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Open Access
Reconstruction of ancestral non-coding RNA sequences using sequential and structural information with tree decomposition
(2024-12-31) Hu, Songdi; Durocher, Stephane (Computer Science); Turgeon, Maxime (Statistics); Tremblay-Savard, Olivier
Ancestral sequence reconstruction aims to infer what was the content of certain biological sequences of interest for ancestral species that do not exist anymore. This is accomplished by comparing and extracting similarities and differences from the sequences in extant (i.e. living) species. Since the search space is quite large, a lot of research has been devoted to the design of efficient and accurate methods to solve different variations of this problem. However, ancestral sequence reconstruction becomes even more complex when the goal is to reconstruct the ancestors of sequences that are not well conserved in extant species. This is the case with non-coding RNA (ncRNA) sequences, for which the structure (formed by base pairing) is more conserved than the actual sequences. One recent approach to tackle the ancestral reconstruction of ncRNA sequences involved considering the sequences of two related ncRNA families simultaneously. Although this helped avoid biases in the reconstruction, some cost calculations had to be simplified for efficiency. In this thesis, the goal was to improve the cost calculation of that approach by using a more advanced structural model and tree decomposition to partition the cost calculation into subproblems. Our results demonstrate an important gain in accuracy and a significant reduction in the number of optimal sequences inferred.
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Open Access
Elucidating factors that influence infection success and the behaviour of gastropod hosts of Echinostoma trivolvis lineage c
(2025-01-03) Hodinka, Cameron; Van Nest, Byron (Biological Sciences); Wyeth, Russell (St. Francis Xavier University); Detwiler, Jillian
Wildlife trematodes are important to study due to their impact on wildlife populations, including the ability to modify the behaviour of their hosts. However, these parasites are challenging to study without a fully elucidated life cycle that can be completed in a laboratory. As such, a model for wildlife trematodes would be a great asset for learning about the ecology and behavioural manipulation found in this group. I chose Echinostoma trivolvis lineage c as a parasite model to study these topics in gastropod hosts. Chapter 1 determined how host species/morphotype, host size and miracidial dose affects infection success of gastropod first intermediate hosts. I confirmed reports from natural infections that Ladislavella elodes is a host along with it’s morphotype Stagnicola reflexa and further determined which size and exposure dose produced the highest infection success. I used this new information to obtain infected hosts for my second chapter of my thesis. Herein, I tested whether light and species influenced the navigational behaviour of potential second intermediates host L. elodes. I determined that snail velocity increased when exposed to a higher light level. Using these higher light conditions, I also found that there was no attraction to infected conspecific hosts by potential second intermediate hosts. Both experiments suggest that abiotic and biotic factors can alter snail navigational behaviour and may even influence whether host behavioural modification is observed. As such, laboratory-based studies of behavioural modification may be over or underestimating the strength and frequency of the behaviours that may be occurring in nature. Examples of naturally occurring behavioural modification may be missed entirely if not tested under the right context in the laboratory.
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Open Access
Public attributions and attitudes toward the not criminally responsible accused in Canada
(2024-12-16) Vallotton, Jamie; Evans, Nicholas (Psychology); Demetrioff, Sabrina (Clinical Health Psychology); Nijdam-Jones, Alicia
Research has found that the public holds negative attitudes towards the NCRMD defence and views individuals using it as dangerous and avoiding punishment (Goossens et al., 2021). Within these attitudes, people appear to attribute behavioural control and stability or consistency across time towards NCRMD adjudicated. Thus, it was hypothesized that these attributions could influence punishment goals and NCRMD attitudes. This study examined public attitudes towards NCRMD-accused using a 2x2 factorial design vignette manipulating two offender characteristics: the amount of control the offender had over their behaviour (high or low) and the stability of their behaviour (high or low). Undergraduate psychology students completed an online survey using the vignette and instruments to assess causal attributions, punishment goals, and NCRMD attitudes. Participant responses were analyzed using qualitative (N = 156) and quantitative (N = 544) analysis. The results did not support attributions affecting punishment preference and NCRMD attitudes. Constructed themes from reflexive thematic analysis included the role of medication in predicting behaviour, interpreting stability as emotionally stable, and perceptions of mental illness and criminality. The results from this study suggest that people do not consider the legal criteria for NCRMD in their attributions of control and that control is changeable in an NCRMD context. Additionally, financial barriers to medication can mitigate public perceptions of control. Finally, attributions of stability may function differently within an NCRMD context than in a carceral context.
