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Recent Submissions

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    Portus: Linking Alloy with SMT-based Finite Model Finding
    (IEEE, 2025-11-25) Dancy, Ryan; Day, Nancy A.; Zila, Owen; Tariq, Khadija; Poremba, Joseph
    Alloy is a well-known, formal, declarative language for modelling systems early in the software development process. Currently, it uses the Kodkod library as a back-end for finite model finding. Kodkod translates the model to a SAT problem; however, this method can often handle only problems of fairly low-size sets and is inherently finite. We present Portus, a method for translating Alloy into an equivalent many-sorted first-order logic problem (MSFOL). Once in MSFOL, the problem can be evaluated by an SMT-based finite model finding method implemented in the Fortress library, creating an alternative back-end for the Alloy Analyzer. Fortress converts the MSFOL finite model finding problem into the logic of uninterpreted functions with equality (EUF), a decidable fragment of first-order logic that is well-supported in many SMT solvers. We compare the performance of Portus with Kodkod on a corpus of 63 Alloy models written by experts. Our method is fully integrated into the Alloy Analyzer.
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    Real-Time Speed of Sound Estimation for Point-of-Care Tissue Health Assessment.
    (University of Waterloo, 2026-02-02) De la Torre Sanchez, Pat
    Speed-of-Sound (SoS) is a fundamental acoustic property that emerging Ultrasound (US) modalities aim to leverage for tissue health assessment and image quality improvement. Tissue SoS has been tied to tumor malignancy classification, muscle health assessment, steatotic liver classification and bone porosity measurement among other. Consequently, leveraging the tissue SoS for more accurate beamforming, not only enables higher resolution imaging, leading to more accurate cyst classification, but also correct for heavy skull aberration and defocusing during High Intensity Focused Ultrasound. Directly measuring the tissue SoS requires multi-site access, thus limiting such methods to the breast and some limbs. Current Pulse-echo SoS estimation algorithms demand high computation time or provide a single global SoS value, either constraining real-time assessment or decreasing accuracy. In this dissertation, I developed: 1) A single-shot SoS estimation algorithm that estimates the global SoS of the media by leveraging the signal consistency across channels from a single transmitting event. 2) Multiple localized SoS estimators that leverage image dissimilarity from multiple transmission events to provide the user with the SoS of the segmented regions in the image, either in stratified media, or arbitrary configurations. By developing custom image formation, segmentation, raytracing and wavefront tracking frameworks, optimal transmission schemes, and GPU acceleration on a portable, research scanner, I’m able to provide robust, accurate, SoS estimation platforms that have been thoroughly validated in vitro, ex vivo and in vivo. This dissertation research aims to bridge the gap between SoS research and other US modalities that can benefit from the SoS information, as well as the gap between the low-level-research side that develops methods for robust US tissue assessment, and the clinical research side that tracks and relates such features to conditions of clinical relevance. With the single-shot algorithm, I provide non-SoS researchers with valuable information to increase the accuracy of their algorithms without the need of long transmitting times or high computational demands, crucial for flow or real time imaging. With the other algorithms, I provide robust avenues for non-invasive tissue health assessment, as well as arming clinicians with access to intrinsic tissue features, that can be used for real time monitoring or for subsequent research that arise from the insights clinicians gain with this novel tool.
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    Psychosocial Outcomes of Youth with Chronic Physical Illness and Siblings
    (University of Waterloo, 2026-02-02) Basque, Dominique
    Youth with chronic physical illness (YwCPI) are more vulnerable to developing psychopathology than their healthy counterparts. Prospective studies show that psychopathology in youth remains stable over time and extends into adulthood. Ongoing symptoms, treatment, and worry about disease progression increase the risk for worsened mental health. Given that health status often impacts physical, mental, and psychosocial health outcomes, health-related quality of life (HRQL) has been a focus in health research. The functional limitations resulting from disability caused by chronic physical illness (CPI) disrupt school participation, peer support, and family relationships, contributing to lower HRQL compared to healthy peers. Existing research on CPI continuity and HRQL is constrained by infrequent assessments and disease-specific approaches, limiting understanding of psychosocial outcomes in YwCPI. CPI in youth also affects siblings. This is consistent with family systems theory, which posits that emotional functioning results from interactions between an individual and their family members, and the family unit and its contextual circumstances. Research finds that CPI negatively impacts sibling mental, physical, and psychosocial health. Siblings of YwCPI are also at higher risk for internalizing and externalizing symptoms compared to controls. However, studies on sibling mental health and HRQL are limited. Few studies use longitudinal methods, limiting the ability to assess the long-term impact of CPI. The aim of this research is to assess psychosocial outcomes in YwCPI and siblings. To address the aforementioned literature gaps, the objectives of this dissertation were to: 1) compare the homotypic and heterotypic continuity of psychopathology in YwCPI and siblings over 48 months, 2) model 48-month trajectories and assess predictors of HRQL in YwCPI and siblings, and 3) assess the mediating effect of sibling psychopathology on the association between YwCPI disability and sibling HRQL. Data come from the Multimorbidity in Children and Youth Across the Life Course Study; data were collected at baseline, 6, 12, 24, and 48 months. Study 1 utilized cross-lagged panel modelling to assess internalizing and externalizing