Innovative Projects Realized

Estimating Optimal Treatment Regimes from Electronic Health Records using Natural Language Processing for Unmeasured Confounding

n precision medicine, optimal dynamic treatment regimes (DTR) are a sequence of decision rules that individualize medical treatments. DTR estimation methods use observational data, such as electronic health records (EHR), which may lack variables that capture doctors’ rationale behind treatment assignment. However, while such variables, also referred as confounders, may not be directly recorded in EHRs, they may be embedded in unstructured medical notes. In this project, our project introduces Relational-variational Graph Autoencoders (R-VGAEs) in precision medicine via DTR estimation. R-VGAEs are particularly well-equipped at identifying latent features within graph-structured data, such as medical notes. We aim to compare our proposed method to DTR estimation via conventional unsupervised natural language processing methods, such as word2vec, doc2vec and ELMo, to showcase its performance. We also apply it on data from MIMIC-IV, a publicly available dataset, to show that the additional use of medical note data can further improve treatment personalization.

Determination of the Mechanical Properties ofWheat Straw for Equipment Design

Harvesting wheat grains require that the plant be cut from the stem and threshed. When the stem (straw) of the wheat bend due to pest and other factors, losses are incurred during harvesting. To minimize losses, breeders have developed pest-resistant wheat (solid stemmed) as compared to the hollow stemmed. The solid stemmed varieties may lead to higher straw strength and energy requirement which consequently will result in higher harvesting cost. Also, farmers are faced with the challenge of increased cost of transporting the straw outside the farm due to their high volume. Further compression of the straw can reduced this cost. The research project sets to investigate the mechanical properties of wheat straw varieties (solid and hollow stemmed) at various moisture and stem height for similarities and differences to help the sponsor (CNH) develop new equipment or improve existing equipment that can harvest agricultural residues and meet farmer’s demand.

Développement d’un inhibiteur de microtubules résistant aux pompes glycoprotéines P, ciblant la poche des maytansinoïdes

Le projet consiste en le développement de nouveaux médicaments pouvant traiter le cancer. La méthodologie utilisée sera par l’inhibition de microtubules, une structure essentielle aux cellules cancéreuses, ce qui mènera
alors à la mort de ces dernières. Ces composés devront être résistant au mécanisme de défenses des cellules cancéreuses, soit les pompes PgP. Ces pompes permettent l’excrétion de molécules toxiques pour la cellule
diminuant ainsi l’accumulation intracellulaire du médicament. Donc un composé étant résistant à ce mécanisme améliorerait grandement son efficacité à tuer les cellules cancéreuses et diminuerait également les effets
secondaires systémiques puisque l’excrétion de molécules toxiques augmente les chances que les cellules saines soient affectées par le médicament toxique. Par la suite, afin de livrer le médicament préférentiellement aux
cellules cancéreuses, ce nouvel inhibiteur des microtubules sera alors transformés en complexe anticorps-médicament permettant alors de cibler exclusivement les cellules cancéreuses améliorant alors l’efficacité des
chimiothérapies offertes pour le traitement du cancer et diminuant les effets non-désirés de la chimiothérapie, les effets secondaires. Ce projet permettra aux partenaires de développer leur propre conjugué anticorps-médicament
dont chaque composante sera propriété du partenaire soit l’anticorps, la petite molécule médicamenteuse, le ‘linker’ et la technique de conjugaison.

Comparison of chemical reactions between cyclone and filter for collection of PM2.5

The project focuses on studying the physicochemical characteristics of cyclone-collected PM2.5 in urban environments. Utilizing advanced techniques like Energy-dispersive X-ray fluorescence (EDXRF) and X-ray absorption fine structure spectroscopy (XAFS), the research aims to provide insights into the composition of fine particulate matter, including metals with varying toxicities such as chromium. The innovative methodology involves cyclonic separation for PM2.5 collection, eliminating traditional filters and minimizing contamination. The project includes a comprehensive multi-day sampling survey, offering an opportunity to collect original data specific to Canadian urban areas. Collaborating with international partners, particularly Dr. Okuda’s team, enriches the project with a global perspective. Through this initiative, the research team anticipates advancing air quality assessment, addressing health risks, and contributing to innovative methodologies in atmospheric science research. The hands-on experience and mentorship provided are expected to catalyze the intern’s growth into an independent researcher.

