Graduate Studieshttps://hdl.handle.net/1880/1000292024-03-29T06:37:28Z2024-03-29T06:37:28Z282011Parallelization of Bayesian Phylogenetics to Greatly Improve Run TimesYang, Davidhttps://hdl.handle.net/1880/1183312024-03-28T09:01:08Z2024-03-24T00:00:00Zdc.title: Parallelization of Bayesian Phylogenetics to Greatly Improve Run Times
dc.contributor.author: Yang, David
dc.description.abstract: Phylogenetic analyses are invaluable to understanding the transmission of viruses, especially during disease outbreaks. In particular, Bayesian phylogenetics has great potential in modeling viral transmission due to the numerous phylogenetic models that can be incorporated. Currently, the availability of user-friendly software and accessibility to sequence data makes phylogenetic analyses easy to perform. However, to date, Bayesian phylogenetic analyses are still limited by long computational run-times which are especially unfavorable during ongoing and evolving disease outbreaks that demand real-time phylogeny results. Current optimization methods of Bayesian phylogenetic analysis mainly focus on iteration-level parallelization and mostly overlook the potential of larger-scale parallelization approaches. In this thesis, we provide an in-depth overview of topics including phylogenetic analysis, relevant biological information, and phylogenetic analysis optimization methods. We also proposed a novel parallelized Markov Chain Monte Carlo method that greatly improved Bayesian phylogenetic run times and integrated the approach into a data pipeline to allow for the direct analysis of viral samples. We demonstrated the validity of our methods by performing phylogenetic analyses on two sets of HIV simulation data and one set of real-world SARS-CoV-2 data. Our results suggested that the parallelization of MCMC in Bayesian phylogenetic analyses drastically reduces run times by 29-fold without causing significant deviations in parameter estimates and predicted phylogenetic trees.
2024-03-24T00:00:00ZAugmented QArt: Interactive Art Recreation by Mobile Augmented RealityBooshehrian, Mahnazhttps://hdl.handle.net/1880/1183212024-03-28T09:01:59Z2024-03-21T00:00:00Zdc.title: Augmented QArt: Interactive Art Recreation by Mobile Augmented Reality
dc.contributor.author: Booshehrian, Mahnaz
dc.description.abstract: The integration of technology into art galleries and museums has opened new avenues for enhancing visitors' experiences and addressing challenges related to accessibility, interactivity, and artistic attraction. Inspired by Picasso’s Cubism paintings and Augmented Reality technology, this thesis explores the design of aesthetically detectable codes, known as QArt codes, to enhance accessibility and visual appeal and to enrich traditional art experiences in settings where space and time are limited. The project aims to answer questions about how technology can be leveraged to enhance artistic environments, offer interactive access to artwork information, and seamlessly blend the actual and virtual realms. Through the implementation of QArt codes, people can easily access and explore various artworks, including Picasso's Harlequin paintings, while saving time and money. This approach offers visitors a chance to learn about different aspects of the artwork, such as style, techniques, and historical context. Interacting with QArt codes provides an engaging and memorable experience, leaving a lasting impression on visitors. A qualitative user study conducted at the end of the project revealed that QArt codes can provide a nuanced understanding of Picasso's artistic range and insight into the Cubism style through multiple dimensions. Overall, QArt codes are an effective and captivating way to share artworks with the world.
