Nadia Al Hashemi
Consultant: Dr. Sarah Symons
Metacognition in the Integrated Science Program
The McMaster Integrated Science program, from its inception in 2009, has been continuously evaluated through research with the goal of improving multiple aspects of the program. Through teaching and learning strategies within projects, students are expected to build on the concepts learned as they progress through the program. However, this hypothetical development of strategies over time within the Integrated Science program has not been directly measured. In this study, a 55-question survey is used to record the perceived awareness in learning, or metacognition, of students of all levels in the Integrated Science program. The survey gives individual scores upon completion of the survey in two aspects of learning: Knowledge About Cognition and Regulation of Cognition. We expect that there will be an overall increase from levels 1-4 when comparing scores in Regulation of Cognition. We find that while there are no significant results, there appears to be a noticeable drop in average scores from the first to second year students followed by an increase in score from the second year onwards. This trend in average scores resembles the Dunning-Kruger effect, in which those with less experience overestimate their abilities, while those with more experience can more accurately discern their abilities. These apparent trends open a new avenue for research for the Integrated Science program, to reassess if there is a significant drop between first and second year of Integrated Science, and if anything could be done to minimize this drop.
Consultant: Dr. Boyang Zhang
Modelling the Barrier and Transport Function of the Syncytiotrophoblast at the Placental-Fetal Interface using the Synoplate™ Platform
The exclusion of pregnant women from clinical trials creates a glaring gap in evidence when trying to determine a drug’s risk-benefit profile and dosage during pregnancy. The placenta plays an essential role in regulating the exchange of endogenous and exogenous materials between mother and fetus. The barrier between the fetal circulation and maternal blood consists of the fetal capillary endothelium and the syncytiotrophoblast. Both organoid technology and organ-on-a-chip microfluidic devices have been used to model the placental barrier in vitro; However, both approaches have limitations. Organoids lack perfusion and vascularization and micro-fluidic devices poorly recreate higher-order structures. Here we present a 3D model that mimics the architecture of the maternal-fetal interface using the SynoPlateTM platform in a 384-well plate format, which can be used for in vitro functional studies. Combining the principles of both approaches we use a unique fabrication technique we termed 4D (3D + time) subtractive manufacturing to create a model that generates 3D tissue structures and that can be perfused. The model achieves intricate vascular-tubular complexes and organ-specific vasculature, and is compatible with dynamic flow conditions. The complex biological features and functionality of this platform enable users to model and investigate higher-level organ structures and their development, thus overcoming the trade-offs of existing placenta models. This project and subsequent studies can help to prevent the disruption of treatment for Canadian women with chronic illnesses as well as acute conditions that necessitate medication without compromising the fetus’ safe and healthy development.
Consultant: Tara Rosewall
Cannabis Use by Cancer Patients: A Thematic Analysis of Patient-Initiated Cancer Blog Posts
Studies regarding the connections between cancer patients and their use of cannabis for pain and symptom management are missing from the current qualitative literature, with an evident clinical need for more information. This study aimed to gain a better understanding of cancer patients’ knowledge, views and questions regarding the use of cannabis as symptom and side effect management. More specifically, the following research questions were addressed: 1) What questions are patients posing about the use of cannabis? 2) What are the benefits/harms expressed by the patients? 3) Are patients sharing information about cannabis use with their health care team?
The use of cancer patient blogs and social media platforms has allowed researchers to collect and analyze qualitative data on patient’s perspectives throughout their cancer journey. In this study, a thematic analysis of cancer patient blog posts pertaining to cannabis use was conducted. The inclusion criteria for blogs required at least one of the individual’s entries to be focused specifically on the cancer experience and the use of any form of cannabis product. To further aid in the understanding of patient demographics using cannabis, it was essential that the blog author indicated their type of cancer, their age, and at what point during their cancer journey cannabis was used. The thematic analysis consisted of three read-throughs of the posts and quote collection in order to compile all the ideas into main themes, ensuring the proposed research questions were answered.
Consultant: Dr. Roxana Vlad
A biomechanical based model to assess vaginal cuff, bladder and rectum motion over the course of radiotherapy for endometrial cancer
A biomechanical model of the female pelvis was built using finite element analysis (FEA) methods to study the interactions between changing rectal and bladder fillings on the internal target motion of the vaginal cuff over the course of radiotherapy treatment in endometrial cancer patients.
Radiation therapy (RT) is a well-established cancer treatment method used to treat the vaginal cuff in endometrial cancer patients at high risk of disease recurrence. A RT treatment plan (RT-TP) is designed to specify the optimal radiation dose to deliver over a set number of days to the target anatomy (vaginal cuff), while minimizing the dose to healthy organs at risk (bladder, rectum). It is known that the vaginal cuff moves over the course of treatment, relative to the RT-TP, in response to changing bladder and rectal fillings. This motion must be quantified to precisely deliver radiation, however, it is difficult to predict; to date it is estimated using clinical experiments and judgement that can be inaccurate. We have built a biomechanical model in the FEA software, HyperMesh, to determine the motion of the vaginal cuff. Using segmented data (bladder, rectum and vaginal cuff) from the planning computed tomography (CT) image and daily treatment cone beam CT images (which reflect daily patient treatment position) a linear elastic biomechanical model was used to assess vaginal cuff motion. The model discusses meshing techniques, assignment of material properties, determination of boundary conditions and applied forces as well as contact constraints to best model anatomical interactions and resulting motion margins.
Consultant: Dr. Patrick Speissegger
Quantum Computing to Improve Machine Learning
Quantum computing (QC) offers potential solutions to problems that modern conventional supercomputers cannot feasibly handle, with one application area being machine learning (ML). The primary goal of this project is to gain insight on how QC could potentially be used to improve ML. This will be done by studying this application through the lens of creating artificial intelligence (AI) programs which play games, such as AlphaGo or OpenAI Five. The paper begins by reviewing classical computing and conventional AI algorithms such as the minimax algorithm, alpha-beta pruning, reinforcement learning, and neural networks. This is followed by an overview of QC and its applications, ending by reviewing and discussing current research on this area of the intersection of QC and ML processes. The main findings were that although most of what is currently known on the subject area is highly speculative, considering the current limitations of quantum hardware, a hybrid quantum-classical framework for neural networks is considered as one of the most promising applications for the subject area. It is also concluded that the development of modern interest in quantum neural networks makes sense when considered from a temporal progression standpoint. It is concluded that, just as the progression of AI as a field has evolved in stride with the capabilities of conventional computing hardware, so too will quantum software develop as quantum computers improve. At the current point in time, the field of QC and ML is still in an exploratory phase.
Cong, I., Choi, S. and Lukin, M.D., 2019. Quantum Convolutional Neural Networks. Nature Physics, 15(12), pp.1273–1278.
