PRISM | Institutional Repository
Communities in PRISM
Select a community to browse its collections.
Recent Submissions
Item
Open Access
Molecular dynamic simulations of bulk nanobubbles: Investigation of factors important to their stability
(2023-03-24) Pathirannehelage, Nihari Sathsarani Pathirannehe; Kusalik, Peter G; Kimura-Hara, Susana; Salahub, Dennis R
Nanobubbles are gas-filled bubbles in liquids with a diameter in the 100 nm range. Due to their
small size and their long-term stability (up to months), there are various applications available in
numerous fields, including medicine, agriculture, water remediation, washing, and mining.
Although there are numerous applications and much research has been performed, there is a lack
of insight into the stability of bulk nanobubbles. Since bubble pressure is an important parameter
for bubble stability, in this project we have used molecular dynamics simulations to investigate
nanobubbles in water and factors affecting the pressure. For all simulations, the TIP4P/2005 water
model was used. A suitable method to calculate the short-range interactions in nanobubble
simulations was explored and the particle mesh Ewald summation method was shown to be
superior to the cut-off method. The pressure in systems with different sized nanobubbles was
measured to examine whether there may be other contributions in addition to the Laplace pressure.
The radii and positions of the bubbles were calculated based on the densities of slices through the
systems. The results confirmed that pressure is impacted by factors other than the Laplace pressure,
where long-range dipole-dipole interactions are found to play an important role. A manifestation
of this was the observation that the distance between adjacent bubbles can effect the pressure.
Item
Open Access
Systematic Review using a Spiral approach with Machine Learning
(2023-03-22) Saeidmehr, Amirhossein; Samavati, Faramarz; Steel, Piers; Maleki, Farhad; Chapman, Derek
Systematic reviews have become increasingly time-consuming and costly due to the accelerating growth of academic literature, doubling every nine years. Machine learning (ML) offers a promising solution to manage the growing corpus of literature, but current approaches still rely on a sequential, two-staged process designed for a purely human approach. In this thesis, we propose and test a spiral or oscillating approach, where full-text screening is done intermittently with title/abstract screening. We examine this approach in three datasets by simulating 360 conditions with different algorithmic classifiers, feature extractions, prioritization rules, data types, and information provided. Our results overwhelmingly support the spiral processing approach with Logistic Regression, TF-IDF for vectorization, and Maximum Probability for prioritization, demonstrating up to a 90\% improvement over previous two-staged ML methodologies over just title-screening, particularly for databases with fewer eligible articles. These advancements have the potential to make systematic review screening functionally achievable for another one to two decades.
Item
Open Access
The impact of morphine on nerve injury recovery and lipid metabolism pathways
(2023-03-30) Stokes-Heck, Sierra; Trang, Tuan; Ousman, Shalina; Stys, Peter
Neuropathic pain resulting from peripheral nerve injury is among the most debilitating types of
chronic pain conditions. Opioid medications are often used despite their poor efficacy in treating
neuropathic pain symptoms and concerns about adverse effects. Notably, emerging evidence
suggests that rather than alleviating neuropathic pain, opioids may worsen mechanical allodynia,
wherein innocuous stimuli elicit pain. Morphine has been shown to exacerbate nerve injury-induced
mechanical allodynia, but the cause is not understood. Both morphine and nerve injury
have been implicated in myelin and oligodendrocyte perturbations. As myelin is primarily
composed of lipids, here I determined whether spinal lipid metabolism alterations are a potential
mechanism underlying morphine exacerbated neuropathic pain. In this study, I characterized
neuropathic pain development and recovery using the chronic constriction injury model (CCI),
which results in robust mechanical allodynia. I demonstrated that delayed morphine treatment of
CCI animals resulted in prolonged mechanical allodynia and recovery from nerve injury, as
compared to nerve injured mice given saline. Using profiling arrays for cholesterol metabolism
and lipoprotein signaling, I found that morphine further increases the CCI-induced lipid
metabolism changes within the spinal cord. More specifically, I found that cholesterol metabolic
and lipoprotein clearance pathways are upregulated in nerve injured animals given saline when
earlier and later timepoints are compared, suggesting their role in recovery. Conversely, these
same pathways are downregulated in morphine treated CCI animals. To confirm these results, I
validated the six most dysregulated gene candidates and found that Cyp11a1 was significantly
upregulated in CCI animals treated with morphine. These results suggest that morphine could be
delaying recovery from CCI by dysregulating lipid metabolism at the spinal cord level. As glial
cells are involved in lipid synthesis and maintenance of myelin, alterations in lipid metabolism
could be linked to changes in oligodendrocytes, astrocytes, microglia, and myelination. These findings could help mitigate adverse opioid effects and improve treatment for people suffering from neuropathic pain.
