VictorJuiz/thesis huggingface dataset:
Temporal Multiplexed Fluorescence Imaging Device for Bead-based Immunoassay Detection

Point-of-care testing devices have received considerable attention due to the growing need. Complex diseases, such as sepsis, put challenges to the current device and require the results of multiple biomarkers. In this work, we demonstratea fluorescence imaging device that can detect multiple biomarkers using temporally multiplexed illumination. Our device is proven to be able to classify three biomarkers and has the potential to achieve higher multiplexing ability. We separately tested three cytokines, IFN-α, IL-5 and IL-6, with different concentrations. The detection range of these three cytokines is 20 pg/ml-2500/pg/ml, 20pg/ml-2500/pg/ml, and 40 pg/ml-5000/pg/ml. The A nine-groups multiplexed test proves that our device can perform classification and quantitative measurements of three cytokines simultaneously. The results demonstrate our device can be used for sepsis diagnosis and potentially other complex diseases where the detection of multiple biomarkers is needed. With further development, we believe our device can contribute to the point-of-care medical service.

Keywords: Bead-based immunoassay
Fluorescence imaging
Multiplexed detection
Point-of-care device
Quantum dots
Sepsis detection
Advisor: Aitchison, Stewart
Conceptualizations of Identities in Bisexual, Pansexual, and Plurisexual Communities

Plurisexual people – individuals who are attracted to multiple genders – are at increased risk for mental health concerns. Internalized sexual stigma, that is, the internalization of negative attitudes towards one’s sexual orientation, is a key contributor to plurisexual mental health. However, extant scales of this construct are few and lack appropriate content. This study aimed to understand individuals’ attitudes towards their plurisexuality, and translate this into questionnaire items. Qualitative interviews were conducted with n = 13 plurisexual people and n = 3 mental health clinicians. Reflexive thematic analysis yielded three themes: (1) Validating vs. Doubting Myself – self-affirmation to combat identity uncertainty, (2) Owning My Truth vs. Avoiding It – accepting plurisexuality as a core part of oneself versus denying it, and (3) Celebrating vs. Shaming Myself – viewing plurisexuality as an overall positive versus negative force in one’s life. Implications for conceptualizations of internalized sexual stigma and quantitative scale development are discussed.

Keywords: Bisexual
Internalized Stigma
Pansexual
Plurisexual
Reflexive Thematic Analysis
Advisor: Gillis, J. Roy
Detecting Multipartite Entangled States with Machine Learning-Derived Witnesses

We are entering a time in which quantum channel capacity is becoming increasingly dependent on having high-dimensional entangled systems. However, existing methods of detecting high-dimensional entanglement are hindered by their need for an unwieldy amount of measurements and computational power. Indeed, the use of entanglement witnesses circumvents this problem by only considering a small subset of the entangled states in Hilbert Space. Although efficient witnesses for 2-qubit Bell States and 3-Qubit GHZ states are well-known, the predominant “fidelity method" witnesses used for detecting multipartite W states remain relatively complex in the amount of measurements that they require. The work outlined in this thesis aims to improve on existing entanglement witnesses by drawing their correspondence with supervised learning techniques, specifically Support Vector Machines. In doing so, one can derive entanglement witnesses whose features (observables obtained via local operations and classical communications) can be ranked according to their impact on the classification of entangled and separable states. This method allows us to derive W state witnesses that require fewer measurements than those derived via the fidelity method. The process of Recursive Feature Elimination is also presented, by which we can define witnesses that can be decomposed into fewer Pauli observables at the cost of inferior tolerance to noise. Finally, we present the practical utility of our derived witnesses through physical experiments performed on the superconducting qubit devices provided by IBM.

