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Improved prediction of gene expression of epigenomics data of lung cancer using machine learning and deep learning models
Get PDFEpigenetics is the study of biological mechanisms that will switch genes on and off, its
alterations are deeply involved in the change of gene expression among various diseases
including cancers. Machine learning is frequently used in cancer diagnosis and
detection. In this research, four types of data are used towards the correct prediction of
lung cancer, including DNA Methylation data, Histone data, Human Genome data, and
RNA-Seq data. Four feature selection methods - ReliefF, Gain Ratio (GR), Principle
Component Analysis (PCA), Correlation-based feature selection (CFS) and seven
different classifiers - Random Forest (RF), Support Vector Machine (SVM) with
Gaussian Kernel function and Linear Kernel function, Logistic Regression (LR), Naive
Bayes (NB), Artificial Neural Network, and Convolutional Neural Network (CNN)
were implemented in this study. The processing of these data sets is done using custom
R-script. The tools that were used for feature selection and classification in the
presented work are Weka 3 and Python. With the help of machine learning and deep
learning methods, we were able to improve the accuracy and area under the curve (AUC)
of the lung cancer prediction from an earlier published work. It was observed that the
CNN model overperformed the other six classification methods
The protective role of hydrogen sulfide from obesity-associated metabolic stress in GLP-1 regulation
Get PDFCirculating palmitic acid (PA) and glycated albumin (GA) are increased in obesity and cause
metabolic stress leading to diabetes. This includes the impairment of the glucoregulatory
hormone glucagon-like peptide-1 (GLP-1) secreted from intestinal L-cells. Recently, the
gasotransmitter hydrogen sulfide (H2S) has been implicated in the enhancement of GLP-1
secretion. We hypothesized that H2S can reduce the oxidative stress caused by PA and GA, and
play a protective role in L-cell function. In mouse and human L-cell models, PA and GA caused
an increase in reactive oxygen species (ROS). The H2S donor GYY4137 partially blocked PA-
ROS induction. In mice, PA-enriched Western diet (WD) elevated body weight in both sexes and
elevated fasting blood glucose and lipid peroxidation in males. A single GYY4137 injection
improved oral glucose tolerance in WD-fed male mice and also enhanced glucose-stimulated
GLP-1 release. To conclude, H2S reduces oxidative stress in GLP-1 cells and can improve
glucose clearance in mice
Emplacement history of mafic-ultramafic volcanic rocks in the northern Pontiac subprovince, Quebec, Canada
No full textDetailed geological mapping of volcanic, sedimentary and intrusive rocks in the northern Pontiac subprovince of the Superior Province has identified multiple volcanic-sedimentary contacts at the margins of a 30 km long volcanic package of high-Fe tholeiites and Munro- to Barbertontype komatiitic flows and sills. Breccias displaying blocky, globular and tendril-like juvenile clasts in a massive sedimentary matrix were observed along the contacts of mafic-ultramafic intrusions with their host sedimentary rocks. These textures are consistent with peperite, a rock formed by the mixing and mingling of magma with wet, unconsolidated sediments. Geochemical data for one of the peperites indicates that the igneous component has a similar trace element composition to spinifex-bearing komatiite flows and the sedimentary component has a similar composition to the Pontiac Group wackes. Additionally, conformable unstrained contacts were observed between effusive volcanic rocks and turbiditic wackes. These relationships indicate a previously unrecognized ca. 2682 Ma mafic and ultramafic volcanic event synchronous with the deposition of the Pontiac subprovince sedimentary rocks. This suggests that the mafic-ultramafic volcanic package is synsedimentary and autochthonous, which
is not consistent with previous interpretations of these rocks as structural thrust panels. We propose that the mafic-ultramafic volcanic package was emplaced during a previously unrecognized plume-related extensional event that facilitated the upward flow of mantle-derived magmas along major, mantle-penetrating structures during Pontiac sedimentation. Shortly after, tectonic compression folded and imbricated the Pontiac rocks and accreted them to the southern margin of the Abitibi subprovince
High-fat diet-induced loss of muramyl dipeptide sensitivity
No full textGlucagon-like peptide-1 (GLP-1) is an insulin-stimulating hormone released from
enteroendocrine cells. Muramyl dipeptide (MDP) is a peptidoglycan motif which has insulin-
sensitizing effects in obesogenic mice by acting through the nucleotide oligomerization domain 2
(NOD2) receptor. We hypothesized that MDP enhances glucose tolerance by inducing intestinal
GLP-1 secretion through NOD2 activation. We observed a significant increase in GLP-1
secretion when L-cells were treated with a fatty acid MDP derivative (L18-MDP). Additionally,
we demonstrated NOD2 expression in mouse intestine and in L-cells. Two intraperitoneal
injections of MDP (5mg/kg) significantly increased fasting total GLP-1 in chow-fed mice; an
effect that was lost during the onset of hyperglycemia during a high-fat diet. No improvement in
oral glucose tolerance was observed in MDP-treated mice. Finally, we demonstrated in L-cells
that hyperglycemic conditions reduce NOD2 and GLP-1 mRNA expression. Together these