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Open Access
Investigating markers of Alzheimer’s disease in posttraumatic stress disorder using machine learning and magnetic resonance imaging
(2024-12-19) Yakemow, Gabriella; Hryniuk, Alexa (Human Anatomy and Cell Science); Bolton, Shay-Lee (Psychiatry); Ko, Ji Hyun
Introduction: Posttraumatic stress disorder (PTSD) is a mental health disorder caused by experiencing or witnessing traumatic events. Recent studies show that patients with PTSD have an increased risk of developing dementia, including Alzheimer’s disease (AD), but there is currently no way to predict which patients will go on to develop AD. The objective of this study was to identify structural and functional neural changes in patients with PTSD that may contribute to the future development of AD. Methods: Neuroimaging (pseudo-continuous arterial spin labelling [pCASL] and structural magnetic resonance imaging [MRI]) and behavioral data for the current study (n = 67) were taken from our non-randomized, open label clinical trial (ClinicalTrials.gov Identifier: NCT03229915) for treatment-seeking individuals with PTSD (n = 40) and age-matched healthy controls (HC; n = 27). Only the baseline measures were utilized for this study. Mean cerebral blood flow (CBF) and grey matter (GM) volume were compared between groups. Additionally, we utilized two previously established machine learning-based algorithms, one representing AD-like brain activity (Machine learning-based AD Designation [MAD]) and the other focused on AD-like brain structural changes (AD-like Brain Structure [ABS]). MAD scores were calculated from pCASL data and ABS scores were calculated from structural T1-MRI images. Correlations between neuroimaging data (regional CBF, GM volume, MAD scores, ABS scores) and PTSD symptom severity scores measured by the clinician-administered PTSD scale for DSM-5 (CAPS-5) were assessed. Results: Decreased CBF was observed in two brain regions (left caudate/striatum and left inferior parietal lobule/middle temporal lobe) in the PTSD group, compared to the HC group. Decreased GM volume was also observed in the PTSD group in the right temporal lobe (parahippocampal gyrus, middle temporal lobe), compared to the HC group. GM volume within the right temporal lobe cluster negatively correlated with CAPS-5 scores and MAD scores in the PTSD group.Conclusion: Results suggest that patients with PTSD with reduced GM volume in the right temporal regions (parahippocampal gyrus) experienced greater symptom severity and showed more AD-like brain activity. These results show potential for early identification of those who may be at an increased risk for future development of AD.
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Open Access
Human-wetland relations in an agricultural landscape: Ojibway and non-Indigenous perspectives from the Swan Lake region, Manitoba
(2024-12-03) Wiebe, Leanna; Vanrobaeys, Jason (Health Canada); Oakes, Jill (Environment & Geography); Scott, David (Swan Lake First Nation); McLachlan, Stephane (Environment & Geography); Baydack, Rick
Wetlands in the Swan Lake region were historically seen as highly valuable parts of the landscape by Ojibway Peoples and early non-Indigenous settlers alike, providing vital food and water on an arid prairie. Contrastingly, wetlands today are often seen as a nuisance, incentivizing their ongoing drainage. As a result, Swan Lake, like other prairie lakes, faces cumulative impacts from wetland drainage including an accumulation of sediment, lowering lake depth, damaged wildlife habitat, as well as increased nutrient loads causing algae blooms and deoxygenation. In short, the introduction of colonial land management and governance systems has transformed the relationship between humans and wetlands from a mutually beneficial to a dysfunctional one. This thesis examines the transformation described above by looking at the influence of historical and individual decision contexts experienced by Ojibway and non-Indigenous land users today in the Swan Lake region. In this thesis, wetlands become a prism refracting a much bigger context, one where dysfunctional relationships between humans and wetlands are part of a polycrisis affecting all earth systems. A gatekeeper sampling method and semi-structured interviews with six Ojibway participants from Swan Lake First Nation, Gaubiskiigamaug, and six non-Indigenous farmers from the surrounding region were used. Data were analyzed using thematic and grounded approaches. Results emerge in five themes: 1) Historical contexts shaping today’s wetland-related decision-making, including colonization and changes in the agricultural industry; 2) Tensions between Ojibway and non-Indigenous worldviews related to wetlands; 3) The influence of individual decision contexts including differences in land use on wetland-related decision-making; 4) Land user perspectives on the future of human-wetland relationships; and 5) The dynamic nature of human-wetland relationships in shaping the landscape itself. This thesis concludes that enduring solutions to today’s wetland crisis can only occur at pace with healing relationships between people and land.