2024-03-21T00:00:00ZNeutrophil- and B cell-mediated host defense against viral and fungal respiratory infectionsSarden, Nicolehttps://hdl.handle.net/1880/1183302024-03-28T09:00:55Z2024-03-21T00:00:00Zdc.title: Neutrophil- and B cell-mediated host defense against viral and fungal respiratory infections
dc.contributor.author: Sarden, Nicole
dc.description.abstract: Infections of the lung continue to be a worldwide annual problem affecting millions of people. Fighting acute respiratory infections requires rapid and collaborative responses involving diverse immune cells. An interesting and unexplained clinical problem that sparked this thesis was the clinical observation that influenza A, a common respiratory virus, increases susceptibility to secondary infections with environmental fungi such as Aspergillus fumigatus (Af). By establishing a mouse model of viral-fungal co-infection and using clinical human samples, I discovered an essential collaboration between an underappreciated innate B lymphocyte, called B1a, which produced natural antibodies against Af, which tagged the fungi for elimination by neutrophils. Following influenza A infections, B1a cells died of apoptosis leading to diminished natural anti-Af antibodies and negating the ability of neutrophils to target and eliminate Af. Disruption of this axis explained susceptibility in viral- and steroid-associated infections. Delving deeper into the requirements of immune cell resistance to influenza and Af as individual infections, I discovered unique roles for neutrophils during influenza and innate B cells in aspergillosis. While there is ample research investigating neutrophils and their roles during infections with extracellular pathogens, it remained unclear how the neutrophil pool is affected following viral infections and subsequent functional outcomes. Additionally, it has been recently proposed that an interferon-responsive neutrophil state with unknown functions emerges following viral infections. In isolated viral infection, I found neutrophils adapt to an anti-viral phenotype which is spatially regulated, requires type I interferon licensing and sympathetic drive. On the other hand, using a genetically engineered mouse, we studied the specific roles of innate B1a cells during Aspergillus infection and found that this rare antibody producing cells was essential for host resistance against isolated Af infection. Moreover, I discovered key molecular requirements of the B1a cells that allow them to traffic and recruit properly in the lung, and I discovered that these cells can be amplified to improve host defense against Af. Altogether, this body of work uncovers neutrophils’ effects following isolated viral infection and during co-infection and demonstrates the tight interconnectedness between neutrophils and B lymphocytes which are critical for anti-fungal immunity.
2024-03-21T00:00:00ZChemical Looping Combustion Process Using Supported Copper Oxide Oxygen CarriersDaneshmandjahromi, Sanazhttps://hdl.handle.net/1880/1183172024-03-23T09:02:02Z2024-03-14T00:00:00Zdc.title: Chemical Looping Combustion Process Using Supported Copper Oxide Oxygen Carriers
dc.contributor.author: Daneshmandjahromi, Sanaz
dc.description.abstract: Chemical looping combustion (CLC) is an innovative and environmentally promising technology for efficient and low-emission combustion of fossil fuels. Unlike conventional combustion processes, CLC operates by utilizing metal oxide particles as oxygen carriers (OCs) to facilitate the combustion of fuel while preventing the mixing of air and fuel, thereby minimizing the formation of nitrogen oxides (NOx) and enabling carbon capture. This unique approach makes CLC an attractive solution for mitigating greenhouse gas emissions from power plants and industrial processes. The oxygen carrier is a pivotal component of the CLC process. Therefore, the development of a highly stable oxygen carrier is of utmost importance for the commercialization of the CLC process. To this end, this thesis investigates the fabrication of synthetic oxygen carriers for the CLC process considering the activity and stability of the OCs in cyclic operation. In this study, CuO was selected as the oxygen carrier because it is relatively cheap, abundant, and highly reactive. The effect of support type and the CuO loading were investigated to optimize the physical properties of the prepared oxygen carriers and their performance in the CLC process. Silica, zirconia, and alumina supports were synthesized by the aerogel method, and CuO was impregnated on the surface of them. Results indicated that zirconia aerogel support exhibited the highest reactivity for methane combustion, and γ-alumina aerogel support displayed the least favorable performance, primarily due to the interaction between copper and alumina and the formation of coke. In order to prevent the interaction between CuO and Al2O3, a new method was employed to synthesize α-Alumina with a significantly increased surface area. It was observed that the alumina support transformed into α-Alumina in the temperature range of 1000-1200 °C, resulting in a surface area between 100-160 m2/g. OCs showed high activity during reduction and oxidation reactions and the conversion was complete after a few minutes because the interaction between CuO and Alumina was prevented. Yolk-shell structured γ-alumina support was also prepared in order to prevent the formation of spinel. It was found that the CuO-impregnated yolk-shell oxygen carrier showed the highest oxygen transport capacity and the highest resistance to coke formation compared to the core-shell and γ-alumina support because the presence of homogeneous coating of zirconia prevented the interaction between alumina and copper oxide and avoided the formation of coke. The effect of the immobilization of the CuO in the structure of the support was investigated in the CLC process. CuO nanoparticles, ranging from 20% to 60% in weight, were encapsulated within the nanochannels of silica and zirconia using a sol-gel technique. The findings suggested that a loading of up to 60 wt.% of CuO on the zirconia support could be achieved without any loss of the OC’s activity and stability. Silica-supported OCs exhibited lower oxygen transport capacity than the anticipated theoretical values. This reduction was a result of both CuO decomposing into Cu2O during the reduction process and the fusion and collapse of mesoporous silica. The kinetics of redox steps in the CLC process were investigated using a modified grain model considering grain size distribution in the OC particles based on their pore size distribution profile and the “pore to sphere” factor.