Farhi, E. and Neven, H., 2018. Classification with Quantum Neural Networks on Near Term Processors. [online] Available at: <https://arxiv.org/abs/1802.06002v2> [Accessed 24 Nov. 2019].
Shen, H., Zhang, P., You, Y.-Z. and Zhai, H., 2019. Information Scrambling in Quantum Neural Networks. arXiv:1909.11887 [cond-mat, physics:quant-ph]. [online] Available at: [Accessed 7 Apr. 2020].
Silver, D., Huang, A., Maddison, C.J., Guez, A., Sifre, L., van den Driessche, G., Schrittwieser, J., Antonoglou, I., Panneershelvam, V., Lanctot, M., Dieleman, S., Grewe, D., Nham, J., Kalchbrenner, N., Sutskever, I., Lillicrap, T., Leach, M., Kavukcuoglu, K., Graepel, T. and Hassabis, D., 2016. Mastering the game of Go with deep neural networks and tree search. Nature, 529(7587), pp.484–489.
Silver, D., Schrittwieser, J., Simonyan, K., Antonoglou, I., Huang, A., Guez, A., Hubert, T., Baker, L., Lai, M., Bolton, A., Chen, Y., Lillicrap, T., Hui, F., Sifre, L., van den Driessche, G., Graepel, T. and Hassabis, D., 2017. Mastering the game of Go without human knowledge. Nature, 550(7676), pp.354–359.
Consultant: Supervisor: Dr. Sandeep Raha
Mentor: Chitman Josan (PhD Candidate)
The Effects of Cannabis on Mammary Gland Development via The Endocannabinoid System
Cannabis is the most commonly used drug during pregnancy, but its impact on the developing organs of the fetus and the physiology of the mother are not well understood. The primary bioactive constituents of cannabis, Δ⁹-tetrahydrocannabinol (THC) and cannabidiol (CBD), may impact mammary gland development via the endocannabinoid system (ECS) present in this organ. These interactions may disrupt the developmental processes of the mammary gland during pregnancy leading to poor nutrition for the neonate.
This research project investigated the effects of THC and CBD on mammary epithelial cell differentiation using the mouse HC11 cell line. The HC11 cells are a model of the mammary epithelium which can be differentiated into a phenotype that produces beta-casein, an important component of breast milk. We hypothesized that the ECS receptors, ECS enzymes, and mammary differentiation genes will be upregulated post-differentiation while THC and CBD treatment will decrease the expression of these genes. The HC11 cells were treated with 10 M THC or 10 M CBD for four days. The effects of cannabis were assessed by RT-qPCR to monitor the relative mRNA levels of genes that encode the ECS and mammary epithelial differentiation. The expression of these genes was also analyzed at the protein level with Western blots. Project findings will be discussed in the presentation. Cannabis exposure during pregnancy may impact the ECS in the mammary gland. Thus, alteration of the ECS may perturb signalling pathways associated with mammary gland development during pregnancy, leading to effects on maternal and infant health.
Consultant: Dr. Laurel Trainor
Investigating Top-Down Processes in Infant Rhythm and Meter Perception
Adults primed to hear an ambiguous rhythm in groups of 2s (duple meter) or 3s (triple meter) show steady state responses (SSRs) in their EEG with more energy at their primed meter. Previously, SSRs were found at frequencies for the beat, duple, and triple meter in unprimed 7-month-old infants. Other neural responses, mismatch negativity (MMN) and P3a, respectively reflect the detection of and attention to a ‘violation’ of a standard, repeating pattern. This study investigated whether priming 6-month-olds to hear a repeating ambiguous six-beat rhythm in either duple or triple meter would be shown in SSRs and MMN. Infants were primed using accents on beats 1, 3, and 5, or 1 and 4 for duple and triple meter respectively, for four repetitions of the rhythm, followed by sixteen unaccented repetitions which contained rare pitch deviants on beats 4 and 5. It was expected that MMN and P3a responses would be present and larger for metrically strong beats (beat 4 for triple, beat 5 for duple). SSR amplitude peaks were found at all frequencies of interest (sextuple, triple, duple, beat), however, no significant differences between peaks were observed in either group, suggesting that infants may not be favourably perceiving one metrical structure. Nearly-significant MMN-like activity was found in frontal left sites, along with significant P3a in both hemispheres for both groups. P3a amplitudes in the duple group were larger for strong beats, perhaps demonstrating an effect of meter on later auditory processing.
Cirelli, L., Spinelli, C., Nozaradan, S. and Trainor, L., 2016. Measuring Neural Entrainment to Beat and Meter in Infants: Effects of Music Background. Frontiers in Neuroscience, 10.
Nozaradan, S., Peretz, I., Missal, M. and Mouraux, A., 2011. Tagging the Neuronal Entrainment to Beat and Meter. Journal of Neuroscience, 31(28), pp.10234-10240.
Consultant: Dr. Sue Becker, Dr. Ranil Sonnadara
Investigating the Effects of Training and Individualization on Virtual Sound Localization Accuracy
A near-field virtual auditory display is any audio delivered through headphones that appears to come from within a meter of the listener’s head. The current study sought to determine the most efficient and effective way to generate near-field virtual auditory displays. Creating virtual auditory displays requires the use of head-related transfer functions (HRTFs) to synthesize spatialized virtual sounds. HRTFs depend upon physical dimensions of the head, torso, and outer ears, making them highly individualized. Many studies have shown that listeners localize virtual auditory displays better when they are presented with an individualized set of HRTFs. More recently, however, studies have shown that listeners improve their localization accuracy of virtual auditory cues that have been synthesized with general HRTFs after completing a training protocol. Many of the reported individualization methods and training protocols are inefficient for practical use, and therefore the current study investigated the effects of an efficient method of HRTF individualization compared to general HRTFs (between subjects condition), and training (within subjects) on participants’ virtual sound localization performance.
We found that both individualization and training improved sound localization performance. The greatest improvement between pre- and post-training was at lateral angles in participants using generic HRTFs. However, participants in the individualized group performed better both pre-training in lateral angles and post-training averaged over all angles. The results indicate that short individualization and training protocols would be worth completing in order to improve virtual sound localization performance. This will help inform future applications of near-field virtual spatialized auditory displays.
Consultant: Dr. Kyla Sask
Determining Protein Conformational Changes Upon Adsorption to Gold and Polyethylene Oxide (PEO) Modified Gold
Blood-contacting biomaterials are widely used for medical devices, including vascular grafts, stents and other devices. However, one of the biggest limitations is thrombosis due to plasma protein adsorption onto the devices which accounts for 30% of cases with blood-contacting devices. Protein adsorption is the accumulation of proteins on a surface (without the protein absorbing into the surface) which triggers the coagulation cascade. This adsorption can be reduced by modifying materials with polymers such as polyethylene oxide (PEO).