Super-resolution microscopy of caveolin-1 dynamics in response to mechanical stress: caveolae, scaffolds and cell signaling

Caveolin-1 (CAV1) is a protein on the plasma membrane that forms cup-shaped structures caveolae, which flatten to protect cells under mechanical stress. However, the relationship between the caveolae and other CAV1 structures, scaffolds and dolines, in the process of caveolae formation and flattening is unclear. A challenge is to differentiate caveolae from scaffolds using conventional imaging methods because of their small size. AI-based network analysis of super-resolution microscopy provides a solution to this problem with its ability to determine nanoscale details. Therefore, we aim to determine how mechanical stress impacts CAV1 structures and their interaction with other proteins present in caveolae using super-resolution microscopy. Our results will help understand how CAV1 structures contribute to stress response of cells and how caveolae form. This collaboration project will enable sharing of complementary expertise on super-resolution network analysis from the Nabi Lab at UBC with the expertise of the Lamaze lab at the Institut Curie to further explore the role of caveolae fragmentation to scaffolds in response to mechanical stress.

Exploring water-light interactions and protein dynamics during simultaneous environmental perturbations using near-infrared spectroscopy and aquaphotomics

This project will explore the interactions between water’s molecular structure and light, and use this knowledge to study the behaviour of proteins within the water sample. The intern will collect data using near-infrared spectroscopy (NIRS), which can provide insight into what a sample contains based on how different materials absorb light. Samples with a high water content are difficult to study with standard NIRS techniques, so the intern will use aquaphotomics, which connects spectroscopy data with specialized processing and analysis methods to obtain more detailed information.
Using NIRS and aquaphotomics, the intern will study the influence of changing environmental conditions (including dissolving additional substances in water and changing temperature, sound, humidity, and lighting) and the ways these changing conditions interact with each other on the water-light interaction and the information obtained about protein behaviour.
Aquaphotomics is a recent and rapidly growing research field. This project will support an understanding of water’s behaviour that will inform future aquaphotomics research design and practical applications.

System Design of a Multi-Criteria Decision Analysis (MCDA) Tool for Repurposing Pit Lakes into Aquaculture Operations

With the mining industry striving to become more sustainable, there is a pressing need to re-evaluate typical open pit restoration practices. Many open pit mining operations are naturally inundated after operations, leaving behind an unproductive lake. These sites neglect the environmental, cultural and socio-economic implications for dependent communities. One promising alternative that generates a positive ecological, social and economic change for the community involves the innovative repurposing of these pit lakes into productive aquaculture operations. The benefits could contribute significantly to the social equity, economic vitality and environmental integrity of mining communities.

With input from international experience and system research training in Japan, this research proposal aims to create a tool that helps identify pit lakes in Ontario that may be suitable for this transformation. This tool, called a multi-criteria decision analysis, evaluates and weighs multiple factors, such as hydrology, water quality, and technical and operational aspects to identify key pits of opportunity. By integrating geographic information system techniques, it also considers proximity to markets, climatic conditions, and socio-economic considerations. Each mine is assigned a score based on the aggregated factors, providing stakeholders with a clear metric to identify the best candidates for repurposing. The tool will be applied to existing pit lake datasets in Ontario, offering a strategic blueprint for sustainable development in the region. By making this tool available to public knowledge users, we generate momentum to deal with the thousands of pit lakes and abandoned open pits that exist in the province today.

Refugee Home Share Program

Happipad is a not-for-profit Canadian corporation which leverages technology to facilitate the matchmaking and support of home-sharing between refugees and hosts in Canada. Launching its pilot projects in Metro Vancouver and Toronto, Happipad wants to assess its effectiveness and benefits for refugees and minimize its potential barriers to make it a replicable framework for implementation in other locations in Canada and Worldwide.
This research study aims to help Happipad with these assessments, identify the barriers and challenges faced by homeowners in hosting refugees and propose potential solutions to overcome these obstacles, analyze the limitations and downsides associated with home sharing with refugees, considering factors such as privacy, cultural differences, and potential conflicts and examine factors impact on the well-being and economic stability of both refugees and hosts.