2024-03-14T00:00:00ZThe distribution of Dopamine Receptors in the Mesencephalic Locomotor Region and colocalization with inhibitory and excitatory cell typesDi Vito, Stephaniehttps://hdl.handle.net/1880/1183112024-03-22T09:00:52Z2024-03-20T00:00:00Zdc.title: The distribution of Dopamine Receptors in the Mesencephalic Locomotor Region and colocalization with inhibitory and excitatory cell types
dc.contributor.author: Di Vito, Stephanie
dc.description.abstract: The dopaminergic (DA) control of motor function has for many decades been thought to be indirect via substantia nigra pars compacta (SNc) projections to the striatum. DA interaction with dopamine D1 or D2 -receptor (D1R or D2R) expressing cells in the striatum leads to locomotion via disinhibition of Mesencephalic Locomotor region (MLR) neurons. The MLR is known to be a key centre for the control of locomotion. It comprises the cuneiform nucleus (CnF) and pedunculopontine nucleus (PPN). These regions are heterogeneous and show differential effects on locomotion following stimulation of either glutamatergic or GABAergic cells. The MLR receives predominantly inhibitory input from the basal ganglia. Recently, our lab discovered that a dopaminergic nucleus within the medial zona incerta (mZI); the A13, projects to the MLR. Direct dopaminergic projections that modulate locomotion, from the SNc to the MLR, have also been identified in lampreys and rats. This suggests at least two direct dopaminergic control pathways to the MLR that lie parallel to the canonical nigrostriatal DA pathway and modulate motor control. However, it is not well understood how dopamine receptors are distributed across cellular subtypes in the MLR. In this thesis I used adult C57BL/6 male and female mice to address this gap. RNAscope® was performed to determine the distribution of DA receptor mRNA on vGLUT2 and vGAT neurons within the PPN and CnF. Overall, D2+5R were the highest expressing subtypes of DARs, while D1,3, and 4R were sparsely expressed. There were no significant differences in D1-5R expression between the PPN and CnF. D5R cells showed colocalization with cells expressing vGLUT2 mRNA, while D2R had significant subpopulations of cells expressing both vGAT and vGLUT2 mRNA. My thesis suggests that DA modulation of MLR neurons are predominantly D2R mediated, and dopamine may play a role in opposing behaviours, due to D2R expression on glutamatergic and GABAergic cells. Further investigation is needed to determine the functional role of dopamine receptors in the MLR and upstream nuclei (A13, SNc, or both) contributing to dopaminergic modulation of the MLR.