This study focuses on determining conformational changes of fibrinogen (Fg) and apolipoprotein-AI (apo-AI), two plasma proteins that are known to adsorb to biomaterial surfaces. By determining conformational changes of Fg and apo-AI once adsorbed onto a gold surface, compared to a PEO-modified gold surface, we can better screen future biomaterials and surface modification methods.
We have used methods including antibody-binding with Quartz Crystal Microbalance with Dissipation (QCM-D) and attenuated total reflection-Fourier-transformed infrared (ATR-FTIR) spectroscopy to determine protein conformational changes. From the QCM-D experiments, we have measured quantities of antibodies bound to the adsorbed protein. These results will allow us to determine whether proteins have changed conformation and bind less antibodies. From ATR-FTIR methods, we are investigating the secondary structure of the proteins by fitting peaks from the Amide I band on the FTIR spectra.
By better understanding the conformational changes of proteins upon adsorption, we can tailor biomaterial surface modification strategies to prevent thrombosis due to plasma protein adsorption.
Stuart McKinlay (Health Sciences, Third Year)
Dr. Bianca Pfaffenseller (Co-supervisor)
Dr. Bianca Wollenhaupt de Aguiar (Co-supervisor)
Dr. Flavio Kapczinski (Supervisor)
Consultant: Supervisor: Dr. Flavio Kapczinski, Co-supervisor: Dr. Bianca Pfaffenseller
Biological Markers and Illness Progression in Bipolar Disorder: A Systematic Review.
Introduction: Studies have shown that bipolar disorder (BD) may undertake a progressive course in a subset of patients, with recent efforts made to understand BD through clinical staging models. The progressive course of BD has led to the hypothesis of neuroprogression, which states that different stages of BD are associated with distinct neurobiological underpinnings.
Objectives: The purpose of this systematic review is twofold: (a) to review current literature available on the differences in biological markers between patients in the early and late stages of BD, and (b) to evaluate whether the evidence suggests that the changes in biological markers are progressive in nature.
Methods: Peer-reviewed articles from 2005 to 2019 were accessed from three different databases: Embase, PsycINFO, and PubMed; the reference lists of the identified studies were also reviewed. Studies were assessed with a focus on biological markers and illness progression in BD. All participants were 15-65 years old, with a diagnosis of BD and a classification into either the early or late stage. Cross-sectional studies, longitudinal studies, prospective studies, retrospective studies, non-randomized trials, and case-control studies were included.
Results: 801 citations were identified; of these, 18 studies were included. The authors of this review expect to find more pronounced changes in biological markers in patients with BD in the late stage compared to individuals in the early stage.
Conclusions: The goal of this review is to synthesize the current literature on biological markers and illness progression in patients with BD. This research hopes to advance prognosis and treatment.
- Andreazza, A. C., Kapczinski, F., Kauer-Sant’Anna, M., Walz, J. C., Bond, D. J., Goncalves, C. A., Young, L. T. and Yatham, L. N., 2009. 3-Nitrotyrosine and glutathione antioxidant system in patients in the early and late stages of bipolar disorder. J Psychiatry Neurosci, 34(4), p. 263-71.
- Ascoli, B. M., Parisi, M. M., Bristot, G., Antqueviezc, B., Gea, L. P., Colombo, R., Kapczinski, F., Guma, F., Brietzke, E., Barbe-Tuana, F. M. and Rosa, A. R., 2019. Attenuated inflammatory response of monocyte-derived macrophage from patients with BD: a preliminary report. Int J Bipolar Disord, 7(13), p. 1-11.
- Barbé-Tuana, F., Parisi, M., Panizzutti, B., Fries, G., Grun, L., Guma, F., Kapczinski, F., Berk, M., Gama, C. and Rosa, A., 2016. Shortened telomere length in bipolar disorder: a comparison of the early and late stages of disease. Braz J Psychiatry, 38(4), p. 281-286.
- Cao, B., Passos, I. C., Mwangi, B., Bauer, I. E., Zunta-Soares, G. B., Kapczinski, F. and Soares, J. C., 2016. Hippocampal volume and verbal memory performance in late-stage bipolar disorder. J Psychiatr Res, 73, p. 102-7.
- Cao, B., Passos, I. C., Wu, M. J., Zunta-Soares, G. B., Mwangi, B. and Soares, J. C., 2017. Brain gyrification and neuroprogression in bipolar disorder. Acta Psychiatr Scand, 135(6), p. 612-3.
- Çinar, K., 2018. Telomere length and hTERT in mania and subsequent remission. Braz J Psychiatry, 40(1), p. 19-25.
- Duarte, J., Massuda, R., Goi, P. D., Vianna-Sulzbach, M., Colombo, R., Kapczinski, F. and Gama, C. S., 2018. White matter volume is decreased in bipolar disorder at early and late stages. Trends Psychiatry Psychother, 40(4), p. 277-84.
- Fries, G. R., Vasconcelos-Moreno, M. P., Gubert, C., Quadros dos Santos, B. T., Sartori, J., Eisele, B., Ferrari, P., Fijtman, A., Ruegg, J., Gassen, N. C., Kapczinski, F., Rein, T. and Kauer-Sant’Anna, M., 2014. Hypothalamic-pituitary-adrenal axis dysfunction and illness progression in bipolar disorder. Int J Neuropsychopharmacol, 18(1), p. 1-10.
- Grande, I., Magalhaes, P. V., Chendo, I., Stertz, L., Panizutti, B., Colpo, G. D., Rosa, A. R., Gama, C. S., Kapczinski, F. and Vieta, E., 2014. Staging bipolar disorder: clinical, biochemical, and functional correlates. Acta Psychiatr Scand, 129(6), p. 437-44.
- Kauer-Sant’Anna, M., Kapczinski, F., Andreazza, A. C., Bond, D. J., Lam, R. W., Young, L. T. and Yatham, L. N., 2009. Brain-derived neurotrophic factor and inflammatory markers in patients with early- vs. late-stage bipolar disorder. Int J Neuropsychopharmacol, 12(4), p. 447-58.
- Lavagnino, L., Cao, B., Mwangi, B., Wu, M., Sanches, M., Zunta-Soares, G., Kapczinski, F. and Soares, J., 2015. Changes in the corpus callosum in women with late-stage bipolar disorder. Acta Psychiatr Scand, 131(6), p. 458-64.
- Panizzutti, B., Gubert, C., Schuh, A. L., Ferrari, P., Bristot, G., Fries, G. R., Massuda, R., Walz, J., Rocha, N. P., Berk, M., Teixeira, A. L. and Gama, C. S., 2015. Increased serum levels of eotaxin/CCL11 in late-stage patients with bipolar disorder: An accelerated aging biomarker? J Affect Disord, 182, p. 64-9.