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Open Access
Tracing an autoethnography to identify opportunities and challenges of implementing backyard biodiversity installations in Winnipeg’s residential spaces
(2025-01-14) Dowie, William; Thompson, Shirley (Natural Resources Institute); Cicek, Nazim (Biosystems Engineering); McCance, Erin (Fisheries and Oceans Canada); Sinclair, John; Baydack, Rick
An autoethnography of a twenty-five-year adult learning journey (formal, non-formal, and informal approaches) is used to trace the processes and dynamics of installing native plants in the City of Winnipeg, Canada. Merging these educational experiences with activities of a homeowner, a horticulture-sector professional, and a researcher gives unique insights and perspectives into adding appropriate biodiversity to the private residential space. Native plants are an important part of the regional ecosystem as these organisms have co-evolved with other organisms for thousands (and even millions) of years. This helps form the basis of the food web creating a stable and resilient life-giving ecology. Further, native plants provide important ecosystem services such as pollination, food provisions, flood protection, control of pollution, heat regulation, carbon sequestration, and healthy soil. Unfortunately, due to various factors including habitat loss due to urbanization, there is a crisis of biodiversity loss (coupled with climate change). Therefore, this thesis reveals the importance of establishing native plants of all forms in the urban realm. Such plantings are an opportunity for city residents to contribute to the restoration of the local ecosystem by supporting the flora and fauna of the corresponding ecodistrict, ecoregion, and ecozone. Since design with, and installation of, native plants in the residential backyard is not a widespread practice, the purpose of this thesis is to understand why the planting of native species is not ubiquitous in urban areas. Management models, archival videos, and professional design-build research reflections are part of the analysis that helps sort out the complexity of residential ecosystem. When keystone woody native plants or modified nativars (trees) are used in purposeful installations, they would benefit a future-forward City of Winnipeg – especially when shifting climate and extreme weather will be prominent. Generally, trees that are suited for the urban forest that can support Lepidoptera larva can also simultaneously contribute to adaptation and mitigation of climate change – one yard at a time.
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Open Access
Disaster capitalism, settler colonialism, and Indigenous environmental justice in the COVID-19 pandemic
(2025-01-02) Curran, Alexandra; Miller, Cary (Indigenous Studies); Erickson, Bruce (Environment & Geography); Neckoway, Nathan (Tataskweyak Cree Nation); McLachlan, Stéphane
While the COVID-19 pandemic was experienced and borne by everyone, the weight of everyone’s burden was not equal; As they have in the past, Indigenous peoples experienced disproportionate impacts during the crisis. This may be largely connected to the ongoing presence of settler colonial ideologies and structures which, among other issues, resulted in a patronizing disregard for Indigenous pandemic decision-making. In conjunction, disaster capitalism ensued throughout the pandemic, a practice defined by Naomi Klein as the exploitation of crises by the powerful to further their own agendas, which worked to further compound and hinder Indigenous efforts to ensure community safety and well-being. However, First Nations nonetheless asserted their self-determination, challenging harmful decision-making and prioritizing community well-being. This project utilizes two cases (Case Study 1: Keeyask Lockdown, Manitoba and Case Study 2: Ring of Fire, Ontario) to examine how the pervasive ideologies of settler colonialism interacted and influenced disaster capitalism during the pandemic, as well as how Indigenous Environmental Justice (IEJ) was then enacted by communities. An analysis of these cases demonstrate that, while disaster capitalism and IEJ were prevalent during COVID-19, the specific circumstances were nonetheless shaped by distinct, place-based histories and relationships among settlers and Indigenous peoples. Moreover, this project explores the narratives surrounding these cases, including how they were presented to the public by various Mainstream, Alternative/Advocacy and Indigenous news outlets by utilizing a media analysis. This analysis notably observed the considerable inclusion of settler narratives/biases by Mainstream sources, while Alternative/Advocacy, and Indigenous sources specifically, highlighted Indigenous voices/experiences and the context of sovereignty. Lastly, the inclusion of a community experience chapter highlights place-based Indigenous experiences and ways of knowing regarding the Keeyask case study; Demonstrating the complexity of Indigenous relationships with industry and settler government, these experiences moreover spoke to a dedication to continue to take action, heal and move forward in a good way. By exploring these subjects of settler colonialism, disaster capitalism and IEJ through various lens’ and by utilizing a two-eyed seeing approach, this project demonstrates the value of employing multiple perspectives and storytelling when striving to formulate contextualized, respectful and meaningful research.