Keywords: Entanglement Detection
Entanglement Witness
Machine Learning
Quantum Information Science
Advisor: Qian, Li
An Online Platform for Manipulating and Understanding Attentional Tunneling: The Development and Assessment of CogLog 2.0

This thesis explores the induction and measurement of attentional tunneling in a display-based visual search task through the development and subsequent analysis of an online platform called CogLog. An overview of the terms and definitions relevant to attentional tunneling, as well as a review of the state-of-the-art of measurement and manipulation of attentional tunneling, are provided. The original CogLog was designed by previous researchers but is no longer accessible for further research as originally intended; therefore, the development and assessment of a more accessible and modular platform called CogLog 2.0 as serves as the major contribution of this thesis. The assessment confirms that CogLog 2.0 performs comparably to its predecessor with the addition of a built-in workload assessment feature. CogLog 2.0 is positioned as a tool for further studying attentional tunneling as well as cognitive countermeasures and adaptive display interventions.

Keywords: attentional processes
attentional tunneling
passive data monitoring
Advisor: Jamieson, Greg
Cell-extracellular Matrix Interactions Contribute to Rapid Embryonic Wound Closure

Embryos repair wounds rapidly, in a process driven by the collective movement of the cells around the wound. The cells adjacent to embryonic wounds polarize the cytoskeletal proteins actin and non-muscle myosin II at the wound edge. Simultaneously, adherens junction proteins including E-cadherin are internalized from the wound border and localize to former tricellular junctions around the wound. Using quantitative microscopy, we found that cells adjacent to embryonic wounds in Drosophila polarized Talin, a core component of cell-extracellular matrix (ECM) adhesions. Integrin knock-down delayed wound closure and was associated with a defect in E-cadherin reinforcement at tricellular junctions along the wound edge. Additionally, depleting integrins caused a reduction in actin levels and an abnormal actin distribution around the wound. Together, our results show that cell-ECM adhesion contributes to embryonic wound repair and reveal an interplay between cell-cell and cell-ECM adhesion for the transmission of forces that drive embryonic wound healing.

Keywords: adherens junctions
cytoskeleton
Drosophila
Extracellular matrix
integrins
wound healing
Advisor: Fernandez-Gonzalez, Rodrigo
Covalent Attachment of Polyaspartic Acid to Experimental Resin-based Materials for the Microinvasive Treatment of White Spot Lesions: An In vitro Pilot Study

Background: Resin infiltrants can be improved through the addition of bioactive molecules. A bioactive molecule capable of promoting hydroxyapatite development is polyaspartic acid, pAsp. Objective: This in vitro study assessed the material properties of experimental resin-based materials. Methods: Artificial white spot lesions on extracted human premolars (n=60) were treated with resin-based materials, Prime&BondTM (Dentsply Sirona, North Carolina, USA) or IconTM (DMG, Hamburg, Germany), containing pAsp (passive or covalent) or unmodified. After remineralization, specimens were assessed for penetration depth (μm) through Confocal Microscopy, and surface nanohardness (GPa) and Young’s modulus (GPa) through Diamond Berkovich Indenter. Two-way ANOVA followed by Tukey post-hoc test was used to analyze data, a=0.05. Results: Covalent attachment of pAsp significantly increased penetration depth compared to passive addition pAsp to resin-based materials (p=0.013). Conclusion: To our knowledge this is the first study to covalently attach pAsp to resin-based materials targeted for the treatment of white spot enamel lesions.

Keywords: Covalent bond
Experimental Infiltrant
Polyaspartic acid
Resin Infiltrant
White spot lesion
Advisor: Prakki, Anuradha
Carneiro, Karina
A Power-Performance Comparison of CMOS Tunable-Delay Clock Buffers

This thesis presents a systematic comparison of the power-supply induced jitter (PSIJ), random jitter (RJ) generation and random jitter amplification (RJA) of different CMOS tunable-delay clock buffers in GF 45-nm PDSOI technology. Under the proposed com- parison methodology, inductive peaking buffer architectures using passive and active inductors were found to have the best jitter performance. Passive inductors require large areas at moderate clock frequencies and thus are impractical for most applications. A novel active inductive peaking buffer architecture is proposed as an alternative, improving upon the state-of-the-art by reducing the self-loading effect and improving jitter atten- uation. The clocks of two different digitally-controlled delay lines (DCDL) using shunt capacitor buffers and the proposed active inductive peaking buffers were used at the final multiplexer stage of a prototype 25 Gb/s NRZ transmitter. The resulting post-layout simulated transmitter output jitter shows a 30% reduction using the proposed active inductive peaking buffer design.