- Pfaffenseller, B., Wollenhaupt-Aguiar, B., Fries, G. R., Colpo, G. D., Burque, R. K., Bristot, G., Ferrari, P., Cereser, K. M., Rosa, A. R., Klamt, F. and Kapczinski, F., 2014. Impaired endoplasmic reticulum stress response in bipolar disorder: cellular evidence of illness progression. Int J Neuropsychopharmacol, 17(9), p. 1453-63.
- Reininghaus, E. Z., Lackner, N., Birner, A., Bengesser, S., Fellendorf, F. T., Platzer, M., Rieger, A., Queissner, R., Kainzbauer, N., Bernd, R., McIntyre, R. S., Mangge, H., Zelzer, S., Fuchs, D., Dejonge, S. and Muller, N., 2016. Extracellular matrix proteins matrix metallopeptidase 9 (MMP9) and soluble intercellular adhesion molecule 1 (sICAM-1) and correlations with clinical staging in euthymic bipolar disorder. Bipolar Disord, 18(2), p. 155-63.
- Siweck, M., Sowa-Kucma, M., Styczen, K., Misztak, P., Szewczyk, B., Topor-Madry, R., Nowak, G., Dudek, D. and Rybakowski, J. K., 2016. Thiobarbituric Acid-Reactive Substances: Markers of an Acute Episode and a Late Stage of Bipolar Disorder. Neuropsychobiology, 73(2), p. 116-22.
- Siweck, M., Sowa-Kucma, M., Styczen, K., Szewczyk, B., Reczynski, W., Misztak, P., Topor-Madry, R., Nowak, G., Dudek, D. and Rybakowski, J. K., 2016. Decreased serum zinc concentration during depressive episode in patients with bipolar disorder. J Affect Disord, 190, p. 272-7.
- Tatay-Manteiga, A., Balanza-Martinez, V., Bristot, G., Tabares-Seisdedos, R., Kapczinski, F. and Cauli, O., 2017. Clinical staging and serum cytokines in bipolar patients during euthymia. Prog Neuropsychopharmacol Biol Psychiatry, 77, p. 194-201.
- Wollenhaupt-Aguiar, B., Pfaffenseller, B., Chagas, V., Castro, M., Passos, I. C., Kauer-Sant’Anna, M., Kapczinski, F. and Klamt, F., 2016. Reduced Neurite Density in Neuronal Cell Cultures Exposed to Serum of Patients with Bipolar Disorder. Int J Neuropsychopharmacol, 19(10), p. 1-5.
Consultant: Dr. Bhagwati Gupta
Investigating the PRY-1/Axin signaling pathway and target genes in stress response and aging
Aging is an inevitable process that is intrinsically linked to a variety of diseases. However, the genetic factors and signaling pathways that regulate longevity remain poorly understood and thus it is difficult to identify potential therapeutic targets for age-associated diseases. Aberrant signaling of the Wnt pathway has been implicated in age-related diseases and thus may be a therapeutic avenue for treatment.
The model organism Caenorhabditis elegans is genetically amenable and possesses many homologous proteins to humans, causing it to be an ideal system in which to study lifespan-regulating genes. PRY-1 is the C. elegans homolog of the human Wnt pathway protein Axin, which controls Wnt target gene expression. Previous research has identified eight genes overexpressed in C. elegans lacking functional PRY-1: ard-1, cdk-1, clsp-1, cpz-1, his-7, rnr-1, rpn-7 and spp-1. Knockdown of each of these genes rescues the cancer phenotype of PRY-1-deficient worms. Thus, it is hypothesized that these genes may regulate cellular responses such as stress and aging.
Here, we investigate the contributions of the Wnt signaling pathway and its eight potential target genes to aging and stress in C. elegans. Results from RT-qPCR and fluorescence microscopy experiments demonstrate that PRY-1 is autoregulated, and this autoregulation is dependent on BAR-1 and POP-1, which are C. elegans homologs of two Wnt pathway proteins. Aging assays also demonstrate that knockdown of cpz-1, rpn-7 and spp-1 via RNA interference extends the lifespan of worms lacking BAR-1, suggesting these genes could serve as therapeutic targets for age-related diseases.
Consultant: Dr. Jianping Xu
Investigation of environment-induced phenotypic plasticity of virulence factors in the Cryptococcus neoformans species complex
The Cryptococcus neoformans species complex (CNSC) is an opportunistic fungal pathogen that can disseminate through the human central nervous system upon infection, leading to meningitis. Melanin pigments and a polysaccharide capsule are the two major virulence factors in CNSC, with both exhibiting pleiotropic expression dependent on external factors. In the CNSC, Serotype A cells are known to be more virulent than Serotype D cells, however it is not known whether virulence factor production will similarly vary. This study investigated virulence factor expression, in a genetically diverse group of CNSC cells, comprised of Serotypes A, D and AD, in response to environmental stressors seen during infection. These results were also compared to the virulence factor expression of the sister species Cryptococcus gattii to determine the impact of species genetic distance on the analyzed factors. Environmental stress was created by adding reactive oxygen and nitrogen species to growth media at four concentrations each. Melanin production was measured using transilluminator-based spot densitometry, while polysaccharide production was measured using phenol-sulfuric acid colorimetry. We found significant differences in melanin production and polysaccharide production among Serotypes and across specific growth conditions. Furthermore, within-group analysis of each serotype revealed environment-dependent effects on the phenotypic plasticity of virulence factors. Overall, this study revealed significant interactions between the genetic background of CNSC cells and environmental stressors in the expression of virulence factors. These results suggest that the ability to modulate the expression of virulence factors likely plays an important role in the in vivo virulence of CNSC.
Consultant: Dr. Lesley MacNeil
Identifying Compounds that Reduce the Virulence of Pseudomonas aeruginosa Using Caenorhabditis elegans as a Pathogenesis Model
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterial pathogen that can infect a broad range of host species through similar infection mechanisms. These bacteria commonly cause hospital-acquired infections and infections in cystic fibrosis patients. There has been an increase in drug resistant P. aeruginosa strains, motivating the search for new compounds to combat infection. Due to common infection mechanisms between hosts, Caenorhabditis elegans – small bacterivorous nematodes– can be used as a whole animal pathogenesis model for identifying the virulence of P. aeruginosa strains and screening compounds that can reduce their virulence.
This study optimized a high-throughput multi-well liquid assay to allow for screening of the 96-well plate compound library: Wright Actinomycetes Collection Pre-Fractionated Library (PFL). The optimized protocol involves addition of 42 nematodes suspended in S-basal, 25µL of 4X Slow Killing Liquid, and 25µL of the bacteria of interest to an OD of 0.1 suspended in S-basal per well. This optimization yielded a protocol that is suitable for screening the PFL.