2024-03-20T00:00:00ZPatient-Reported Outcome Measures to Inform Measurement-based Care for Youth Living with Mental Health Concerns: A mixed method studyThapa Bajgain, Kalpanahttps://hdl.handle.net/1880/1183052024-03-21T09:00:44Z2024-03-19T00:00:00Zdc.title: Patient-Reported Outcome Measures to Inform Measurement-based Care for Youth Living with Mental Health Concerns: A mixed method study
dc.contributor.author: Thapa Bajgain, Kalpana
dc.description.abstract: Measurement-based care (MBC) describes the process of routinely using outcome measurement to guide treatment decisions supporting Patient-centered Care (PCC). Patient-reported Outcome Measures (PROMs) play a vital role in MBC supporting the delivery of PCC. Despite the evidence on the benefits of using PROMs in clinical care, some barriers hinder the selection of the PROMs, such as the different age groups for youth and poor consensus on which measurements are best practices and most appropriate for this population. This mixed-methods, multi-phased study addresses some of these gaps by focusing on identifying, selecting, and prioritizing the PROMs to be implemented in the clinical care of youth with depression and/or anxiety to inform the MBC program at the Summit Center. The first phase of this thesis work includes three stages: 1) a systematic review to identify, evaluate, and synthesize the global evidence on the use of PROMs in youth mental health clinical care 2) In the second stage, we create and combine a database of PROMs from different sources. In the third step, we selected the top 10 PROMs to prioritize in Phase 2. The selected top 10 PROMs were: Beck Depression Inventory (BDI), Child Behavioral Checklist (CBC), Child Health Questionnaire (CHQ), KIDSCREEN 10, Pediatric Quality of Life Inventory (PedsQL), Revised Children's Anxiety and Depression Scale (RCAD 25), Spence Children’s Anxiety Scale (SCAC), Screen for Child Anxiety Related Disorder (SCARED), Strength and Difficulties Questionnaires (SDQ), and The Young Person’s Core (YP-CORE). Then, in Phase 2, we conducted the Nominal Group Technique (NGT) with youth living with depression and anxiety and their family caregivers to prioritize these top 10 PROMs. The top PROMs ranked by youth were RCAD 25, BDI, YP-CORE, SCAS, SCARED, CBCL, PedsQl, SDQ, KIDSCREEN 10, and CHQ, while families/caregivers top-ranked RCAD 25, SCARED, YP-CORE, KIDSCREEN 10, SCAS, CBCL, PedsQl, SDQ, BDI, and CHQ. In summary, the findings of this study informed the MBC program at the Summit Center and presented an excellent opportunity to leverage the findings of this study to support the scale-up implementation of PROMs in the clinical care for youth living with mental health in Alberta.
2024-03-19T00:00:00ZViscous Fingering Instability of Complex Fluids in a Radial Hele-Shaw CellLee, Young Hoonhttps://hdl.handle.net/1880/1183012024-03-20T09:00:51Z2024-03-15T00:00:00Zdc.title: Viscous Fingering Instability of Complex Fluids in a Radial Hele-Shaw Cell
dc.contributor.author: Lee, Young Hoon
dc.description.abstract: When a less-viscous fluid displaces another fluid of higher viscosity in a porous medium, instability can develop at the interface between the two fluids. The instability manifests itself in the form of finger-like patterns of the displacing fluid propagating through the displaced one. In this work, viscous fingering instabilities involving complex fluids in a radial Hele-Shaw is investigated. Many fluids in our lives such as shaving foams, glues, flour-water dough, mayonnaise, and paints are complex fluids which exhibit multiple non-Newtonian properties simultaneously such as shear-thinning or shear-thickening, yield stress, and viscoelastic effects. First, the effects of normal stress differences of dilute low molecular weight poly(ethylene oxide) (PEO) solutions on viscous fingering instability are studied. Second, we investigate the instabilities associated with air invading foam in Hele-Shaw cell. Third, we examine the effects of water in viscous fingering instabilities of air displacing mineral oil. Fourth, the instability at the interface between two parallel flows of immiscible liquids through a uniform planar pore is studied by using linear stability analysis. We pose important questions: How does normal stresses affect immiscible radial viscous fingering? How does fingering occur into foam? Is it similar to that of a single-phase liquid? The experimental observations reveal nonmonotonic and opposing effects are evident depending on the molecular weight of the PEO and the stage of the radial viscous fingering evolution. We have identified three different flow regimes in the immiscible radial displacement flows of air invading foam in Hele-Shaw cell. The presence of a small volume of water leads to significantly different fingering patterns than that when no water is present. The outcomes are significant because the results demonstrate new behaviors for displacement flow of complex fluids.
