Lakehead University Knowledge Commons

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Pathway-based multi-omics survival modeling: evaluating weak-modality contributions and robustness across cancer types
(2026) Guo, Jingfeng; Alkhateeb, Abedalrhman; Alsmadi, Malek; Ahmed, Saad B.
Multi-omics survival prediction must distinguish whether a modality enters a model from whether it improves prediction. This thesis evaluated the contributions of copy number variation (CNV) and somatic mutation (MUT) beyond clinical variables and ribonucleic acid (RNA) expression, together with the effects of pathway-based modeling and missing-modality training. Data from The Cancer Genome Atlas (TCGA) covered liver hepatocellular carcinoma (LIHC), breast invasive carcinoma (BRCA), and lower-grade glioma (LGG). Complete-case cohorts comprised 346 and 345 patients for LIHC progression-free interval (PFI) and overall survival (OS), respectively; 778 patients for each BRCA endpoint; and 503 patients for LGG OS. Gene set variation analysis (GSVA) mapped RNA expression to Hallmark pathways, each combined with seven CNV and four MUT summaries. Pathway-grouped composite minimax concave penalty (cMCP) Cox models were compared with Elastic Net using identical features and five frozen train–test splits. A gated residual model tested additional CNV/MUT information beyond a clinical-plus-RNA baseline. Paired bootstrap and permutation controls supported evaluation. Matched ensembles trained with and without modality dropout were tested under synthetic and natural missingness. Elastic Net assigned zero coefficients to at least one molecular block in every cancer–endpoint combination. Relative to same-feature Elastic Net, cMCP improved the mean concordance index (C-index) by 0.0374 for BRCA PFI and 0.0658 for BRCA OS, with both paired confidence intervals above zero. These discrimination gains did not consistently reduce absolute-risk prediction error. Conditional CNV/MUT increment was supported only for LGG OS, with a paired C-index increase of 0.0164 and a 95% confidence interval of [0.0051, 0.0300]; residual corrections were zero in all LIHC and BRCA splits. Modality dropout improved mean discrimination under synthetic missingness for LIHC and LGG but reduced it for BRCA, while natural-incompleteness results varied by endpoint. Exploratory graph ablations did not support a biological-topology advantage, and mediation analysis yielded 11 indirect statistical associations without establishing causality. The results separate penalization benefit, conditional modality information, and robustness to missing inputs. BRCA supported structured penalization, whereas LGG supported conditional weak-modality increment. These internally validated findings define endpoint-specific benefit boundaries without establishing universal model superiority or clinical utility.
The impact of ammonia inhalants on neuromuscular function during fatigued isometric contractions
(2026) Puskas, Liam; Klarner Read, Taryn; Zerpa, Carlos; Sanzo, Paolo
Ammonia inhalants (AIs) are commonly used by athletes to increase arousal and prepare for maximal physical effort; however, evidence supporting their ergogenic effects remains insignificant and/or inconsistent, particularly when exercise is performed under fatigued conditions. The purpose of this study was to determine the effect of ammonia inhalation on neuromuscular function following fatiguing exercise. Fourteen male varsity athletes completed a randomized, counterbalanced crossover design consisting of an AI condition and a control condition separated by one week. During each visit, participants completed a baseline 30-s maximal voluntary isometric contraction (MVIC) of the elbow flexors, followed by a standardized dynamic biceps fatigue protocol and a subsequent 30-s fatigued MVIC. Force and surface electromyography (sEMG) were recorded concurrently. Maximal isometric force, rate of force development to peak force production (RTP), time to maximal force (T2M), biceps sEMG amplitude, rate of force decline (RFDDecline), and mean power frequency (MPF) were assessed. Repeated-measures statistical analyses of variance were used to evaluate differences between treatment conditions and fatigue states. Maximal isometric force significantly decreased following the fatigue protocol (p < .001), with reductions of approximately 20% in both treatment conditions. However, no significant treatment × fatigue state interactions were observed for maximal force, RTP, T2M, biceps sEMG amplitude, or RFDDecline (p > .05). MPF progressively decreased across the 30-s fatigued contraction (p < .001), consistent with the frequency shift phenomenon and the development of myoelectric fatigue; however, neither the treatment effect nor treatment × time interaction was significant (p > .05). Collectively, the results provided evidence that the experimental protocol produced measurable mechanical and myoelectric manifestations of fatigue but did not provide evidence that ammonia inhalation significantly altered the measured indices of neuromuscular function during fatigued sustained isometric contractions in male varsity athletes. These finding suggest that athletes, coaches, and sport practitioners should not rely on AIs to preserve neuromuscular performance during sustained isometric exercise with performed under fatigue. Instead, performance preparation should prioritize evidence-based strategies for managing fatigue and recovery.