This optimized liquid assay was used to study the virulence of Prairie Epidemic Strain isolates of P. aeruginosa isolated from cystic fibrosis patients in the Canadian Prairies. Results from this assay were compared to an established solid agar-based killing protocol. Isolates determined to be highly virulent in the solid killing assay include P1113 and P749 whereas the liquid assay also found P196, P24, and P7 to be highly virulent (although considered avirulent in solid). This indicates potentially different methods of P. aeruginosa virulence between the assays.
Consultant: Dr. Joyce Obeid, Inna Ushcatz, Emily Hauck
An Investigation of Natural Killer Cell Receptors Response to High Intensity Continuous and Intermittent Cycling in a Pediatric Population.
Natural killer (NK) cells are regulatory cells capable of facilitating immunity against abnormal cells (e.g. tumor and virally infected cells) without the need of prior familiarization. Therefore, increasing the number of circulating NK cells and improving their functionality is an area of interest to many clinicians and scientists. NK cell function is partly determined by the expression of receptors on the cell which facilitate interactions with the environment. Two main classes of these receptors are inhibitory and activating. The objectives of this project are to (1) understand the deployment of NK cells which express NKG2A (an inhibitory receptor) and NKG2D (an activating receptor) in a pediatric population in response to exercise and (2) understand the extent of variation between exercise protocol in terms of NKG2A and NKG2D response. To meet these objectives, ten children were recruited as part of the ExiD study. Each participant completed a high-intensity continuous (30 min) or intermittent (20×15 sec) cycling protocol, performed in a randomized order over two separate visits. During each visit, blood was drawn before exercise, immediately after exercise, 30 minutes and 60 minutes after exercise. Whole blood was lysed and stained with fluorescently labeled antibodies to identify NK cells and further quantified to determine NKG2A and NKG2D expression using flow cytometry. Our findings will help to elucidate potential mechanisms through which exercise modifies NK cell activity, and may provide insight into NK cell functional capacities based on receptor expression dynamics.
Consultant: Dr. Brent McKnight
Assessing How Exposure influences Disaster Preparedness: A Study of Mining Firms in Canada’s Boreal Region
Climate change is increasing the frequency and intensity of wildfires and floods facing mining sites in Canada’s boreal forest. Decision-makers at these mining sites must decide whether and how to prepare for these events. To better understand this decision making, we undertook a quasi-inductive research design employing qualitative comparative analysis (QCA). QCA is a method that identifies configurations of conditions that, when present together, are necessary and/or sufficient for an outcome of interest. In our case, this outcome was firm decisions regarding their disaster preparation efforts. Informed by both the attention-based view (ABV) of the firm and construal level theory (CLT) we gathered mining site data, manager perspectives and corporate level information.
Surveys were created and distributed directly to mining site managers operating in Canada’s boreal region. The surveys evaluated the respondents’ perception of the controllability of extreme weather events on operations, and their psychological distance from climate change, their firm’s experience with natural disasters, and their degree of disaster preparedness. Additionally, we tested the influence of the exposure of the mining sites to wildfires and floods using historic wildfire and flood data. This allows us to integrate climate change adaptation research across physical and social sciences.
In this research, we explore how different combinations of conditions at the geographic site, manager decision-making and corporate context configure together to result in prepared or unprepared mining firms. This research will shed light on how firms prepare for disasters and how preparation is influenced by perceptions of climate change and exposure.
Consultant: Dr. Joanna Wilson
The Effects of Tamoxifen on Hermaphroditism and Reproduction of the annelid Capitella teleta
The estrogen receptor (ER) is important in the development, behavior, and reproduction of vertebrate species, yet the role of ERs in invertebrates is not well described. Capitella teleta is an opportunistic marine annelid that is found in the sediments along the coasts of North America, Japan, and the Mediterranean. C. teleta reproduces sexually and the population is composed of morphologically distinct males, females, and hermaphrodites. To determine the role of the ER on hermaphroditism and reproduction of C. teleta, a 6-week tamoxifen exposure was conducted in sexually isolated C. teleta populations. Tamoxifen is a selective estrogen receptor modulator (SERM) that has been shown to bind to annelid ERs and produce reproductive effects in both invertebrate and vertebrate species. Female-only and male-only populations of C. teleta were made in isolated bowls to encourage the development of hermaphrodites. Bowls were then subjected to 150µg/L, 300µg/L and 500µg/L tamoxifen or acted as seawater or vehicle controls (1% DMSO). The development of hermaphrodites and the production of brood tubes was monitored weekly over the experimental period and was compared between tamoxifen treatments and controls. There was found to be a dose-dependent decrease in the mean percentage of hermaphrodites across tamoxifen treatments in the male-only groups. No difference in brood tube production was observed across any treatments. This research will help elucidate the physiological role of the ER in C. teleta, the evolutionary role of the ER in invertebrate species, as well as the effects of endocrine disrupting substances in an aquatic environment.
Consultant: Dr. Elizabeth Weretilnyk
Effect of Phosphate Levels on Eutrema salsugineum Populations from the Yukon
Agricultural soils around the world are becoming increasingly unsuitable for crop growth. Specifically, phosphorus (P), an essential nutrient, is limiting in many soils and must be added as fertilizer to sustain crops. Eutrema salsugineum, a halophytic plant found in the Canadian Yukon, shows an exceptional capacity to grow under P-limited conditions. In this study, Eutrema plants harvested from different Yukon field sites were studied to determine if a capacity to use P efficiently varies among different, geographically separate Eutrema populations. To this end, Eutrema seedlings from seeds originally collected in the Yukon were grown on defined nutrient agar with (0.5 mM) or without (0 mM) P. Root morphology was evaluated from photos using ImageJ. Following 9 to 12 days, seedling root and shoot biomass were measured, after which tissues were frozen and stored at -80°C. RNA was extracted from frozen roots and shoots and used for cDNA synthesis to determine the level of Induced by Phosphate Starvation2 (IPS2) transcripts by RT-PCR. Preliminary results suggest that different seed lines show variable root growth responses to low P. RT-PCR testing is underway and IPS2 expression is predicted to vary among the different lines as well. Overall, this thesis will help determine whether Yukon Eutrema populations show heritable variability with respect to high P efficiency. Identifying genes responsible for Eutrema’s ability to thrive on low P would enable breeding of crops for improved P use efficiency with greater precision.