Keywords: Clock Buffering
Digitally-Controlled Delay Line
Power-Supply Induced Jitter
Random Jitter
Random Jitter Amplification
Wireline Communications
Advisor: Chan Carusone, Anthony
Effects of Maternal High Fat Diet on Microglia Activation in Rat Offspring

Maternal consumption of high saturated-fat diets (mHFD) leads to anxiety-like phenotypes in offspring. Prior evidence suggests that enhanced reactivity of the hypothalamic-pituitary-adrenal axis, which regulates the stress response and neuroinflammation through glucocorticoid receptor (GR) activity, contributes to these phenotypes. Microglia sustain long-lasting phenotypes in response to mHFD, but their role in early-life GR-mediated neuroinflammation is relatively unknown. The objectives of this study were: (1) measure inflammatory gene expression in P7 (neonatal) offspring after mHFD exposure; (2) study changes in microglia density, activation, and morphology; (3) purify microglia from P60 (adult) offspring and characterize their immunophenotype. I hypothesized mHFD would alter offspring microglia to become more activated and pro-inflammatory. My results showed microglia changed their immunophenotype and became activated after mHFD exposure during neonatal stages. Adult microglia immunophenotypes were altered in a sex-specific manner. This research provides insight into mechanisms that drive stress-related mental health outcomes associated with developmental mHFD exposure.

Keywords: Amygdala
High-fat diet
Immunophenotype
Inflammation
Microglia
NFKB
Advisor: McGowan, Patrick O
Upper and Lower Body Intersegmental Coordination During Unsupervised Gait of Older Adults with Dementia

People with dementia are at a high risk of falls, and changes in coordination of the upper and lower body segments may contribute to this risk. Using data obtained from a vision-based gait monitoring system, the temporal cross correlation between trunk and thigh displacement (right and left) in the mediolateral direction, expressed as a percent of the gait cycle (%lag time), was measured in 52 people with dementia. Participants with dementia who fell during the study had more negative %lag times, representing a pattern of gait coordination where trunk motion lagged behind thigh motion. Negative %lag times were associated with number of falls during the study and a history of falls. Negative %lag times were also associated with older age, lower balance test scores, increased agitation scores and spatiotemporal gait measures reflecting decreased stability. Negative %lag times are a marker for impaired stability and fall risk in people with dementia.

Keywords: Coordination
Dementia
Falls
Gait
Video-based Analysis
Advisor: Iaboni, Andrea
Primary Sclerosing Cholangitis-Individual Patient International Meta-analysis of Biochemical and Clinical Predictors of Outcome

PSC is an autoimmune disease of the biliary tracts that affects males more than females. Patients with PSC have a variable disease course. The disease hallmark is strictures and dilations involving the bile ducts with an increased risk of cholangiocarcinoma. PSC has a close association with IBD predominantly UC with a higher hazard of developing colon cancer. Risk stratification of PSC patients is crucial for patient education and to guide clinical decisions and transplant efforts. Multiple risk stratification strategies and models have been proposed. In this study, we sought to explore novel risk stratification strategies in addition to longitudinal risk stratification models to identify patients with progressive disease. ALP, TB, Albumin and platelets have a distinctive pattern and levels for patients with progressive disease and can identify them up to 10 years before experiencing death or transplant. Additionally, total bilirubin ULN can be used to discriminate high-risk patients.

Keywords: Autoimmune Liver Disease
Elastography
End Stage Liver Disease
Liver Biochemistry
Liver Disease
Primary Sclerosing cholangitis
Advisor: Hansen, Bettina
A Framework For Bayesian Optimization of Probabilistic Robustness Metrics

In this thesis, we consider the problem of optimizing probabilistic robustness metrics that depend on the outputs of expensive black-box simulators. In the present work, Gaussian process models of the black-box simulators are leveraged as surrogates to construct sample-based approximations of acquisition functions that can then be used to guide Bayesian optimization algorithms towards the optimum of the probabilistic robustness metric. Sample-based approximations enable accelerated optimization of some acquisition functions using stochastic gradient descent methods, while enabling our framework to accommodate arbitrary robustness metrics. An approach is presented to address the challenges associated with visualizing convergence of probabilistic robustness metrics calculated using surrogate models that are updated sequentially with each observation. A prototype GUI is developed to allow users to specify their problem statement while ensuring all parameters and data are correctly defined. Lastly, numerical studies are presented to illustrate the efficacy of the proposed approach.

