functions within a steady-state Kalman framework, employing data equations to accurately predict the dynamics of the multi-input multi-output (MIMO) network. The performance of the structured BSS method is evaluated by comparing the results of estimating the independent sources obtained through structured state matrices against those generated by conventional subspace methods with unstructured state matrices. The simulation results indicate that structured BSS, given the network topology, offers superior accuracy and robustness in source estimation. This progress in BSS shows how having prior knowledge about the network structure can help separate sources more efficiently and reliably in complex networks.Item Embargo Application of Cellulose Nanocrystals in Water-based Drilling Fluids(2025-01-29) Torres, Eliana; Nassar, Nashaat; Aguilera, Roberto; Hu, JinguangNanotechnology has shown great promise in tackling various challenges in oil and gas drilling operations. The incorporation of nanoparticles in drilling fluids has been found to improve their rheological behavior and overcome common challenges associated with drilling operations by reducing fluid loss, minimizing formation damage, improving heat transfer properties, and decreasing friction between the drill pipe and surrounding formation. Most available literature, however, focuses on using inorganic and non-biodegradable nanomaterials that could be expensive to scale up and might pose some environmental issues. Cellulose-based nanomaterials are among the most produced naturally derived nanomaterials. Research on the application of these nanomaterials in drilling fluids has been limited to evaluating the rheological behaviour and filtration properties of bentonite-based drilling fluids, neglecting the effect of nano-cellulose on the lubricity of drilling fluid. Accordingly, this study aims to investigate the performance of bentonite and non-bentonite water-based drilling fluids in the presence of cellulose nanocrystals (CNCs) at varying content (0.5, 1.0, and 2.0 wt%). The performance of these drilling fluids was evaluated in terms of lubricity, filtration properties, and rheological behaviour before and after high temperature (76 oC) aging. The results show that the incorporation of CNCs into water-based drilling fluids enhanced their lubricity leading to significant torque reductions. This improvement in lubricity was more pronounced in bentonite polymer-free drilling fluids. Furthermore, lower filtrate volume and more uniform filter cake were observed for nano-modified drilling fluids compared to the reference fluids indicating decreased fluid loss. The presence of CNCs also led to higher yield point, viscosity, and gel strength than the reference fluids. This thesis holds valuable insights for the application of CNCs in oil and gas drilling operations, especially in sustainably reducing torque and drag, while maintaining excellent performance.Item Embargo Detection, Identification, and Modeling of Emerging Dynamics for Machine Health Condition Monitoring(2024-10-24) Fernando, Kurukulasuriya Joseph Sunimal; Sun, Qiao; Ghasemloonia, Ahmad; Leung, Henry; Mohamad, Mustafa; Shen, Hua; Zhang, ChrisUnplanned downtime in industrial machinery costs an estimated $50 billion USD per year in the manufacturing sector alone, due to broken parts, additional maintenance expenses, and lost productivity [1]. This highlights the need for more advanced condition monitoring approaches, which may be enabled through the use of models that can predict and prevent potential issues before they occur. While a model that represents the original, or baseline, state of the system is useful for fault detection and diagnostics, updating the model as faults occur is an even more desirable goal. Integrating faults into a systems model can provide us with detailed information such as the progression of a fault over time, its effect on other components, and how and when a failure in the system may occur. In this thesis, a combination of physics-based and data-driven modeling techniques are applied to the problem of updating a systems model as faults initiate, focusing on a class of faults that has received relatively little attention in literature. Faults can manifest either as changes in system parameter values, or as changes to the mathematical structure of the system, the latter of which we refer to as emerging dynamics. These faults introduce additional dynamics which are not present in the baseline system and may involve invalidation of assumed boundary conditions. While there are many established methods for updating model parameters over time [10, 43], considerably less work deals with integrating emerging dynamics into a model. This thesis work aims to address this gap through the development of a comprehensive framework for integrating emerging dynamics behaviours into a systems model to enable predictive condition monitoring analyses. Key framework components include methodologies which have been developed for the detection, identification, and modeling of emerging dynamics. Each involved addressing fundamental theoretical challenges and associated gaps in the literature. The effectiveness of the proposed framework is demonstrated using a test rig. A selected emerging dynamics