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Geostatistical analysis and integration of soil chemistry data with remote sensing information in the Sudbury area, Ontario.
Get PDFThe presence of anomalous concentrations of metals within the soil profile can strongly affect its
biological availability to plants, causing potential toxicity when exceeding threshold concentrations,
and favoring numerous chemical exchanges. These interactions further facilitate metal dispersion in
the hydrogeological and ecological systems, in response to weathering and erosion. Studies of the
geospatial distribution of trace metal contaminants in Sudbury soils is thus important to unravel the
dominant processes controlling dispersion patterns, contributing to sustainability of mining practice.
A kriging geostatistical approach was applied to geochemical data obtained from the Sudbury Soil
Survey to map multiscale geographic, enrichment trends in metal concentrations. Ordinary kriging
prediction maps were developed to re-evaluate the multiscale spatial distribution of the chemicals of
concern. Results show an anomalous distribution of metals centered on historical smelters, forming
dominant northeast and southwest enrichment trends. The existence of these trends was validated by
implementing a geostatistical Gaussian conditional simulation method, which reproduced the same
spatial variability observed in the ordinary kriging maps and efficiently replicated the observed
trends. The correlation analysis of the trends with remote sensing data, suggests that prevailing wind
directions are likely one of the dominant driving forces controlling the trends. Integrating these
results with satellite data showed improved vegetation regrowth patterns consistent with the
geochemical northeast-southwest trend providing further, independent validation of the kriging
results. Re-evaluation of the regional, geospatial distribution of the measured trace element
concentrations will assist the monitoring and improved understanding of soil contamination trends and
their impact on vegetation and other aspects of the biosphere in the Greater Sudbury area.Master of Science (MSc) in Geolog
Nickel and copper translocation in Pinus resinosa (red pine) and their effects on the expression of genes associated with nickel and copper resistance
Get PDFMetals are required in plant tissues at small concentrations for several physiological processes;
however, excess metal can cause toxicity. The City of Greater Sudbury Region (CGS) has a rich
mining history that has resulted in contaminating emissions that damaged surrounding ecosystems.
The main objectives were to 1) investigate metal accumulation and translocation in Pinus spp., 2)
evaluate the effects of different concentrations of nickel and copper on P. resinosa genotypes, and 3)
determine the effects of different concentrations of nickel and copper on gene expression in Pinus
resinosa. Soil, roots, and shoots of P. resinosa were sampled in the CGS. Additionally, seedlings were
treated with different concentrations of nickel nitrate and copper sulphate and corresponding salt
controls in growth chamber screening tests. P. resinosa accumulate nickel and copper in roots and
shoots. Susceptibility to nickel exposure increased with seedling age. Resistance to copper on the
other hand increased in old genotypes. The expression of genes associated with nickel resistance
including 1-aminocyclopropane-1-carboxylic acid deaminase (ACC deaminase), glutathione-Stransferase (GST), High-affinity Ni transporter (NiCoT or AT2G16800), natural resistance-associated
macrophage protein 3 (NRAMP3) and Serine acetyltransferase (SAT) were analyzed using qPCR.