Keywords: Gaussian processes
Machine Learning
Optimization
Robustness Metrics
Uncertainty
Advisor: Nair, Prasanth B
Characterization of PRR20A, FCBR3B and KLHL40 as Proximity-Dependent Effectors of Protein Stability

Proteasomal degradation, a natural process that degrades proteins, is used in targeted protein degradation (TPD) therapeutics to cure diseases. To find potential degraders for TPD, the Taipale lab screened for proteins that induce protein degradation or stabilization in a proximity-dependent manner. I characterized the degraders PRR20A and FCGR3B and the stabilizer KLHL40. I made mutants of PRR20A to identify residues in its degron and identified some residues that might be involved in it. I performed a CRISPR screen on cells expressing FCGR3B-vhhGFP or KLHL40-vhhGFP, with the vhhGFP nanobody binding a GFP construct. In the FCGR3B samples there were kinases and GPI-anchor biogenesis proteins. There were chaperones and phosphorylases in the KLHL40 samples. These proteins can be inhibited to see if they are involved in the KLHL40 or FCGR3B mechanism. The PRR20A residues can help identify an E3 acting on it. Characterizing these proteins could help in developing proximity drugs.

Keywords: FCGR3B
KLHL40
Proximity-Dependent degradtion
PRR20A
Advisor: Taipale, Mikko MT
Play-in-Development: An Examination of the Role of Free Play and the University in the Sport-for-Development Sector

The following research examined student experiences with the community service-learning (CSL) course Play Around the World (PAW), offered by the Faculty of Kinesiology, Sport, and Recreation (KSR) at the University of Alberta (U of A). This research sought to understand the nature and objectives of the program, and to analyze PAW student experiences with the program to answer the following research questions: 1) What is the role of the university within the sport for development (SFD) sector, and 2) What is the role of “free play” within the sport for development sector: with a third research question having emerged as the research process unfolded: 3) How can the PAW program inform the SFD sector moving forward? Key findings revealed that the university and their use of the free play methodology created critically reflexive environments which allowed student practitioners to challenge the neoliberal and neo-colonial features associated with traditional SFD programs.

Keywords: Community Service-Learning
Play
Post-secondary
Sport-for-development
University
Advisor: Darnell, Simon
Assessment of Oral Microbial Flora in Subjects with Inreased Severity of Early Childhood Caries - A Pilot Study

BACKGROUND: Comparative and site-specific microbial differences in subjects with early childhood caries (ECC) have yielded inconclusive data. OBJECTIVE: To conduct a pilot study and identify site-specific relationships between microbiome and increasing caries severity. METHODS: Microbiome analysis was conducted on supragingival plaque from two specific tooth sites of subjects of three groups with increasing caries severity. RESULTS: No differences in bacterial diversity between tooth sites observed within individual subjects; significant differences found between individuals and between three caries groups. Increased abundance of cariogenic bacteria with decrease in health-associated bacteria associated with increase in the severity of caries. Additionally, specific distinctive bacterial genera dominated the least and most severe caries groups. CONCLUSION: Presence of specific bacterial groups in ECC subjects with varying severity of caries could be used to identify degree of severity of diseased state with potential to predict caries progression in ECC, a finding to be verified with longitudinal studies.

Advisor: Gong, Dr. Siew-Ging
Predicting Oxygen Transport Properties of Polymer Electrolyte Membrane Fuel Cell Gas Diffusion Layers with Local Saturation Considerations: A Pore Network Modelling Approach

Polymer electrolyte membrane (PEM) fuel cells are a promising means of reducing anthropogenic greenhouse gas emissions. However, mass transport losses hinder the performance of PEM fuel cells, impeding their commercialization. This thesis comprises of two studies that determine the impact of liquid water within the substrate on the oxygen transport behaviour of the fuel cell. First, the impact of channel and land region saturation on the oxygen transport properties of the substrate were determined. The oxygen transport properties of the substrate were severely affected by channel region saturation, while land region saturation had a relatively minor impact. Next, the contribution of the substrate to the oxygen transport resistance of a PEM fuel cell was determined. It was determined that significant oxygen transport resistance arises from the catalyst layer (CL) or CL-microporous layer interface. This thesis offers insight into designing next-generation components for improved PEM fuel cell performance.