fault is modeled in an experimental setup, detected and identified as it develops in a rotating machinery system, and finally, integrated into the baseline model.Item Embargo Encapsulation of an Organic Phase Change Material in Wheat Straw Derived Cellulose by Spray Drying(2025-01-27) Ulrich, Anna; De la Hoz Siegler, Hector; Lu, Qingye Gemma; Mahinpey, NaderPhase change materials (PCMs) have the potential to provide valuable thermal energy storage. However, PCMs are not widely used due to challenges with their implementation. Factors including leakage, high-cost materials, energy-intensive processes, and the presence of potentially toxic chemicals are barriers to the widespread use of PCMs. A promising approach is to use biomass derived materials for the encapsulation of PCMs, providing inexpensive and non-toxic wall materials. Spray drying processes are more favorable for large scale production than other encapsulation methods. Many studies have used cellulose or cellulose derivatives to encapsulate PCMs, however most of these methods pose significant challenges to scale up, either due to costs, toxicity, or difficulties with the method itself. This work aims to develop a process for the microencapsulation of a PCM using biomass derived wall materials and a spray drying process. This involved the isolation of cellulose from wheat straw, size reduction of cellulose, design and testing of a laboratory scale spray dryer, and spray drying of a cellulose stabilized PCM emulsion. It was found that cellulose could effectively be isolated from wheat straw, and several methods for size reduction were promising for encapsulation. In addition, two spray dryer prototypes were developed, which were able to successfully spray dry during testing, however they had low solids recovery. Successful microencapsulation of the PCM in cellulose by spray drying appears to have occurred based on SEM analysis. Further work is needed to improve cellulose size reduction, emulsion formation for encapsulation, spray dryer performance and operation, as well as rigorous evaluation of the produced microcapsules.Item Embargo Driving Behaviours of Older Adults: Insights into Driver Identification and Real-World Navigational Patterns(2025-01-24) Derafshi, Reihaneh; Bayat, Sayeh; De Souza, Roberto; Vrkljan, BrendaMaintaining driving independence is crucial for older adults, yet cognitive decline poses challenges that impact their safety and decision-making on the road. Additionally, the ability to identify drivers based on unique behavioural patterns has significant implications for vehicle security, personalized driver assistance, and road safety. This thesis explores these interconnected themes through two complementary studies that leverage real-world driving data to gain insights into navigational behaviors and driver identification. The first study examines the relationship between cognitive impairment and driving patterns in older adults. Using GPS data from 246 participants, including 230 cognitively normal individuals and 16 with incident cognitive impairment, spatial clustering and hashing algorithms revealed significant differences in driving behaviours. Participants with cognitive impairment demonstrated reduced route variability and reliance on fewer distinct paths to common destinations, offering evidence for driving as a potential digital biomarker for early detection and monitoring of cognitive decline. The second study presents a privacy-preserving methodology for driver identification using gas and brake data recorded during maneuvers. An unsupervised acceleration-based maneuver detection method was developed, followed by a supervised Long Short-Term Memory (LSTM) model for predicting driver identity. Results demonstrated the efficacy of this approach, achieving an average accuracy of 90.9% across crossvalidation folds. The findings highlight the existence of personal driving signatures embedded in gas and brake patterns, offering a scalable and privacy-conscious solution for driver identification. Together, these studies aim to uncover insights into how cognitive health and individual driving behaviours shape real-world navigational patterns, advancing our understanding of driving as both a digital biomarker and a personal identifier. By integrating behavioural analysis with scalable computational models, this thesis advances the potential for personalized driver systems, digital health monitoring, and vehicle security in naturalistic driving environments.Item Embargo Modelling and Validation of a Cable-Assisted Robotic System for Machining Application(2025-01-29) Sajjad, Omer; Lee, Jihyun; Dankers, Arne; Bisheban, MahdisIn the rapidly evolving landscape of manufacturing processes, robotic systems have gained prominence for their precision and efficiency. A cable-assisted robotic system (CARS) tailored for machining operations, offering enhanced stiffness is presented in this thesis. This thesis aims to understand CARS dynamic behaviour by experimentally examining the system under various conditions. These conditions include equilibrium and imbalance states, varying the robot postures, and varying the pulley locations. Understanding the influence of these variables aids in determining the feasibility of such a system. Additionally, the