Each gene was downregulated in genotypes treated with the 1,600 mg/kg nickel, while GST
expression was increased six folds compared to the water control. The expression of MRP4 and RAN1
genes associated with copper resistance was also investigated. Only the lowest concentrations (13
mg/kg) of copper ions suppressed the expression of these genes while higher concentrations had no
effects. This research suggests that P. resinosa is in general resistant to nickel and copper
contaminants. Nickel and copper ions affect gene expression, even at low concentrations.Master of Science (MSc) in Biolog
Identification of radiation induced miRNA biomarkers using the CGL1 cell model system
Get PDFThe overall aim of this study was to identify novel radiation induced miRNA biomarkers for low
dose radiation (LDR) exposures. MicroRNAs (miRNAs) have emerged as a potential class of
biomolecules for diagnostic biomarker applications. miRNAs are small non-coding RNA
molecules produced and released by cells in response to various stimuli. miRNAs also
demonstrate remarkable stability in a wide range of biological fluids, in extreme pH fluctuations,
and after multiple freeze-thaw cycles. Given these advantages, identification of microRNA-based
biomarkers for radiation exposures can contribute to the development of reliable biological
dosimetry methods, especially for LDR exposures. In this study, an miRNAome next-generation
sequencing (NGS) approach was utilized to identify novel radiation induced miRNA gene
changes within the CGL1 human cell line. Here, irradiations of 10, 100, and 1000 mGy were
performed and samples collected 1, 6 and 24 h post-irradiation. Corroboration of the NGS results
with RT-qPCR verification confirmed the identification of numerous radiation-induced miRNA
expression changes at all doses assessed. Further evaluation of select radiation induced miRNAs
including miR-1228-3p and miR-758-5p, as well as their downstream mRNA targets UBE2D2,
PPP2R2D and ID2 demonstrated significantly dysregulated reciprocal expression patterns. In
order to explore the miRNA profile in a sub-background ultra-low dose radiation (ULDR)
environment, the CGL1 cells were grown in the underground SNOLAB laboratory in a
specialized tissue culture incubator (STCI) designed to lower natural background radiation by a
27-fold difference relative to surface. Here, the cells were grown in the ULDR environment and
natural background radiation (NBR) controls for a period of three months. Total RNA was
periodically extracted to assess miRNA expression levels. Here, miR-502-3p was significantly
upregulated in CGL1 cells cultured in the ULDR environment compared to the NBR control cells. Taken together, this study has identified novel radiation induced miRNA biomarkers at
various radiation dose ranges, spanning from ULDR, LDR (10 and 100 mGy) and high dose (1
Gy) radiation exposures. Further evaluation is needed to determine whether the candidate
miRNA biomarkers identified from this study can serve as suitable targets for radiation
biodosimetry applications.Master of Science (MSc) in Chemical Science
Machine reading comprehension to answer COVID19 queries using Bio-Bert and multi-task learning
No full textIn recent years, with the development of artificial intelligence technology in many fields, the
question-answering system has brought significant change to knowledge acquisition
mechanism. The question-answering system based on machine reading comprehension can
obtain short and accurate answers compared with the traditional retrieval question-answering
system. This thesis designs an intelligent question-answering method based on information
retrieval and multi-document machine reading comprehension. Firstly, a two-stage information
retrieval recall strategy is designed. After the information retrieval by using Bm 25, a structure
called Dual Bio-Bert Retrieval is designed, which uses two Bio-Bert to extract semantic
features in questions and paragraphs respectively in the training stage. Then, the information
between the two Bio-Bert is interacted by utilizing Performer. At the reading comprehension
stage, an additional method—Matching Tech is designed to improve the model. Compared
with other common methods, the results of the information retrieval and reading
comprehension shows that the models designed in this research have good performance.Master of Science (MSc) in Computational Scienc
Design enabled: the everyday refuge for a neuro-inclusive city
No full textOne of the most pressing issues within
the built environment is the ever-evolving
conversation of accessibility and its relationship
to obsolete building standards from the past.
Standards such as the Ontario Building Code and
the Accessibility for Ontarians with Disabilities
Act (AODA) provide insufficient solutions to users
with invisible disabilities, particularly the underrecognized realm of neurodiversity. This thesis
explores the possibility for a new set of design
guidelines, adopting principles to enable the
users’ senses and, in turn, create a neuro-inclusive
environment. It also presents the design of a neuroinclusive library centre with a secondary urban
park to mitigate the challenges neurodivergents
experience at both a human and city-wide scale.
By designing a community-oriented project within
the already-established arts and cultural hub of
downtown Sudbury, this thesis creates a network
of inclusive, user-centered, and sensorial design
that can begin to decode the issue of accessibilityMaster of Architecture (M.Arch
The impact of finance and political ideology on income inequality: empirical analyses
Get PDFIn order to better understand how finance causes income inequality and to comprehend the
ontology of this relationship, I started the ‘minor’ part of this thesis with the fundamental
assumption that the knowledge sphere exists independently of our knowledge and regardless of
personal subjective experience.
The overall (minor plus major) objective of this thesis is to gain a better understanding of the
relationship between finance and income inequality. To achieve this objective, I examine both
the theoretical and a large empirical literature on the subject. At the level of theory, the thesis
combines the orthodox and heterodox mechanisms through which finance generates income
inequality in modern capitalist countries. Empirically, the thesis develops a Dynamic Panel
Autoregressive Distributed Lag (ARDL) model that controls for indicators of globalization,
rising monopoly power, business cycles, and other variables in an attempt to isolate the unbiased
causal effects of financial variables on income inequality.