2024-03-15T00:00:00ZProduction Forecasting in Unconventional Reservoirs: A Workflow for Data-Driven AnalysisRahmanifard, Hamidhttps://hdl.handle.net/1880/1182992024-03-20T09:00:35Z2024-03-13T00:00:00Zdc.title: Production Forecasting in Unconventional Reservoirs: A Workflow for Data-Driven Analysis
dc.contributor.author: Rahmanifard, Hamid
dc.description.abstract: The oil and gas industry has experienced a significant transformation in recent years, with the use of advanced data analytics and machine learning (ML) techniques. These innovations have opened new opportunities in reservoir engineering, allowing engineers to make data-driven decisions and optimize well completion parameters. The accuracy of forecasts in predicting hydrocarbon production from unconventional reservoirs has become very important, as it directly affects energy security, economic growth, and sustainable resource management. This thesis presents a novel and comprehensive automated multistep workflow that includes data collection, data preparation, feature selection, hyperparameter tuning, ML algorithm selection, and well completion parameter optimization. In the workflow, we also propose novel methods for outlier detection, feature selection, and a modified optimization algorithm. To verify the accuracy of the workflow, we applied it to various synthetic and field databases and considered different objective functions, such as oil and gas cumulative production and monthly/daily production rates. The proposed integrated workflow enhanced the accuracy and reliability of production forecasting, as well as the assessment and improvement of well performance in unconventional formations. It also helped us determine how geology, reservoir characteristics, and completion designs influence production, and how to adjust them to achieve better outcomes. Moreover, we used the workflow to find the best completion design and estimate the production loss due to sub-optimal completion practices for the wells in the unconventional plays. These results of the research offer valuable insights for the stakeholders in the energy sector who operate in unconventional resources to make informed decisions about well completions, field development, resource extraction, and operational costs.
2024-03-13T00:00:00ZPredicting the Movement of Occluded Objects Using Motion Models and Statistical TrackingGrond, Marco Martenhttps://hdl.handle.net/1880/1182902024-03-19T09:01:16Z2024-03-14T00:00:00Zdc.title: Predicting the Movement of Occluded Objects Using Motion Models and Statistical Tracking
dc.contributor.author: Grond, Marco Marten
dc.description.abstract: Long-term occlusions pose a significant challenge to tracking systems, resulting in broken tracks which obfuscate results and lead to ambiguity when analysing a scene. My proposed solution to this problem, which I call the Occluded Trajectory Modelling (OTM) system, predicts the movement of occluded objects with a statistically-learned model of their movements while occluded, allowing for seamless tracking across occlusions. The model detailing the movement of occluded objects is extracted from unannotated data using Network Tomography and an objective function which extracts object occlusion times. I create a hybrid system, consisting of the OTM working in conjunction with an adapted Multiple Hypothesis Tracker, that is able to seamlessly transition between tracking visible objects and predicting their movement while they are occluded. This is done in real time without the need for visual features. I test my system on two datasets: the first consisting of drone footage with multiple environmental occlusions, and the second containing scenes with multiple non-overlapping cameras. The experimental results obtained from both of these datasets show that my system outperforms existing visual tracking systems in terms of correctly re-identifying objects after occlusion, without suffering a performance trade-off.
2024-03-14T00:00:00ZHomo Emigraturus: Exploring the Collective Yearning for Migration, The Case of IranAsayesh, Omidhttps://hdl.handle.net/1880/1182822024-03-15T09:01:47Z2024-03-12T00:00:00Zdc.title: Homo Emigraturus: Exploring the Collective Yearning for Migration, The Case of Iran
dc.contributor.author: Asayesh, Omid
dc.description.abstract: This study addresses the implications of unrealized international migration aspirations for the lives of various groups in a population, including those who want to migrate, those who prefer to stay, emigrants, and return migrants. The central argument of the study is that the unique combination of a high desire for migration and a low chance of its realization of actual migration reshapes the social landscape in profound ways. This impact extends to the lifestyles, social engagements, political attitudes, and behaviours of individuals in any of the four above-mentioned groups. Some of the concepts that have emerged out of empirical data of this study include the Homo Emigraturus (those ‘about to leave’) who experience ‘imagined migration’; the Anti-Emigraturus (those decidedly avoiding migration) and their ‘anti-migration narrative’; a high-migration-desire society and its ‘culture of migration.’ In this multimethod study, I have utilized two sets of data: a) semi-structured in-depth interviews and b) an analysis of the contents of the online data from the social media debates among Iranians on the issue of migration on Twitter, as well as the Google Trends data. The former is based on 71 interviews with Iranian adults, and the latter is based on a thematic analysis of more than 200,000 tweets in Farsi utilizing recent developments in Natural Language Processing and Machine Learning techniques. The findings demonstrate how a culture of migration in a mobility-restricted population society can significantly reorientate its sociopolitical and cultural landscape, economic dynamics, and civic engagements. The study provides valuable insights into the changing landscape of international migration in a world where the longing to migrate is a prevailing force, even in the absence of substantial actual emigration.
2024-03-12T00:00:00Z