Consultant: Dr. Karen Kidd
The Effect of Forest Management Practices on Mercury Contamination in Streams of Forested Catchments
Forested catchments support an important ecological relationship between forests and streams. For example, forests filter nutrients and sediments from runoff and contribute terrestrial energy inputs (e.g. leaf litter) that support aquatic food webs. Forest disturbance can affect this transport of matter, and a growing concern is the role of forestry in mobilizing mercury (Hg) from terrestrial sources into streams, which is poorly understood at catchment-sized scales. Stable isotopes of carbon, nitrogen, and hydrogen can be measured to help distinguish the relative contributions of terrestrial and aquatic sources to diet and trace the movement of Hg across trophic levels. The objectives of my thesis were to evaluate the effect of forest management on spatial distributions of Hg in slimy sculpin (Cottus Cognatus) within and between three watersheds managed at different intensities in New Brunswick: minimally, extensively, and intensively harvested. During the fall of 2017, sculpin were sampled from five or six upstream to downstream reaches in each watershed. Where possible, 10 males and 10 females from each reach were selected for analyses. Total Hg (THg) was measured in dried, homogenized muscle tissue (n = 245) using a Direct Mercury Analyzer, and δ13C, δ15N, and δ2H were measured in whole body tissue (n = 258). Within all three watersheds, the effect of stream order on THg concentration was significant (ANOVA, p < 0.01). Results will contribute to a better understanding of how forestry affects the spatial distribution of Hg across catchment-sized scales.
Consultant: Dr. Greg Flynn
Assessing Acceptance and Application of Forensic DNA Identification Technology by the Judiciary in the Canadian Criminal Court System
While the experimental research on forensic identification methods including early techniques (e.g. RFLP, PCR, STR) and more recent applications (e.g. AIM, RNA profiling, DNA phenotyping) is extensive, their interpretation and admissibility determined by Canadian courts is not well-understood. Unlike the United States which has clear tests providing direction to judges on when to admit evidence, namely, the Daubert analysis, Canada does not have a direct equivalent.
This article studies judges’ application of forensic identification techniques in criminal cases using a random sample of 64 appellate court-level decisions from the legal database CanLII. Case-specific information is extrapolated to include: technology discussed, facts of the case, issues (if any) related to admissibility or use of the technology, analysis given by judge(s) if pertinent to technology, holding, and referenced precedent. Analysis reveals varying thresholds and justifications for acceptability but shared emphasis on protecting genetic data. Much of the discussion by judges concerns the purpose of DNA orders, warrants, collection, and use, and whether the purpose is balanced when juxtaposed with questions of constitutional validity (using Criminal Code clauses and the Charter of Rights and Freedoms). The task of determining the validity of techniques is left to expert witnesses, indicating that judges take a lesser role as gatekeepers of scientific evidence. Novel techniques also elicit limited discussion compared to their pre- to mid-1990 counterparts in the courts. These findings suggest that courts may benefit from discussing scientific methods, possibly incorporated through the inclusion of forensics in law curriculum or training for judges.
Consultant: Dr. Marie Elliot
Investigating the role of predicted regulatory proteins in Streptomyces venezuelae
Streptomyces are a widely studied genus of bacteria because of their production of industrially relevant secondary metabolites. Under specific growth conditions, 10% of Streptomyces species undergo a new mode of growth called exploration. Exploration is characterized by the rapid growth of non-branching, vegetative hyphae over solid surfaces at ten times the rate of regular growth. The regulatory factors and pathways involved in exploration initiation and development, as well as those governing classical growth, requires further study. This study focused on the role of YlqC (sven_5287) and Mfd (sven_2926), a predicted nucleoid associated protein and a bacterial DNA translocase protein, respectively, in classical growth, exploration, glycerol metabolism and secondary metabolite production.
PCR targeting was used to create sven_5287 and sven_2926 deletion strains. Growth curves for the deletion and wild type strains were performed using OD600 measurements. The growth curve indicated that the Δsven_5287 deletion strain were delayed in liquid growth while Δsven_2926 is similar to wild type growth. The phenotypes of the strains during regular and exploratory growth on a variety of solid media were also compared. During exploration, Δsven_2926 produced explorers with a greater number of “escapers”. On medium supplemented with glycerol, Δsven_5287 exhibited delayed growth. Antibiotic activity assays assessed the secondary metabolite production of the deletion strains against a variety of microorganisms. No zones of inhibition were observed. These results indicate Mfd may have a role in maintaining genome integrity and this role would be amplified during rapid exploration. Additionally, YlqC may have a role in classical development and glycerol metabolism.
Consultant: Dr. Todd Hoare
The Controllable Delivery of Hydrophilic and Hydrophobic Drugs Using Starch Nanoparticle-Based Clusters
Despite the number of treatment methods currently available, cancer remains one of the leading causes of death in Canada and worldwide. It is therefore critical that new and more effective means of combating this disease be developed. Nanoparticles have been heavily investigated for their use in cancer diagnostics, imaging, and most critically in chemotherapeutic drug delivery. One such example is starch nanoparticles (SNPs) which can penetrate tumours based on their small size and have the capacity to be functionalized and loaded with different types of drugs. The size of SNPs, however, limits their potential to reach tumours due to their rapid clearance from the body. To address this challenge, we have fabricated SNP clusters, or nanoclusters, of 100-160 nm in size that are comprised of cationic SNPs (~20 nm diameter) complexed with an anionic polymer with charge-switchable properties. These nanoclusters are able to remain stable at physiological pH (7.4) and disassemble to release the highly penetrable SNPs when exposed to the acidic (6.5) microenvironment associated with tumours. Furthermore, recent research has indicated that the administration of certain combinations of chemotherapeutic agents can increase the efficacy of targeted cancer therapy while reducing the necessary dose to achieve remission. One example of this is the administration of the hydrophobic EGFR inhibitor erlotinib (Erl), which can synergize cancer cell apoptosis with the hydrophilic DNA damaging agent doxorubicin (Dox). Here, we reveal the ability to engineer two functionalized SNP variants capable of loading either Dox or Erl that can subsequently be used in nanocluster formation to deliver synergistic anti-tumour therapy in vitro and in vivo. Though drug loading and dual-SNP carrying nanocluster formation remain to be assessed, SNP variant synthesis is an important step towards generating multi-drug carrying nanoclusters.
Consultant: Dr. David Earn
Determining the Effectiveness of Using a “Canonical Path” to Understand the Factors that Lead to the Elimination of Measles in the United States
As one of the most contagious infectious diseases, the elimination of measles is of key interest to the World Health Organization (WHO). Until recently, the progress towards the elimination of measles has been based solely on goals set by the WHO. However, in 2019 “Measles and the Canonical Path to Elimination” by Graham et al. defined a novel method for understanding the factors that lead to the elimination of measles on a country scale. This thesis aims to determine whether the method created by Graham et al. can be adapted for use on a smaller scale like that of the United States. First, measles incidence data and United States population data is collected from online sources and combined into a single working file. This data is then used to create a 2-dimensional incidence space using the weighted mean incidence per 100,000 people and the coefficient of variation. This is then used to define a “canonical path” which each state follows while progressing towards the elimination of measles. The results of this thesis are still pending, however, determining the usefulness of this method within the United States is important. If successful, the model can provide a better understanding of the dynamics of measles incidence along the path to the elimination of measles in the United States.