Three-dimensional geometric morphometric analysis of the intermediate cuneiform in anthropoids
(2026) Zachariasz, Jessica; Tocheri, Matthew; Varney, Tamara; Knigge, Ryan; Patel, Biren
The primate foot exhibits substantial morphological variation associated with locomotor behaviour, substrate use, and phylogenetic history. Despite its central role in load transmission, stability, and mobility during locomotion, the intermediate cuneiform remains one of the least studied tarsal bones in comparative morphology. This study uses three-dimensional geometric morphometrics (3DGM) to investigate variation in intermediate cuneiform morphology among anthropoids and assess the extent to which shape variation reflects locomotor behaviour, functional adaptation, and/or phylogenetic relationships. The sample for this study consists of 403 intermediate cuneiforms across various anthropoid species and focuses specifically on the facets that articulate with the navicular and second metatarsal bones and their impact on intermediate cuneiform shape. Digital 3D models derived from previously acquired laser scans of primate intermediate cuneiforms were analyzed using 3DGM of landmark and semi-landmark data. Analyses were conducted using generalized Procrustes analysis (GPA), principal component analysis (PCA), and Procrustes analysis of variance (PERMANOVA). Across all analyses, the first few principal components captured a substantial proportion of total shape variation, with the first three components explaining over half of the total variance. The results demonstrated that intermediate cuneiform morphology largely reflects phylogeny rather than any simple relationship with locomotor behaviour alone. Closely related taxa generally clustered together, whereas more distantly related taxa with similar locomotor behaviours frequently occupied different regions of morphospace. Atelids and colobus monkeys, for instance, clustered at opposite ends of the morphospace, despite both being primarily arboreal quadrupeds. The Procrustes analysis of variance further supports the interpretation that variation in the intermediate cuneiform is structured by phylogeny as well as locomotor behaviour, as it indicated that taxonomy and locomotor behaviour both explain a substantial proportion of total shape variation among anthropoids. Atelids, in particular, have short and stout intermediate cuneiforms that are unlike any other anthropoid in this study. Gorillas (and colobus monkeys to a degree) also have distinctive intermediate cuneiforms that are tall and narrow in shape. In addition to strong separation from other taxa, gorillas exhibit unusually high levels of interspecific and intraspecific variation in intermediate cuneiform morphology, suggesting that this variation is likely caused by lineage-specific evolutionary history. Unexpectedly, modern humans and fossil hominins occupied a relatively central position within the morphospace rather than forming a highly distinct cluster and consistently overlapped or clustered near orangutans despite major differences in locomotor behaviour. Overall, humans and most other anthropoids follow a similar structural framework for intermediate cuneiform morphology, with only minor differences occurring in the shape of this bone between species. These results suggest that the intermediate cuneiform is morphologically constrained, with phylogenetic history acting as the primary driver of variation while locomotor behaviour contributes secondarily.
Digital emotional intelligence
(2026) Maiorova, Yuliia; Hoechsmann, Michael; Kaefer, Tanya
My first child was born almost ten years ago, and even before she was born, I watched my younger brother grow up, beginning in 1998. Even then, I realized how different his childhood was from mine. Being nine years apart, I was closely involved in my younger brother’s upbringing as his older sister, which very much revolved around the stationary computer in our living room. I wouldn’t say that this affected him in a negative way, but his childhood was definitely very different from how I spent my days from the age of six onward. At the same time, he was very active and involved in our street boys’ squad, jumping from garages, climbing poles, and riding his bike across half the city. Building my approach to motherhood upon my previous experience as an older sibling was an exciting journey. I read extensively about children’s psychology, and by 2015, there was already a growing body of international research and statistics on the pioneers of digital childhood. These children were now around my brother’s age, and the findings made me want to be prepared to make a difference in my own children’s lives and to take a more intentional approach to technology in childhood. At the same time, something seemingly unrelated at first glance was happening in my homeland. Crimea, part of Ukrainian territory, was annexed by the Russian Federation, and my entire family had to adjust to living under a different legal system. Travelling became much harder for them as the territorial dispute continued and became increasingly dangerous. For me, travelling to see them increased from 14 hours door-to-door to 36 hours or more, including crossing the border on foot for about a kilometre because transportation from both sides was only allowed up to the border. Because the Crimean Peninsula is connected to the mainland by a very narrow strip of land, this was the only route available. I did this many times, in all seasons, travelling with a stroller, two children, and two suitcases. I physically experienced what it meant to navigate a changing environment without having control over the system. As much as I wanted to blame the circumstances that made it three times harder for my children and me to see our family, I had to find solutions, navigate a new system, protect my values, and find ways to work within its constraints. And I had to do it quickly—children do not stay children for long. I wanted them to inherit and benefit from both cultures