I estimate the ARDL model against two-panel datasets. I use the first dataset (48 countries from
1993 to 2017) to study how financial development, financial liberalization, and financial
structure affect the Gini- measure income inequality across high, middle, and low-income
countries. I employ the second dataset (14 OECD countries from 1980 to 2017) to study the
long-run effects of financialization and neoliberalism on several alternative measures of income
inequality across countries classified as neoliberal (the United States, the United Kingdom,
Canada, and Australia); Nordic (Denmark, Finland, Sweden, and Norway) and social-corporatist
(France and Germany).
The primary finding of this research is that financial indicator variables exert a significant effect
on income inequality in the long run across high, middle, and low-income countries.
Second, countries with a more market-based financial structure promote more equitable income
distribution, while countries with faster growth tend to generate greater income disparity. Third,
increased trade openness leads to increased income disparity, while lower competition helps to reduce inequality. Our evidence does not support the inverted “U-shape” theory1 concerning
financial development and income inequality. Finally, neoliberalism and financialization have
increased disposable income disparity in the upper-tail and the lower-tail of income distribution
within countries.Doctor of Philosophy (Ph.D.) in Human Studie
Transcriptome and methylome analysis of trembling aspen (Populus tremuloides) under nickel stress.
No full textNickel is an essential micronutrient required at low concentrations for adequate plant growth and
health. However, excessive amounts of bioavailable nickel ions in the surrounding soil can result
in plant toxicity symptoms. Plants have evolved heavy metal tolerance mechanisms to adapt and
cope with this abiotic stressor. The main objectives of the present research were to 1) further
characterize the P. tremuloides transcriptome 2) compare gene expression dynamics between
nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT)
sequencing, 3) determine the effects of different nickel concentrations on P. tremuloides gene
expression and, 4) assess global methylation levels in P. tremuloides under nickel stress.
Trembling aspen (Populus tremuloides) seedlings treated with varying concentrations of nickel
nitrates (150 mg Ni / 1 kg of dry soil, 800 mg / kg, and 1, 600 mg / kg) showed phenotypic
segregation of physical toxicity symptoms at the highest nickel dose of 1, 600 mg / kg. This study
revealed that a metal transport protein (Potrs038704g29436 – ATOX1-related copper transport)
was among the top upregulated genes in resistant genotypes when compared to susceptible plants.
Other upregulated genes associated with abiotic stress were identified including a Dirigent Protein
10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar
transporter, and thiamine thiazole synthase. Overall, an upregulation in ribosomal and translation
activities was identified as the main response to Ni toxicity in the resistant plants. The results of
the dosage analysis suggested that the 800 mg / kg nickel dose is the threshold at which an early
abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two
calcium binding proteins when compared to water. The cluster of genes that had increased gene
expression with increasing nickel dose also had multiple enriched GO terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal
activity.
Lastly, the initial screen for potential global methylation differences between nickel-resistant
genotypes and water showed no significant difference in overall methylation levels. However, the
potassium nitrate control for the 1,600 mg / kg dose did show significantl hypomethylation in
comparison to the nickel-treated or water control samples. Future experiments could use targetspecific methylation and gene expression assays to investigate the biological significance of the
heavy metal stress candidate genes identified in this top-down study in trembling aspen.
Understanding the heavy metal tolerance mechanisms and responses used by hardy species like
trembling aspen is important for environment bioremediation and maintenance of healthy
ecosystems.Doctorate (PhD) in Biomolecular Science
16N calibration and background studies for SNO+
No full textSNO+ is a multipurpose scintillator based neutrino experiment which is located 2km underground at SNOLAB, Creighton mine, Sudbury. The primary physics goal of the experiment
is the search for the elusive process of neutrino-less double beta decay with 130Te loaded
into the liquid scintillator cocktail. In addition, SNO+ will be able to detect low energy
solar neutrinos, geo- and reactor-antineutrinos, as well as supernova neutrinos. SNO+ has
completed its water phase in 2019. During the water phase SNO+ made measurements
of 8B neutrinos, and improved the limits on the lifetime of nucleon decay. Aside from the
physics goals, the optical and energy calibration of the detector was accomplished in water
phase. SNO+ has finished filling the detector in May 2022, and preparing for the 130Te
phase.
This thesis consists of author’s major contributions to the experiment: i) calibration analysis described in chapter 7, and ii) the background analyses discussed in chapter 6 and
chapter 7.
