University of Lethbridge Theses

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    Initial characterization of the functional cycle of YihA
    (Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, 2023) Capatos, Dora; University of Lethbridge. Faculty of Arts and Science; Wieden, Hans-Joachim
    The worldwide shortage of new and effective antibiotics is becoming of increasing concern. New antibiotic targets are needed for testing and validation in the development of a new generation of antibiotics. This thesis investigates a potential antibiotic target, the essential GTPase YihA. The objective of this thesis was to gain a greater understanding of the mechanisms that regulate YihA’s functional cycle. Small angle X-ray scattering (SAXS) was used to obtain a low resolution solution structure of YihA and to provide information about the hydrodynamic characteristics of YihA including size, shape and flexibility. Further analysis of the SAXS data by disorder prediction programs and by modelling suggested that YihA in solution contains a folded core with flexible N-terminal and C-terminal tails. The SAXS structure of YihA, the SAXS-based modelling and the solution properties of YihA all supported dimerization of YihA in solution. Additionally, analytical gel filtration chromatography at concentrations of YihA closer to physiological concentrations revealed dimerization of YihA. The characteristics of the dimerization interface in the E. coli YihA crystal structure suggest that dimerization of YihA may play an important role in the functional cycle of YihA. Thus, these studies lay the groundwork for future structural and biochemical studies on the mechanism and significance of dimerization of YihA.
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    Accuracy of horse affect assessments: a comparison of equine assisted mental health professionals, non-equine assisted mental health professionals, and laypeople
    (Lethbridge, Alta. : University of Lethbridge, Faculty of Education, 2023) Fox, Sebastian A.; University of Lethbridge. Faculty of Education; Greidanus, Elaine
    In order to know whether a horse’s welfare has been compromised, the professional needs to be able to assess the animal’s behaviour and meaningfully interpret it. Misinterpretation of a horse’s mental state may lead to further misunderstandings of the animal’s behaviour, breakdowns in horse-human communication, and jeopardized wellbeing (Gronqvist et al., 2016; see also Horseman et al., 2016; Mcbride & Long, 2001; Merkies et al., 2018). This study investigated the abilities of (EAMHPs) to assess the affective states of horses. First, an instrument for measuring accuracy was developed by showing a panel of 12 equine behaviour experts 20 videos of horses and asking them to describe the emotional states of the animals. Using the QBA and FCP method, the 10 videos with the highest inter-observer consensus and their associated terms (used to create answer keys) were retained. In the prediction testing phase, those 10 videos were shown to EAMHPs (n = 55), laypeople (n = 94), and non-equine assisted mental health professionals (NEAMHPs; n = 51), who were also asked to generate affectively descriptive terms. These three groups were then graded using the answer keys and awarded total assessment accuracy scores representing how similar their answers were to those of the experts. The participants of the three groups also self-rated their perceived level of horse experience and filled out a related questionnaire. The results found that EAMHPs and laypeople scored significantly higher than the NEAMHPs. However, when horse experience scores were controlled for, the EAMHPs no longer scored significantly higher than the NEAMHPs. Profession and horse experience scores significantly accounted for variation in the total assessment accuracy scores, and the horse experience scores were positively correlated with self-rated levels of horse experience. Those participants who believed they had a high level of horse experience scored significantly higher than those who said they had no horse experience or a low level of experience. The finding that EAMHPs and NEAMHPs score similarly, yet laypeople (significantly) outperform the latter and the former (non-significantly) when assessing the affective states of horses is perplexing. More research is needed to further investigate the involvement of horses in equine assisted therapy practices to ensure that their use remains ethical and that their welfare is not being compromised in exchange for aiding clients.