Consultant: Dr. George Dragomir and Dr. Traian Pirvu
Estimating the Economic Impact of Natural Disasters
As the current climate crisis becomes more serious, natural disasters have the threat of becoming more numerous and increasingly damaging. Both the inevitability of their occurrence and the expected increase in severity make researching the economic impact of natural disasters worthwhile. This thesis quantifies the negative impact that natural disasters have on certain Central and South American economies. By using historical disaster and economic data from the past 60 years, a numerical tool is developed to forecast the future impact of natural disasters on gross domestic product (GDP). The tool uses past disaster damage figures and GDP growth rate to yield an expected annual loss in GDP due to disaster. For each country, the expected loss is expressed as a percentage of GDP. This analysis could provide policymakers with new insight into the ways damages caused by natural disasters can be mitigated effectively, such as through the purchasing of insurance or the allocation of emergency funds. Economies at a greater predicted risk of financial losses due to natural disasters may find the consideration of alternative mitigation strategies useful in order to preserve or improve their current economic standing. Some of these strategies will also be discussed.
Consultant: Dr. Jonathon Stone
Evidence of Rudiment Regression and Regrowth in Sea Urchin Lytechinus variegatus
Phenotypic flexibility (reversible change in phenotype) is an evolved developmental adaptation that increases organism survivability in variable environments. For example, sea urchin larvae may express phenotypic flexibility in response to changes in exogenous nutrient availability. There is evidence to suggest that sea urchin rudiments (structures which grow in the larvae until they are expelled as juveniles during metamorphosis) are resorbed in response to starvation. This study investigates rudiment phenotypic flexibility in sea urchin Lytechinus variegatus by determining whether rudiment resorption is reversible when food is reintroduced. Sixty-six rudiment-containing larvae were placed into either a control group or treatment group, and their development was monitored for 66 days. Larvae within the control group were fed every other day while individuals of the treatment group were starved. Once evidence of rudiment resorption was demonstrated in the treatment group, the starved individuals were fed and monitored for changes in development. If larvae are phenotypically flexible, we would expect that the rudiments of the control group would reach metamorphosis, whereas the rudiments of the treatment group would regress during starvation and regrow after refeeding. In this study, we show evidence of rudiment regression and regrowth in four surviving members of the treatment group. Notably, only one member of the control group reached metamorphosis. Therefore, additional stress may have been present in the larvae population to affect rudiment development. Overall, these findings will contribute to current understandings of marine developmental biology and the adaptive mechanisms in place to increase organism survivability under environmental stress.
Consultant: Dr. Sue Becker
The Effect of Imagery Vividness and Perspective on the Relationship Between Episodic Future Thinking and Delay Discounting
Episodic Future Thinking (EFT) is someone’s ability to mentally travel forward in time. People who are good at envisioning themselves in the future tend to be farsighted decision makers and vice versa. But this relationship between future thinking and decision making isn’t simple; it’s modulated by trait imagery vividness and imagery perspective. Imagery vividness is the detail with which an individual imagines a scenario, such as the specific number of people present. Imagery perspective can be either first- or third-person. First-person is your own perspective, how you would view the event if you were there. Third-person perspective adopts the viewpoint of an onlooker, as if watching yourself from the outside. In order to quantify these traits, participants completed the Plymouth Sensory Imagery Questionnaire, the Dissociative Experiences Scale, an EFT writing task, and a monetary choice task. While full results are pending, we anticipate the following: regression analysis should reveal that monetary choices tagged with a cue word from the EFT task should be discounted at a less steep rate than un-cued decisions. Additionally, we anticipate that analysis of variance will reveal that high levels of imagery vividness and low levels of dissociation (which predicts first-person imagery) should heighten the effects of EFT, thereby decreasing rates of discounting. This investigation will contribute to the growing body of literature in cognitive neuroscience around the utility of imaging future events. This will have clinical application in populations affected by PTSD or addiction disorders, where high rates of dissociation and delay discounting are prevalent.
Consultant: Dr. Kari Dalnoki-Veress
The Granular Drop Weight Experiment
Aggregates made of adhesive frictionless droplets have been observed to display properties analogous to those of continuous substances. Thus, well understood experiments capable of characterizing continuous materials can be used to explore novel properties of granular media. Here we present methodology for conduction a variation of the drop weight experiment capable of measuring an effective interfacial tension between a granular aggregate and a surrounding fluid. The granular aggregate is created using a collection of monodisperse oil microdroplets which are forced through a narrow opening. Droplet size and polydispersity are key parameters in the creation of granular drops, since they impact buoyancy and adhesion of the aggregate. In the experiment presented, buoyancy drives the oil droplets through an opening while adhesion between droplets causes the creation of granular pendant drops. This outcome is similar to the interaction between gravity and surface tension which drives the creation of water droplets in the conventional drop weight experiment. As such, the effective interfacial tension between a granular material and a fluid can begin to be probed with the methods proposed here.
Consultant: Dr. André Bédard
Investigating the Physiological Roles of TMEM16F and CDK6 in Quiescent Chicken Embryo Fibroblasts
Cells in unfavourable conditions may enter a state of reversible growth arrest known as quiescence or phase G0. Quiescent cells are non-dividing but metabolically active and viable. Investigating the growth arrest-specific genes that allow cells to enter, maintain, and exit quiescence will enhance our understanding of the mechanisms involved in cell survival and homeostasis. TMEM16F and CDK6 are proteins that have potential physiological roles related to stress mitigation in quiescent cells. This study aims to contribute to a greater understanding of their roles in quiescent cells. This study planned to optimize antibodies specific to TMEM16F and CDK6 to enable further investigation of protein expression, validate the upregulation of TMEM16F and CDK6 at the protein level in quiescent cells, and compare the intracellular localization patterns of these proteins in proliferating versus quiescent cells. Quiescence was induced by culturing chicken embryo fibroblasts (CEF) in conditions of contact inhibition, hypoxia (1.8% O2), or serum starvation. Western blotting and indirect immunofluorescence microscopy was performed to analyze the expression and localization of each protein in proliferating versus quiescent cells. While gene profiling analysis had suggested an up-regulation of both TMEM16F and CDK6 transcript levels, preliminary results suggest that only CDK6 is induced in CEF by hypoxia and serum starvation. Immunofluorescence analysis highlights an interesting localization pattern of TMEM16F in hypoxic CEF. These results characterize the expression of TMEM16F and CDK6 in quiescent cells, which will lead to a better understanding of their functions in relation to the complex mechanisms involved in cell survival and homeostasis.
Consultant: Dr. Dan Perri and Carmine Nieuwstraten
A Statistical Analysis of Opioid-Related Medication Incidents and Near Misses at St. Joseph’s Healthcare Hamilton
The leading cause of avoidable harm in healthcare is medication incidents, which are errors in the medication process that have the potential to result in patient harm. Separate from medication incidents, near misses are events that could have caused harm but were remedied before they reached the patient. Opioid-related medication incidents are of particular concern due to the associated risks of these drugs and the current opioid crisis. Medication incidents can be analyzed to determine where in the medication process (prescribing, dispensing or administration) the errors occurred, allowing preventative measures to be implemented.