findings suggest MDP may play a role in enhancing GLP-1 during euglycemia but loses its
ability to do so in hyperglycemia
Mitigating the impacts of the First Nation water crisis in Ontario using Indigenous approaches
No full textThe purpose of this study is to speak with First Nation community members across Ontario to
assess how they’ve been impacted by water insecurity and to share their perspectives on potential
solutions and recommendations. While several reports and studies have been conducted over the
past two decades by both levels of government, Indigenous and non-Indigenous organizations and
individuals, little progress has been made toward achieving water security for First Nations. The
research question for this thesis is what are Indigenous peoples saying about solutions to their
water insecurity challenges
Twitter sentiment analysis of the 2019 Indian election
No full textWith easily available internet services in India and the rest of the world in the recent past,
there is more and more traction towards social media like Facebook, Twitter, Instagram,
YouTube, etc. This has enabled individuals the freedom of speech and to display their
sentiments and emotions towards society. Social media has brought people closer than ever
before and has provided a common platform for individuals to communicate. Some
influencers promote products on social media platforms, while politicians run their
campaigns online for broader reach. Social media has become the fuel for globalization. In
2019, the Indian Lok Sabha Elections saw around 360 million tweets on Twitter, giving their
opinions and showing their sentiment towards the political leaders and their parties.
Sentiment analysis is the computational investigation of opinions, evaluations, views, and
feelings expressed in a text. The political parties have used this technique to run their
campaigns and understand the opinions of the public. This also enables them to modify their
campaigns accordingly. In this research text mining was performed on approximately
200,000 thousand tweets collected over four months that referenced four national political
parties in India during the campaigning period for the Lok Sabha elections in 2019. The
sentiments of Twitter users were identified towards each of the considered Indian political
parties, Congress, Bhartiya Janata Party (BJP), Aam Aadmi Party (AAP) and Bahujan Samaj
Party (BSP) using VADER (Valence Aware Dictionary and sEntiment Reasoner). A lexicon
and rule-based sentiment analysis engine was created that is the principal platform to evaluate
the opinions expressed in social media. The results of the analysis show that Bhartiya Janata
Party (BJP) being a lead runner in the elections of 2019 received more positive intent and
emotions towards their campaigns and their leader Narendra Modi as compared to the other
parties and their leaders
New methods for the interpolation and interpretation of lineaments in aeromagnetic data
No full textAeromagnetic data is one of the most widely collected types of geophysical data. In mineral
exploration it can assist in mapping geological features, as well as indicate potential locations of
economic interest. Due to the method in which aeromagnetic surveys are flown, an interpolation
process must be completed before any map-based interpretation can be accomplished. One
artifact common to many interpolation methods is that of “beading”, which is a discontinuous
sequence of circular magnetic features that are at acute angles to the traverses, often caused by
thin, linear geologic features such as dykes. Developing an interpolation method that “trends” or
images these beads as continuous features on magnetic images would allow automatic and
reliable quantitative methods to be used for interpretation by geologists and geophysicists. First, a new interpolation method was developed for aeromagnetic data. Utilizing a Taylor
derivative expansion and structure tensors, it iteratively enhances trends evident across flight
lines to manifest as linear features on the interpolated grid. When applied to both synthetic data
and field data, the new method showed improvement over standard bidirectional gridding,
minimum curvature, and kriging methods for interpolating thin, linear features at acute angles to the flight lines .Following this, a machine-learning interpolation approach was developed for aeromagnetic data
using support vector machines and random forests. By using multiple standard interpolation
methods as input to the machine-learning models, a filter-like approach was developed. These
models could produce aeromagnetic maps that were overall more accurate than any single
interpolation method, but not as effective as the Taylor derivative expansion method on lineament features. Finally, convolution neural networks were applied to estimate the source parameters
characterizing lineament anomalies. A synthetic aeromagnetic data modeler was used to vary
relevant physical parameters, and a representative dataset of approximately 1.4 million images
was developed. These were then used for training convolution neural networks to estimate the
strike and depth of sources. Applying the trained networks to a real-world dataset that was
interpolated by the Taylor derivative expansion method, they located a dyke and estimated a depth consistent with a previous borehole investigation
Effects of nickel toxicity on expression of genes associated with nickel resistance in white spruce (Picea glauca): Nickel translocation in plant tissues.