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    Neural correlates of narrative structure during naturalistic audiovisual film using functional magnetic resonance imaging
    (Lethbridge, Alta. : University of Lethbridge, Dept. of Neuroscience, 2023) Haines, Christina; Ekstrand, Chelsea; Gibb, Robbin
    A narrative is defined as a description of interconnected events, whereby forming narratives requires sustained attention and simultaneous integration of information to navigate and track events and assign them along an immersive timeline (Martinez-Conde et al., 2019). Narratives, in the form of film, plays, and television, offer a unique opportunity to assess brain functions in situations more akin to the “real-world”. However, most neuroimaging studies examining narrative formation have used static stimuli (e.g., still images, disconnected sentences, or incoherent narratives) that do not encapsulate the complexity of narrative formation in the everyday life. It is currently unknown how the brain processes “real-world” information into coherent narrative events. The current research uses data from the Naturalistic Neuroimaging Database (Aliko et al., 2020) to examine the neural correlates of narrative processing using functional magnetic resonance imaging (fMRI). In four experiments, we assessed neural synchrony patterns implicated in long-term narrative processing and identified networks associated with distinct phases of narrative processing and conveyed the dynamic changes of cognitive demands as a narrative evolves. Results from this study emphasize the evolving cognitive demands intrinsic to narrative structure, reflecting dynamic changes in neural synchrony. These findings extend beyond research advancement, by bridging the gap between cognitive neuroscience and “real-world” narrative processing.
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    Molecular standards for analytical ultracentrifugation: investigating the suitability of double-stranded DNA
    (Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, 2023) Ranasinghe, Maduni Charuni; University of Lethbridge. Faculty of Arts and Science; Demeler, Borries
    This thesis focuses on the development of molecular standards to validate analytical ultracentrifugation (AUC) instruments, alongside an exploration of multiple applications of AUC. The goal of the main study is to address the critical need to develop a robust molecular standard for validating AUC instruments, with a specific emphasis on evaluating double-stranded DNA molecules as a potential candidate. By extensive investigation into the hydrodynamic properties of different topologies of double-stranded DNA at a wide range of temperatures, this study reveals the potential of linear and nicked double-stranded DNA as a reliable standard for AUC, contributing to the accurate characterization of macromolecules in solution. Supplementary research findings, as detailed in the attached publications presented in the attached appendix, further illustrate the versatility of AUC in various scientific domains. In one study, we employed AUC as a powerful technique to measure the sedimentation and diffusion coefficients of DNA minicircles to validate the elastic theory results obtained from our other collaborator. Also, it explores the impact of DNA supercoiling-induced shapes on minicircle hydrodynamics. In another collaborative effort, we study the oligomerization behavior of a de novo designed metalloprotein for photocatalytic hydrogen evolution, leveraging AUC for comprehensive characterization. These collective studies highlight the indispensable role of AUC in the characterization of macromolecules in solution, with applications ranging from DNA dynamics to functional protein characterization, and they demonstrate the crucial importance of reliable molecular standards in enhancing the accuracy of AUC measurements. Together, they contribute to the advancement of analytical science and its applications across diverse research domains.
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    Measuring developer experience with abstract syntax trees
    (Lethbridge, Alta. : University of Lethbridge, Dept. of Mathematics and Computer Science, 2023) Deutekom, Steven M.; University of Lethbridge. Faculty of Arts and Science; Rice, Jacqueline E.; Anvik, John
    Accurately representing a developer's programming knowledge and experience is difficult. Traditional metrics rely on counting the number of times a developer has used or made changes to pieces of code. When a developer has modified a file in the past they are less likely to introduce defects with a change. However, these metrics do not contain any general information on the structure or purpose of a piece of code and are only useful when developers work on a piece of code more than once. We investigated the use of several new metrics based on abstract syntax trees (ASTs) as a possible way to more completely measure a developer's experience. By using the ASTs of code previously modified by a developer we may be able to identify their experience with a piece of code they are modifying even if they have never modified that specific code before. Through statistical analysis and machine learning predictions we show that AST-based metrics capture a more general programming experience than count-based metrics. In their current form, AST-based metrics do not offer any significant improvements over existing metrics for defect prediction. However, our work offers a starting point for future use of ASTs for representation of knowledge and experience in defect prediction and other relevant areas.