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Open Access
The impact of COVID-19 on the roles and responsibilities of respiratory therapists in primary care in Ontario, Canada
(2025-01-15) Biesheuvel, Sandra; Hatala, Andrew (Community Health Sciences); Camp, Pat (University of British Columbia); Chartrand, Louise
Background/Introduction: The COVID-19 pandemic impacted health care providers as their roles changed in providing care for patients with chronic respiratory disease. The impact of the pandemic was significant in Ontario, Canada, where the already strained health care system responded by reducing in-person primary care visits and replacing them with virtual visits. Some respiratory therapists working in primary care pivoted to the provision of virtual care, while others were redeployed to acute care to manage the patient surge. Few articles explore the roles and responsibilities of respiratory therapists working in primary care. Purpose: The purpose of this qualitative case study is to describe the impact of the COVID-19 pandemic on the roles and responsibilities of respiratory therapists working in primary care in Ontario, Canada. The research objectives are to define the roles and responsibilities of respiratory therapists working in primary care, explore the extent of role ambiguity, and describe how COVID-19 has impacted their practice. Methods: Using case study methodology, virtual semi-structured interviews were conducted with four respiratory therapists working in primary care in Ontario. Data was analyzed using Stake’s method of case study analysis. Results: Respiratory therapists are a well-respected member of the interprofessional health care team, they appreciate the autonomy of their roles in primary care, and these roles were adapted during the pandemic to continue providing care to patients with chronic respiratory disease. The challenges posed by the pandemic resulted in some primary care clinics moving to virtual care, while other clinics suspended services at the peak of the pandemic. Public fear of contracting the COVID-19 virus prompted some patients to discontinue care with their primary care team, and respiratory therapists felt devalued and disconnected from their patients. Discussion: The COVID-19 pandemic highlighted the strengths and vulnerabilities within the primary care setting and identified that there is a need for more respiratory therapists working in primary care to utilize their skill set in managing patients with chronic respiratory disease. Pivoting the role of the respiratory therapists to provide virtual care provides insight into how to prepare for future pandemics and minimize the disruption of care. Conclusion: Future research into the roles and responsibilities of respiratory therapists working in primary care could demonstrate the need for these health care professionals in reducing the burden of chronic respiratory disease on the health care system and increase patient outcomes.