Keywords: gas diffusion layer
local saturation
oxygen transport resistance
polymer electrolyte membrane fuel cell
Advisor: Bazylak, Aimy
Student Reflections of their Experiences with French as a Second Language Programs in Ontario

By documenting student perspectives on French as a Second Language (FSL) in Ontario, this study gains a better understanding of the degree to which students appreciate their FSL programs. The literature review reveals that research on FSL focuses primarily on teachers’ working conditions, pedagogy, and student proficiency and motivation. This study aims to provide the voice of students on their experiences of FSL. Participants were university students (n=24) who had previously completed a FSL program in Ontario. Data were collected using a questionnaire and individual interviews (n=8) and were analysed via a mixed method approach through a Complexity Theory framework. Findings revealed that participants generally appreciated their FSL programs, however they also wished to be more proficient in their oral skills, particularly university-level French-studies students who felt underprepared for their French studies. Participants expressed wanting to have more agency and authentic learning in their FSL programs at the elementary/secondary levels. En documentant les points de vue des étudiants sur le français langue seconde (FLS) en Ontario, cette étude permet de mieux comprendre dans quelle mesure ils apprécient leurs programmes de FLS. L'analyse documentaire révèle que la recherche sur le FLS porte principalement sur les enseignants, la pédagogie et la compétence et la motivation des élèves. Les participants étaient des étudiants universitaires (n=24) qui avaient déjà suivi un programme de FLS en Ontario. Les données ont été recueillies par un questionnaire et d'entretiens individuels (n=8) et ont été analysées via une approche de méthode mixte dans un cadre de théorie de la complexité. Les résultats ont révélé que les participants appréciaient généralement leurs programmes de FLS, mais qu'ils souhaitaient également être plus compétents dans leurs compétences orales. Les participants ont exprimé le désir d'avoir plus de pouvoir et l’apprentissage authentique dans leurs programmes de FLS aux niveaux élémentaire/secondaire.

Keywords: core french
French as a second language
french immersion
FSL
Ontario
second language
Advisor: Rehner, Katherine
Topological Properties of Causal Spaces

In this paper, we study causal spaces, i.e. spaces equipped with a time separation function. We introduce some natural topologies on this space and study their properties. We study how causal path-connectedness simplifies the topologies, and induces desirable properties such as first count- ability. We also study the compatibility of these topologies with subspaces and products. Finally we introduce an analog of the Hausdorff distance for metric spaces, called the Hausdorff time separation.

Keywords: General Topology
Mathematical Relativity
Metric Geometry
Advisor: McCann, Robert
DropMAVE: A High-throughput Droplet Microfluidic Platform for Non-localized Protein Variant Effect Assays

Genome variant interpretation becomes increasingly important as next-generation sequencing discovers more genomic variation. Precision medicine seeks to leverage genomic data to better inform clinical decision making. Because most variants are classified as variants of uncertain significance, genomic data often do not have functional annotations to inform clinical decision making. Of the currently available variant interpretation methods, multiplexed assays of variant effect (MAVEs) are the only methods that can provide strong functional evidence for variant pathogenicity at scale. Because of technical challenges, scalable variant effect assays are limited for non-localized genes are limited, e.g., genes encoding secreted proteins or genes encoding enzymes with diffusible enzymes. I developed DropMAVE, a droplet microfluidic platform for scalable non-localized gene variant function assays. This platform is accessible to most life science research laboratories and generalizable to improve variant interpretation for many non-localized genes.

Keywords: droplet microfluidics
missense variation
multiplexed functional assay
single-cell analysis
variant interpretation
Advisor: Roth, Frederick P