symptom continuity in YwCPI and siblings. Auto-regressive pathways assessed homotypic continuity and cross-lagged pathways assessed heterotypic continuity. Separate models were computed for YwCPI and siblings. The method of variance estimates recovery (MOVER) assessed how patterns of continuity in YwCPI differed from siblings. Significant (p<0.05) autoregressive pathways were detected between all time points for internalizing and externalizing symptoms in YwCPI and siblings. Few cross-lagged paths were significant in either model. The MOVER showed no significant differences in the magnitude of any path estimates between YwCPI and siblings. Study 2 delineated trajectories of change for each domain of HRQL (physical well-being, psychological-being, autonomy and parent relations, peer and social support, school environment) using latent class growth analysis. Models were computed for YwCPI and siblings independently. Backward stepwise regression assessed predictors of trajectory group membership. The number of trajectory groups ranged from two to four, and class size ranged from 5% to 80%. Over half of the models included an increasing, no change, and decreasing group, with most changes occurring at earlier time points. The proportion of siblings having no change in HRQL was greater than YwCPI. Group membership predictors were age, income, and parenting stress. In Study 3, linear mixed-effect models assessed the mediating effect of sibling psychopathology on the association between YwCPI disability and sibling HRQL. YwCPI disability predicted increased sibling psychopathology, which was associated with lower sibling HRQL on all domains. Mediation effects were statistically significant in all models. Given the homotypic continuity of symptoms of psychopathology, health services should promote early and routine mental health screening for YwCPI and siblings. Early changes in YwCPI and sibling HRQL trajectories highlight critical opportunities for family-centred approaches to pediatric care. The mediating effect of sibling psychopathology in the association between YwCPI disability and sibling HRQL underscores the importance of integrating siblings into family-centred care, with targeted mental health screening and interventions that aim to mitigate negative psychosocial outcomes.
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    Navigating the Politics of Food System Futures: Post-Disaster Food Sovereignty in Puerto Rico
    (University of Waterloo, 2026-02-02) Diaz, Ileana
    Puerto Rico has been devastated by protracted economic collapse. Hurricanes Irma and Maria’s landfall in 2017 shattered the archipelago, followed by earthquakes in 2020, the COVID-19 pandemic, and Hurricane Fiona in 2022. There have been chronic issues with recovery post-disasters. In the context of economic, political, and ecological uncertainty, one of the most pressing concerns for Puerto Rico now and in the future will be its food supply. This research explores the effects of sequential disasters on the people of Puerto Rico and their food system. The study investigates food insecurity, government responses, and the will toward food sovereignty. The study is derived from individual in-depth interviews (n=84), archives (legal/court documents), media analysis (newspapers/photographs), and government data. The research adopts a critical and decolonial framework to the study of post-disaster Puerto Rico.
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    Development of Hybrid Non-Enveloped Viral Vectors Using the Bacterial Miniphagemid Platform
    (University of Waterloo, 2026-01-30) Hosseinali, Mehraveh
    Gene therapy holds significant promise for treating various diseases, with Adeno-associated virus (AAV) vectors being among the most widely used delivery systems. However, current standard AAV production methods relying on costly and inefficient mammalian cell culture limit scalability and clinical accessibility. A similar human virus, Torque teno virus (TTV), also holds great potential for gene therapy; however, it also suffers from problems in its production. To address this manufacturing bottleneck, this study aimed to develop a novel, cost-effective platform for hybrid viral vector production entirely within Escherichia coli. This work advances research on the use of miniphagemids, phages that package a minimal vector genome, to achieve in-bacterial assembly of novel hybrid AAV serotype 2 (AAV2)-based and TTV genotype 19 (TTV19)-based vectors. The hypothesis being tested is that the co-production of single stranded DNA using miniphagemid technology and key AAV or TTV proteins in Escherichia coli can result in AAV-based or TTV-based vectors. The key objectives were therefore: 1) showing recombinant expression of heterologous capsid proteins AAV2 VP1/VP2/VP3 and TTV19 ORF1 in E. coli; 2) producing ssDNA minigenomes flanked by either AAV2 inverted terminal repeat (ITR) or TTV19 untranslated terminal repeat (UTR) sequences; and 3) showing that co-producing protein(s) and ssDNA results in AAV2- or TTV19-based vectors. Results confirmed that AAV2 VP2 and VP3 could be produced in E. coli, albeit expressed primarily as insoluble inclusion bodies. Transformation of cells with a plasmid encoding VP1 resulted in reduced growth and no VP1 was recovered. Expression of TTV19 ORF1 in E. coli produced two histidine-tagged protein products approximately half the size of the expected protein (as previously reported). The ssDNA minigenomes were successfully produced and purified, exhibiting high purity (Objective 2). The central finding was the successful in-bacterial production and purification of functional hybrid vectors, termed AAV-based and TTV-based (Objective 3). Iodixanol gradient ultracentrifugation confirmed particle assembly and density separation. Subsequent qPCR quantification demonstrated high genomic titers in the purified fractions, providing strong evidence of successful ssDNA encapsulation by the heterologous capsids within the E. coli host. The study further found that the TTV19 UTRs likely enhance packaging efficiency in the TTV-based hybrid vector system. In conclusion, this research establishes a robust and scalable E. coli-based platform for producing non-enveloped hybrid viral vectors. This achievement represents a significant step toward revolutionizing gene therapy vector manufacturing, offering a pathway to highly purified, consistent, and affordable therapeutic vectors.