Item
Open Access
The Controls of Porosity on Mineral Alteration Processes in the Shallow Oceanic Lithosphere at Slow-Spreading Ridges
(2023-03-20) Pujatti, Simone; Tutolo, Benjamin Michael; Lecumberri-Sanchez, Pilar; Pattison, David Robert Maitlan; Nair, Rajeev Kumar Sasidharan; Lauer, Rachel Mollie; Tutolo, Benjamin Michael; Shugar, Daniel H
Porosity exerts strong controls on mineral replacement and alteration processes mediated by the action of fluids. These processes are ubiquitous in the Earth’s crust, but even more so within the oceanic lithosphere, an environment saturated by infiltrating fluids that can range in composition from hot hydrothermal fluids to low-temperature seawater. This thesis presents examples of fluid-rock interactions that affect mafic and ultramafic lithologies recovered via drilling from the subseafloor of the slow-spreading Mid-Atlantic Ridge. These reactions are enabled by the presence of pores that provide flow pathways for fluids to reach the reaction front of altering minerals. Chapter 2 explores the genesis of petrographic textures observed in samples recovered from the Trans-Atlantic Geotraverse, a hydrothermal sulfide mound that shows black smoker activity. The textures form due to the replacement of anhydrite by pyrite under the action of hot hydrothermal fluids generated via heating of seawater entrained within the oceanic crust, and involved growth of quartz into open space. Intensive investigation of the observed textures detailed in this Chapter provides a mechanistic explanation for the attainment of the sulfur isotopic signatures found in sulfide precipitate within the hydrothermal mound. In Chapter 3, tomographic analysis of serpentinized peridotite at nanometer and micrometer scales reveals the presence of dissolution pores located at the grain boundaries of olivine, which show significant connectivity, suggesting that soluble Mg and Si sourced from the dissolution of olivine are exported to seawater, affecting its chemical budget, alkalinity, and consequently the coupled carbonate-silicate cycle. Chapter 4 tests the hypothesis that the porosity and Fe3+ contents of serpentinized peridotite increase with increasing serpentinization degree, suggested by correlations between density and magnetic susceptibility of serpentinites established in earlier work. The hypothesis was tested by applying statistical analysis to geochemical and porosity data collected on serpentinite samples recovered from 10 different drilling sites, revealing complex alteration patterns that involve seafloor weathering processes and thus extend beyond the transformation imparted by serpentinization reactions. Together, the scientific investigations conducted in this thesis demonstrate the importance and complexities of porosity generation and evolution during alteration of the shallow oceanic lithosphere.
Item
Open Access
George Platt Lynes: Visualizing Queerness Through the Fluid Male Nude
(2023-03-15) Young, Marcus Baron; Rudd, Annie; Johnston, Dawn Elizabeth Belle; Guglietti, Maria Victoria
This thesis proposes a reading of George Platt Lynes’ homoerotic photographs as queer countertexts – media that subvert and transgress heteronormative codes. Lynes created male nude images from the 1930s to the 1950s. His work, however, was concealed because of American laws that prevented queer identities to exist and thrive in public. A key effect of homoerotic photography is its unapologetic presentation of queerness, and Lynes adapted this form to elevate queer identity through artistic illustrations of the male body as symbols of queer desire. The central argument of this study is that Lynes’ homoerotic photographs queered hetero masculinity by making fluid presentations of the male body. By departing from traditional and “ideal” depictions of maleness that privilege hard and rigid patterns, Lynes offered a way to view the male gender through the subversion of hetero visual expectations. At the theoretical level, this study builds upon Sara Ahmed’s concept of queerness as deviation. Lynes queered hetero masculinity by showing spectators that there are more ways to portray maleness beyond the muscular physiques that were celebrated in the early 20th century. To this end, the thesis engages with a body of theoretical work that considers photography as a means to reveal queer identity, an identity that has been historically marginalised, and approaches Lynes’ nudes through the intersection of homoeroticism and queerness. At the methodological level, this thesis articulates how rejected queerness re-emerges as an acknowledged and beautiful idea through Lynes’ capturing of the male nude. Through a visual discourse analysis, this thesis examines the political, visual, and narrative dimensions of Lynes work as responses to 20th-century American homophobia.