With this in mind, this project aimed to discover trends in the frequency and nature of reported and unreported opioid-related medication incidents and near misses at St. Joseph’s Healthcare Hamilton, along with their reporting rate.
Voluntarily reported opioid-related medication incidents and near misses from December 2017 to October 2019 were analyzed using descriptive and comparative statistics. Additionally, naloxone administrations and patient vitals were used to determine St. Joseph’s opioid-related medication incident reporting rate, by matching the medical record numbers of the patients who received naloxone to the patient numbers in the reported incidents. The reporting rate was determined to be between 0-1.84%. The most frequently reported incident severity was ‘error, no harm’ and the most commonly involved opioid in both reported and unreported incidents was hydromorphone. The results of this analysis will be used to make recommendations and implement changes at St. Joseph’s to limit opioid-related medication incidents and near misses, along with increasing their reporting rate.
Consultant: Dr. John Maclachlan, Mr. Hartley Jafine
Designing a medical improvisation Continuing Professional Development course to enhance CanMEDS roles
In today’s interdisciplinary clinical environment, the inability for physicians to communicate effectively with their healthcare team poses a threat to patient outcomes and to the improvement of treatments and standards of care. We propose that medical improvisation (improv), the application of improvisational theatre activities to enhance specific CanMEDS roles (six roles a physician must fill to be considered a medical expert), can be an effective tool to teach clinical competencies to medical professionals in Canada. Improv activities isolate specific skills in a non-medical context and allow for reflection and awareness which can then be applied to future medical contexts.
We created a unique 12-hour medical improv Continuing Professional Development course for physicians to explore key skills with an emphasis on experiential learning and reflective debrief. The key component of the course is a refined personal reflection survey which acts both as a debriefing tool and as a method of quantitatively analyzing changes in participants’ perceptions of their communication skills over the course of the workshop. The workshop curriculum, along with the ethics approval documentation comprises a package that can be implemented in future medical improvisation projects.
This curriculum and package for further study will contribute to the growing body of quantitative literature on medical education in Canada. With the recent shift towards Competency-Based Medical Education, this work will add to the limited number of Continuing Professional Development courses that emphasize intrinsic skills over discipline-specific knowledge, in order to improve the clinical skills of physicians in Canada.
Consultant: Dr. Cheryl Quenneville
The Effects of Ankle Posture on Foot Impact Response for Frontal Automotive Collision Applications
Frontal automotive collisions can cause debilitating, long-term foot injuries. Typical collision safety testing uses Anthropomorphic Test Devices (ATDs, or ‘crash test dummies’) equipped with force sensors, as cadaveric testing is impractical for industry. However, current ATDs neglect data collection at the foot, relying on tibial load cells to predict lower limb injury risk. Previous studies have demonstrated that load distribution in the foot varies with ankle posture, likely influencing injury risk mechanisms. This highlights a need for an analysis of foot impact response at non-neutral postures in cadaveric feet. The present work modified an existing ATD to accept a cadaveric foot (adapted leg) wearing an instrumented boot, allowing analysis of both tibial load cell data (industry standard metric) and foot fractures (to identify tolerance). A pneumatic impacting apparatus delivered sub-injurious impacts replicating frontal collisions to the adapted leg, and an ATD. Feet were positioned in two ankle postures commonly assumed by occupants: external rotation combined with either inversion or eversion. Force data were collected at the tibia and boot insole. Higher tibial forces were recorded in the ATD than the adapted leg, with no difference between postures. This indicates higher stiffness in the ATD. Total insole force did not differ between test limbs or postures, suggesting that the ATD responds similarly to the adapted leg in these conditions. Regionally, heel forces were highest for all test limbs and postures. This demonstrates that regionalized insole force measurement is relevant and may help predict localized injury risk to the foot.Emily Xiang – Confidential, not for website at this time, Statement posted April 7
Consultant: Dr. Laurel Trainor
Developmental priors on musical rhythm by iterated reproduction
This abstract has been omitted from our website due to a confidentiality agreement between the student and their supervisor.
Consultant: Dr. Benzhong Zhao
Gravity fingering in heterogeneous porous media: an experimental study using microfluidics
Gravity fingering is the phenomenon by which preferential channels, also known as fingers, form when water infiltrates into dry porous media. In soil, gravity fingering is associated with moisture deficits for plants, as infiltrating rainwater bypasses the shallow root zone, as well as accelerated contaminant transport. A definitive understanding of fingering development and propagation, especially at the pore-scale, has yet to be achieved.
Here, we test several design iterations of a novel microfluidic cell that simulates dry heterogeneous soil in 2D, allowing for pore-scale observations enabling hypotheses on the origin of gravity fingering. Time-lapse images of water travelling through the cells are collected, and properties such as saturation and propagation speed are analyzed in MATLAB. The findings are also contrasted with the propagation pattern predicted by the classical Richards equation. A method for saturation determination based on greyscale image intensity is presented. The Richards equation is shown to be an insufficient predictor of infiltration pattern, failing to predict the saturation evolution associated with gravity fingering.
These findings will serve as a basis for further study on gravity fingering. We have created a framework for image analysis in MATLAB and were successful in describing the strengths and weaknesses of a 2D microfluidic cell approach to studying infiltration in heterogeneous porous media.
Consultant: Dr. Tristan Carter
Development of an Application for Simplified, Real-Time Analysis of Archaeological Data
Archaeology as a discipline is the study of the material past; once excavated, materials are quickly digitized, only to be waylaid by a potentially years-long delay before these data are combined to produce useful information. This delay is based in two key problems: 1) archaeological data are complex, meaning that exploration of these data requires knowledge of often-intimidating computer software and of limitations of different statistical models, and 2) analysis is completed ‘after the fact’, leading to inefficiencies as data must be reformatted and researchers must retroactively determine what analytical method best fits their research questions.
The objective of this thesis is to address these problems by creating a web application to interface with an archaeological database (from the Stelida Naxos Archaeological Project) and facilitate simple, time-effective analysis. The application is coded using the Shiny programming language in RStudio software to interface with data in a MySQL relational database system; all software and packages are free and open-source, making the code itself modifiable and accessible. The finished application provides intuitive graphical and numerical outputs that come with written explanations and are customizable by period, material, artefact type, and locus.
The application addresses identified problems by 1) automatically generating a variety of exploratory data visualizations, useable without advanced computing knowledge, and 2) connecting to a database in real-time, eliminating the need to export and ‘clean’ data and allowing researchers to explore possible trends as soon as data are digitized. The existence of this application will reduce the delay between data collection and analysis, subsequently facilitating data-driven decision making in the field, refinement of research questions, and formation of new ideas.