Design and Analysis of Disaster Warning and Evacuation Systems Using the Network Modelling Approach

Canada’s West coast is prone to tsunamis induced from local megathrust earthquakes that can be generated from the Cascadia Subduction Zone (CSZ). The main objective of this research is to study, analyze and simulate the current detection, notification and response systems for an earthquake and resulting tsunami and develop a comprehensive solution using the network modelling approach to mitigate the impact of future disasters. We will use the results and inferences derived from a tornado mitigation analysis to conduct this research. An activity network is developed to represent the information flow from tsunami detection point to the warning communication point. It is simulated using the Simphony software to obtain the overall time consumption. The network is further refined to analyze the system in the presence of some branch failures. A more detailed modelling work is conducted using the emergency and disaster management modelling expertise and simulation software. The outcome results are used to validate the simulation exercise and to develop a more informative way of using the network modelling approach for different disasters.

Safe, Legal… and Inclusive? A Mixed-Methods Study Exploring Trans People’s Experiences Accessing Abortion Care in Canada

Abortion is an essential component of comprehensive healthcare, where lack of access to safe, affordable, timely and respectful abortion is, according to the World Health Organization, a “critical public health and human rights issue.” Trans people are often left out of abortion research, as well as the clinical delivery of abortion care, which focuses on the experiences and needs of cisgender women. A small handful of USA-based research studies have found that trans people experience oftentimes quite profound barriers to accessing affirming abortion care. Little is known, however, about the abortion experiences of trans people in Canada. This project aims to address this gap, using survey, interview and arts-based methods. Results from this project will be used to create a purpose-built tool that abortion providers can use to assess their space and the services offered therein, to ensure that they would be accessible, as well as safe, affordable, timely and respectful to trans people seeking pregnancy termination. This project will be housed in the Centre for Gender and Sexual Health Equity, a research institute whose mission is to advance gender equity in all facets of sexual and reproductive health. Recent research within the centre highlights unmet needs for culturally safe sexual and reproductive health for equity-seeking groups, including sex workers, im/migrants, queer and trans people, and people with HIV. Dr. Lowik’s project will further advance the CGSHE’s work in this area, with a focus on mobilizing research towards policy and practice recommendations, and the delivery of equitable, patient-centred healthcare.

False promises of environmental protection? An historical analysis of the Fisheries Act and ecosystem destruction in the Jordan River Watershed, Vancouver Island, BC

Since the Fisheries Act was enacted in 1868, a year after Confederation, it has been regarded as one of Canada’s oldest and most important environmental laws. Despite the powerful environmental protections provided by the Fisheries Act, various environmental impact studies conducted throughout the Jordan River watershed show high concentrations of copper, hydrocarbon, and wood waste leaching into the river. In 2014, due to high-level of heavy metal contamination, BC’s ministry of environment designated sites along the river as high risk. This ongoing degradation of fish populations and habitat, in the face of the Fisheries Act whose mandate has been to safeguard from this outcome, raises larger important questions about the extent to which current Federal Fisheries laws can achieve these ends. This research examines the ecological disruption operationalized through the Fisheries Act, a principle piece of Canadian environmental legislation.

Machine learning developer interns within cross-functional teams to develop and commercialize AI-powered solutions (16)

AltaML is an innovative company capitalizing on a major technological trend: artificial intelligence (AI) technologies, enabled by big data, are driving a fourth industrial revolution. AI will transform all industries, but traditional industries face challenges in implementing AI. AltaML has a unique business model to overcome barriers to adoption of AI solutions by industry, which is to bring the innovating startup together with the large organization, thereby bringing together rich datasets, AI talent with a playbook for industry application and the close collaboration of subject matter experts and AI experts–with a mindset for change. In addition to AI expertise, we bring agility that our large, corporate partners often lack, and which is so essential for innovation. With a strategic focus on AI adoption and product, AltaML works across industries as well as with the public sector using a co-development approach to create applied AI solutions as well as joint AI ventures. This rich, complex multisectoral environment provides the breadth that enables insights in one area to be applied in new areas, leading to ever increasing opportunities for innovation.

The project comprises internships in a variety of technical and business roles, which are: associate machine learning developer, business development associate, communications associate, finance associate, associate business solutions consultant, and project delivery associate. Outcomes will include algorithm creation and deployment, data visualizations, market research reports, sales collateral, competitive landscape analysis, feasibility analysis; key messages and content writing such as case studies and feature articles, financial model development, data analysis, financial reports and variance analysis, customer workflow mapping, business case reports, resource allocation plans, project update reports, and project plans.