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Open Access
Extraction of phenolic compounds from wheat by developing a rapid and reliable microwave-assisted method
(2025-01-15) Kirusnaruban, Kemashalini; Eskin, Michael (Food and Human Nutritional Sciences); Netticadan, Thomas (Physiology and Pathophysiology); Rosell, Cristina
Phenolic compounds (PC) are vital secondary plant metabolites with recognized health benefits, including antioxidant and anti-inflammatory properties. These compounds help plants manage environmental stress and contribute to their resilience, with a higher concentration found in the outer layers of wheat, particularly in the bran. Current extraction methods are time-consuming and often involve the use of acids, alkalis, and organic solvents, which pose environmental concerns. Therefore, efficient, green, and rapid methods for extracting these phenolic compounds are essential, especially in the food industry, which has an increasing demand for sustainable processes. We hypothesize that Microwave-Assisted Extraction (MAE) will serve as a superior methodology for phenolic compound extraction from wheat, offering improved yield, faster processing, and enhanced environmental sustainability compared to conventional extraction (CE). This study aims to validate MAE as a green and efficient alternative to CE for quantifying phenolic compounds in Canada Western Red Spring wheat kernels, utilizing whole grains and flour. Additionally, MAE was applied to wheat kernels with varying degrees of pearling to assess its effectiveness across different wheat layers. Two solvent systems were tested: 80% ethanol (v/v) and water, with MAE conditions including temperatures between 140°C and 180°C and extraction times of 5, 10, and 15 minutes. A solid-to-liquid ratio of 1:9 was used for whole kernels, and 1:99 for flour fractions, to prevent starch gelatinization. Results showed that MAE outperformed CE in terms of TPC yield, with water as a solvent leading the highest TPC of 5.41 ± 0.10 mg/g DW (p < 0.05) at 170°C for 10 minutes, compared to 80% ethanol extracts at 3.52 ± 0.24 mg/g DW (p < 0.05). CE yielded the lowest TPC at 2.78 ± 0.18 mg/g DW (p < 0.05). Among individual phenolic acids, gallic acid was found to be the most prominent in all MAE extracts. Additionally, phenolic acid extraction was evaluated in six pearled fractions of wheat subjected to different pearling time, ranging from 50 to 450 seconds. Shorter pearling times resulted in higher phenolic acid concentration. Also, TPC values were found to be higher in the outer bran layers, supporting the conclusion that PCs are more concentrated in these parts of the wheat grain. A significant negative correlation was observed between pearling time and phenolic acid content, emphasizing the importance of optimizing pearling times for enhanced phenolic yields. It must be stressed that for the first time, a method for extracting phenolic acids is proposed using water as a solvent and extracting the compounds directly from the wheat kernel. This study highlights the efficiency and sustainability of MAE for phenolic extraction, offering a faster, greener alternative to traditional methods. The findings provide insights into enhancing the phenolic content of wheat-based products, with implications for functional food development and wheat breeding.
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Open Access
For God, King, and the soul of Canada: Christianity, First World War remembrance culture, and early Canadian nationalism
(2024-12-31) Bass, Jennifer; Valenti, Jean (Université de Saint-Boniface); Noël, Patrick (Université de Saint-Boniface); Morris, Paul
The depth to which Christianity influenced Canadian culture and war mobilization has been insufficiently considered. The Churches have long been understood to have played a supporting role in Canada’s First World War, but where major studies have looked at Britain and Germany’s participation in terms of ‘holy war,’ Canada has generally been considered only for its place in the British Empire and not for its own religious motivations. Similarly, the start of Canadian nationalism is often deemed a result of the First World War. This study challenges these ideas by looking at the place the Churches and religion played in Canadian culture at the time, exploring in depth the huge influence religion had in Canadian society and through their support of the war and the significant impact they had on Canada’s participation and national sentiments. It explores how the Churches’ concern for the “soul of Canada,” a term used which appeared even before the war to describe Canada’s character and identity, drove the Churches’ active involvement in, and their understanding of, events. Because of their desire to keep Canada Christian and British, goals they thought could be achieve through the war, they whole-heartedly embraced the First World War. The Churches’ motivations and the results of their support, from the ways they justified participation in the war to the effects they had on the Canadian population, ensured that a Christian interpretation of the war and the deaths of soldiers became the dominant cultural interpretation of the war. The Churches’ long-standing desire to shape “Canada’s soul,” combined with Canadians' desire for meaning in the First World War, led to increased nationalistic sentiments. This impacted the development of a robust “remembrance culture” in Canada, one that favoured religious and national interpretation of the war and continues to influence Canadian symbols and ceremonies. Combining the results of Christian cultural influence, religious justification and memorialisation of the war, and the Churches’ concern for the “soul of Canada,” this study shows the strong Christian culture influence and the religious-based development of remembrance culture and early Canadian nationalism.