they belonged to, as well as from their grandparents’ culture and language. When the time came to make decisions about my children’s media education, I realized that I had been here before. I had to navigate a system that I did not necessarily agree with; however, the process of finding ways to make things work within those conditions was familiar to me. In my personal experience, the first step was always to face the facts: I could not change the circumstances themselves, but I could decide how to navigate them while protecting the values that mattered to me. I began to see the same principle applying to children’s media education. Media culture is already deeply embedded in children’s lives; technology is widely used in schools, and children socialize in environments shaped by digital media and algorithms. We cannot simply wish these realities away, and I did not want my response to be limited to resisting them through measures such as banning social media. Instead, I wanted to understand the environment children are growing up in and explore how parents and educators can navigate it more intentionally. In both situations, I was confronted with a system larger than myself that I did not fully agree with, but that I could not simply ignore. My experience with my family’s circumstances in Crimea did not directly lead me to Digital Literacy, but it shaped the way I approached it. I had already learned that rejecting a system does not make it disappear. Sometimes the more productive response is to understand the system, identify what can be changed, protect what matters, and learn how to navigate what cannot immediately be changed. This approach is reflected in this M.Ed. portfolio made up of three components intended for three distinct (and sometimes overlapping) audiences. Each of the three parts of the portfolio offers a different entry point into the topic. First, is the literature review which is intended for an academic audience of educators. Here, I began the process of developing this portfolio by gathering and examining a representative sample of research from different perspectives that examines digital childhoods and digital literacy. Second, is a website intended for parents and teachers, where I translated some of this complex information into more accessible language while also providing a collection of resources for further exploration. I intentionally included different types of sources - research papers, books, and videos - because I recognize that people approach information from different educational backgrounds, experiences, and learning preferences. Rather than presenting one definitive approach to the issues, I wanted to create a starting point that would allow parents and educators to explore the problems at hand at different levels of depth, develop their own understanding, and make more informed decisions about children and technology. The third component is a fictional children’s book called How My Grandmother Fell Under Surveillance that uses the story telling format to raise awareness through some cautionary and possibly humorous points. I chose to focus the narrative particularly on algorithms because they are one of the most difficult aspects of children’s digital experiences to explain to kids and the adults in their lives. Focusing on the basics of how algorithms work and what are their impacts, I tried to make the underlying concepts understandable through a story. Grandma’s Story was produced using scrollytelling software and for ease of access I have embedded it in the Web site, but it is intended as a distinct unit of this portfolio. The portfolio is the product of a learning journey for me, not only involving some research and reflection, but also the development of new digital skills which were essential to produce a Web site and a scrollytelling essay. Ultimately, this portfolio reflects who I am, the experiences that brought these issues to my attention, and the questions I believe are important for children, parents, and educators to consider.
Investigating childhood health in the Central Zagros Mountains during the Chalcolithic: a visual assessment of subadult human remains from Seh Gabi
(2026) Woodley, Claire; Varney, Tamara; Merrett, Deborah; Kaiser, Tim; Waters-Rist, Andrea
This thesis explores the relationship between subsistence strategies in a marginal environment and how it can impact human health. It includes a comparison of all the types of metabolic bone disease (MBD) and their associated lesions and how this informs different possible diagnoses. The residents of the Chalcolithic site of Seh Gabi, Iran (about 6850 to 5100 cal BP) lived in a marginal environment which, when coupled with the intensification of agricultural practices and the use of animal husbandry, could have left the population susceptible to the type of stressors associated with both vitamin C (VCD) and D deficiencies (VDD). This thesis was designed to determine whether the subadult population at Seh Gabi, represented by 32 individuals, experienced VCD and VDD throughout its period of occupancy. The radiographs and excavated skeletal remains of these individuals were macroscopically assessed for any morphology beyond the range of normal. Probable and possible diagnoses of VCD and VDD were made based on the number of diagnostic and suggestive lesions that individuals demonstrated. Probable VCD was evident in 10.7% of the subadult population; all these probable scurvy cases occurred in individuals less than six months old. While there were no probable cases of VDD, two individuals had a possible comorbid case of rickets and scurvy but there was insufficient skeletal evidence to make a probable diagnosis. Extrapolations of maternal health were made based on these subadult health findings given that those under the age of six months were still likely being breastfed. The environmental context and subsistence strategy used by this population, along with these diagnoses, suggest that vitamin C deficiency was likely experienced by this population.