Get PDFThe main objectives of this study were to determine a) nickel accumulation and
translocation within tissues and b) nickel effects on gene expression in white spruce (Picea
glauca). The results of the study revealed that even at the highest dose of 1,600 mg of Ni /kg of
soil, there was no physical evidence of toxicity to P. glauca seedlings screened. P. glauca was
found to be a nickel avoider, as the bioaccumulation factor as well as translocation factors for
roots to aerial tissues were less than 1.0. Expression of SAT, GR, ACC, NAS, Nramp, and
AT2G16800 genes in roots and needles were investigated. Expression of ACC and NRAMP were
upregulated in the presence of nickel, whereas GR was downregulated at the lowest dose (150
mg/kg) and upregulated at the highest dose (1,600 mg/kg). There were significant differences
between ACC expression in roots and needles. The results of the present study also show that
that potassium nitrate (a common plant fertilizer) does have an effect on gene expression and can
lead to toxicity in P. glauca plants at high concentrations. Overall, the findings of this research
suggest that the low level of bioavailable nickel in mining sites in Northern Ontario and other
mining regions can trigger changes in gene expression
Auditor professional skepticism – a cross-cultural study in the global International Financial Reporting Standards environment: the case of Canada and Brazil
Get PDFThe global financial reporting environment is undergoing significant change, with a
global trend toward more countries adopting the International Financial Reporting Standards for
public companies. Concerns exist as to potential barriers to harmonization, such as culture;
therefore, it is important to draw on institutional mechanisms, such as auditing, to encourage
compliance and harmonization. With this, there is a need to better understand the factors
affecting the quality of such audits. Auditors’ professional skepticism is a key factor in ensuring
audit quality.
This exploratory quantitative study explores an area that is not well researched:
specifically, the cross-cultural professional skepticism of auditors. Through a correlational
design, the study provides insights as to whether auditors from different cultures make different
skeptical judgments and decisions. This study also investigates whether prior research linking
skeptical traits to increased professional skepticism in auditors is exportable from one culture to
another. The major finding of this study is that there is no significant difference in the
professionally skeptical judgments and decisions of entry-level auditors from Canada and Brazil.
Culture is not associated with the professional skepticism of these auditors. The study also
highlights that skepticism, as a trait does not correlate with professional skepticism of auditors
across all cultures, specifically in Canada and Brazil.
This study fills a major void in the literature concerning the study of cross-cultural
professional skepticism and it extends prior research regarding the associations between
skepticism as a trait and auditors’ professional skepticism by investigating auditors from two
very different cultures. This study provides insights that are relevant to practitioners such as regulators, auditors and auditing firms, as well as academics in auditing, accounting, psychology
and cultural studies
Going back to the Lodge: an architectural exploration of Haliburton cottage culture.
No full textNew buildings designed by architects can
sometimes be described as cold. Whereas a
cabin in the woods that has been in families
for generations, built by grandparents, can be
described as warm. What is it about ‘Cottages’ of the past that creates this architectural
feeling?
The idea of the ‘cottage’ versus the ‘home’
has become conflated; there is no longer a
separation of these two experiences. ‘Cottage’ and ‘home’ have essentially become the
same structure in a different environment as
we build more and more ‘permanent’ ‘cottages’.
The change is that new families are beginning
to downsize. First, there is the tiny house
movement, and then the trend noticed in
Haliburton, of young families renting a ‘home’
near their place of work, but owning a
‘cottage’ outside of the cit