Chapter 5 focuses on the calibration of SNO+ detector using 16N calibration source. The
tagged 6.1 MeV γ’s from 16N provided the primary energy calibration data in the water
phase. Furthermore, the source was deployed externally throughout the scintillator filling
process, and the data was used for various calibration purposes such as studying the scintillation light yield, verifying the reconstruction algorithms, characterizing the scintillation
timing, and studying the Cherenkov signal in liquid scintillator.
The second part of my analysis focuses on background analyses in SNO+. Chapter 6 describes a model that I have used to estimate the effective attenuation length of the detector
in scintillator phase. The model was used to fit the tagged 214Po events in scintillator phase,
and estimate the effective attenuation length. The result is consistent with other studies. Moreover, chapter 7 focuses on the external backgrounds. A set of timing and angular classifiers have been developed, and originally optimised to distinguish the external backgrounds
from 0νββ signal. I have utilised these classifiers to investigate their performance for the
detectable solar ν signals. The classifiers found effective, however it is demonstrated that
the performance can be significantly improved by taking advantage of supervised learning
methods. ROOT TMVA was used for this classification study. Furthermore, I have used the
partial-fill scintillator data to estimate the level of the external backgrounds. The 2.6 MeV
γ signal from the external 208Tl is identified in partial-fill. Furthermore, the level of external 208Tl γ’s from the hold-down ropes are estimated by taking advantage of their angular
symmetry. The estimated result is consistent with previous measurements taken in water
phase.
Moreover, I have used the vertical displacements of the AV to estimate the creep rate of
the hold-down rope system during the partial-fill period. This analysis is described in appendix A. Furthermore, the long-term stability tests of the Tensylon fibres are described
in the second part of appendix A. Finally, the leaching model is briefly described in appendix B. I have developed this model as part of my MSc. research. During my first year of
Ph.D, I had the chance to complete the model and develop a simple python tool to estimate
the surface activity, and the level of leached isotopes for different filling scenarios.Doctor of Philosophy (PhD) in Material Science
Microbiota and species conservation: drivers of gut microbial communities variation in the context of captive breeding programs
No full textIn this PhD study, I investigated two broad classes of drivers of gut microbial communities’
variation in threatened species under conservation breeding programs. Firstly, heritable
drivers are potentially not reversible, or if so, over multiple host generations and therefore
operate at long-term scales. Second, immediate drivers could induce variation in microbial
community composition in a reversible manner and at the individual level of the host. I
hypothesized that host genotype and birth location are heritable drivers, and host diet,
biology (such as hibernation) and environment (captivity and geography) are short-term
immediate drivers.Doctor of Philosophy (PhD) in Boreal Ecology and Doctor (PhD) in Science
Set for success: ecological factors facilitating restoration of self-sustaining Lake Trout (Salvelinus namaycush) populations in acid-damaged lakes
No full textSudbury, Ontario, Canada is a site of extreme biodiversity loss due to widespread
acidification from over a century of metal mining and smelting. Lake trout (Salvelinus
namaycush) were the most widely and severely impacted of the resident sportfish but with
massive emission reduction in recent years, their populations have since shown significant signs
of recovery. The objective of my study was to identify conditions associated with lake trout
recolonization and recruitment by conducting fish and water quality surveys on 31 oncedamaged lakes across Sudbury’s historic acid deposition zone. Lake trout biomass and odds of
lake trout recruitment success increased in lakes with more depth of usable lake trout habitat,
higher zooplankton biomass and a lower concentration of dissolved organic carbon. A history of
hatchery stocking of lake trout was a top predictor of total lake trout biomass in standardized
gillnet surveys but did not emerge in top models for predicting natural recruitment or the total
biomass of natural lake trout in the lake.
These results demonstrate the importance of lake-specific ecological factors in the
reestablishment of lake trout populations, regardless of whether the source of the population was
hatchery stocking, migration from neighbouring lakes or residual populations that survived
acidification. Overall, my study shows evidence that Sudbury’s historically damaged lakes have
been extensively recolonized and are no longer limited by acidic conditions. In many cases, they
have shifted to simplified fish communities in which zooplankton may be a primary prey source
for lake trout. Water chemistry factors, in particular the increase in concentration of dissolved
organic carbon and the associated decrease in water clarity also emerged as potential factors
shaping lake trout recovery in my study lakes.(MSc) in Biolog