influence of the cables on the systems is examined. Cable types are varied from solid to stranded, as well as the number of cables and the size of the cables. The cable tension is also manipulated and the effects are investigated. The cables act as massless redundant links providing the robot with additional stiffness, however the extent to which additional stiffness is applied needs to be determined. CARS is also examined in a quasi-static state. The quasi-static state differs from the static, impacting the stability limits at the low frequencies and giving a better understanding of the dynamics of the system for machining applications. Finally, CARS is tested in machining by performing chatter tests under the use of different cables. Furthermore, this thesis presents a novel mathematical model for CARS, consisting of a semi-empirical cable model integrated with a serial robot model. The cable properties are identified experimentally, while the robot properties are determined using optimization techniques. The model is derived using the Euler-Lagrange method, and is validated by simulating CARS response and comparing it to the results obtained through experimentation. Finally, the model is optimized using a genetic algorithm to determine the cable configuration that maximizes the dynamic stiffness. These findings have implications for robotic machining applications and broader industrial robotics.Item Embargo Surfactant-Modified Nanoparticles for Enhanced Oil Recovery in Sandstone and Carbonate Reservoirs(2025-01-29) Aboabdulla, Jomaa Ahmed Melad; Nassar, Nashaat; Hassanzadeh, Hassan; Sumon, Kazi Z.; Mohamad, Abdulmajeed; Dejam, MortezaThis work delves into the realm of enhanced oil recovery (EOR) from carbonate and sandstone reservoirs by using cetyltrimethylammonium and alpha-olefin sulphonate (AOS) grafted on silica nanoparticles with low salinity water (LSW). The research investigates the mechanisms underlying the grafting of surfactants onto silica nanoparticles for carbonates and sandstone core applications, forming surfactant nano-based nanofluids. When coupled with LSW, these nanofluids offer a transformative strategy for chemical EOR. Rigorous experiments were conducted, ranging from material and fluid characterization, interfacial tension (IFT) measurements, wettability assessment using contact angle, spontaneous imbibition, and nuclear magnetic resonance (NMR) measurements and followed with core flooding experiments on different core plug samples both for carbonates and sandstones. For carbonate core plugs, limestone cores consisting of low (50 mD) and higher permeability (200 mD) scenarios were used. For sandstone core plugs, Brea sandstone of permeability in the range of 60-100 mD was used. The outcomes of these experiments clarified key insights into oil recovery. The reduction in IFT, particularly at elevated pH levels, emerged as a critical mechanism. For the case of carbonate reservoirs, while contact angle measurements indicated a significant shift from oil-wet to water-wet conditions, NMR and Amott index measurements indicated no wettability change upon the application of nanofluids. In the core flood experiments, the effectiveness of hexadecyltrimethylammonium bromide (CTAB) alone was contrasted with that of CTAB-grafted silica nanoparticles. For 200 mD cores, CTAB alone had an additional recovery of 22.4% over 6 pore volumes (PV), whereas CTAB-grafted silica nanoparticles at higher pH levels (SE) showed a higher recovery of 34.7%. In the case of 50 mD cores, CTAB alone yielded a recovery of 15%, while SE resulted in 20% of the oil originally in place (OOIP). These findings underscore the unparalleled potential of CTAB-grafted silica nanoparticles at elevated pH levels as a pioneering method, offering an economically viable, efficient, and highly effective approach for implementing surfactant-nanoparticle solutions in carbonate reservoirs, covering both low and high-permeability reservoirs. For the sandstone application, AOS surfactants and silica nanoparticles were tested for EOR applications via a series of tests, facilitating the mobilization of trapped oil. The study presented a new approach to the integration of silica-grafted AOS when dispersed in LSW for EOR applications in sandstone reservoirs. The formulated fluids comprised formation water (FW), LSW, silica nanofluids, AOS surfactant, and AOS+ silica (pH 9). Recovery at the tertiary stage was as follows: FW (0.00%), LSW (1.43%), silica nanofluids (2.85%), AOS (5.71%), and AOS+Silica (pH 9) (15.71%). The significant additional recovery observed in AOS and AOS-assisted nanofluids was attributed mainly to the ultra-low interfacial tension, which resulted in a change in capillary number magnitude (10-5 to 10-3) that facilitated the displacement of trapped oil since the wettability change was not significant. This study demonstrated the potential of integrating AOS-silica nanofluids with low-salinity water for enhanced oil recovery, providing valuable insights for optimizing EOR strategies in sandstone reservoirs. This research contributes significantly to the academic discourse surrounding EOR and holds immense promise for the petroleum industry, heralding a new era of enhanced recovery techniques in challenging reservoirs.