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PPISHES - An Enhanced Physicochemical Approach For Predicting Protein Interaction Sites Using Graph Neural Networks
No full textAccurate prediction of protein interaction sites is key to understanding underlying mechanisms of many biological processes. Most state-of-the-art methods for prediction of protein interaction sites accomplish this task by leveraging sequence features and incorporating spatial neighborhood information. Some methods capture local and global structural, evolutionary, and sequence-based features; however, they overlook physicochemical properties that are crucial in protein interactions and struggle with feature redundancy, which limits their overall performance. By addressing these gaps, we aim to enhance the predictive power of graph neural networks and introduce new feature sets that significantly improve the model's performance. We propose an enhanced model, called Prediction of Protein Interaction Sites based on Solvent Accessible Surface Area, Hydrogen-Bonding Propensity, and Electrostatic Potential Sites (PPISHES), which is built upon incorporating three fundamental physicochemical features—electrostatic potential, hydrogen-bonding propensity, and solvent-accessible-surface-area—to, used to enrich the feature representation of protein structure, and thereby improving site prediction for both obligate and non-obligate complexes. To enhance interpretability and feature selection, we applied feature ablation analysis, systematically masking individual features and identifying the most important features of the model. We evaluated PPISHES on widely-used benchmark datasets, achieving a substantial improvement in the Area Under the Precision-Recall Curve (AUPRC), with increases of up to 42.8% and 29.3% for Test_315 and Test_71 respectively. PPISHES was also evaluated on key metrics including accuracy, precision, recall, area under the curve, and Matthews correlation coefficient, confirming its superior overall performance and surpassing current state-of-the-art
Great Lakes Focus on Water Quality: vol.4 iss.1
No full textOn April 27, Robert J. Sugarman was sworn in as a new Commissioner of the International Joint Commission. He has succeeded Henry P. Smith, lll, as Chairman of the United States Section, following Mr. Smith's recent resignation. Mr. Sugarman is a graduate of Harvard Law School, Stanford University (History) and Brown University (Classics). He is a partner in the Philadelphia law firm of Dechert, Price and Rhodes and on the Legal Advisory Committee of the Environmental Defense Fund
Focus on International Joint Commission Activities (ISSN 0832-6673): vol.19 iss.3
No full textEnlightened public opinion ultimately set things right in the Reserve Mining case. Following US. District Judge Miles Lord’s order of April 20, 1974 to cease all taconite tailings discharge to Lake Superior, it took much additional effort by the State of Minnesota, intervening environmental groups and the US. Government to stop the 25-year dumping of hundreds of millions of tons of tailings into the world’s fresh- water treasure. It finally happened in the spring of 198
SALing the OCEAN Blue: A Systematic Literature Review of Student Approaches to Learning and Big Five Personality Traits
No full textKeywords: personality; approaches to learning; educational psychology; Big Five; R-SPQ-2F Student approaches to learning (SAL) are a measure of a student’s perception of the learning environment (Biggs et al., 2001). Meanwhile in personality psychology, the Big Five personality traits (i.e., openness, conscientiousness, extroversion, agreeableness, and neuroticism) have been used extensively to characterize trends in human behavior (Costa & McRae, 1992). These two complementary measures can tell us a lot about a student, but together, are underexplored. The purpose of our research is to understand the relationships between student approaches to learning and the Big Five personality traits. We conducted a systematic literature review (SLR) using keyword database searches of ProQuest and APA Psycnet, which after applying specific criteria, led to a pool of 26 studies for analysis. We tracked the relationships between SAL and Big Five in each of the 26 studies. We identified that openness, extraversion, and conscientiousness were significantly positively correlated with the deep approach, while neuroticism was significantly positively correlated with the surface approach. Conversely, neuroticism was significantly negatively correlated with the deep approach, and openness, agreeableness, and conscientiousness were significantly negatively correlated with the surface approach. In short, students may be partially drawn to a specific approach based on their personality. This project fits the open challenge because it looks beyond specific designated groups of learners. SAL and Big Five are theories that affect human behavior beyond the context of the other grand challenges. We see this work as interdisciplinary and of importance to anyone interested in knowing more about how students approach their learning
Stalin’s Foreign Policy “Shift”: Cautious Expansionism, USSR-DPRK Relations 1945 – 1950 and the Origins of the Korean War
Get PDFDespite initially denying Kim IL Sung’s requests for a military reunification in 1949, Josef Stalin decided to support an invasion of South Korea in 1950. This paper explores the origins of the Korean War and the roles of both the Soviet Civil Administration and Kim IL Sung in convincing Stalin that the invasion was necessary, and that it would be neither prolonged, nor involve American interference. Throughout the initial occupation of North Korea, Stalin preferred to maintain the status quo on the peninsula, as he was open to, but deeply suspicious of plans for reunification and restrained Kim’s ambitions. However, both the SCA and Kim manipulated Stalin and played off both his fears of a southern led invasion, and potentially losing a communist ally to China. By 1949 Stalin had already been convinced by them of the necessity for a military reunification and cautiously approved Kim’s plans
"In the Name of Progress": Postwar Urban Renewal and the Razing of Black Spaces in Windsor, Ontario, 1957-1980
Get PDFIn the mid-1950s, Windsor, Ontario embarked on a comprehensive fifteen-year urban renewal initiative aimed at redeveloping the city’s downtown core into a modern, municipal hub and locale for both private and commercial interests and cross-border tourism. The initial focus of this strategy was a neighbourhood situated just east of the commercial district, which had been home to much of the Windsor’s Black population for more than a century. Rooted in a complex interplay of social and economic factors, Windsor’s renewal efforts, guided by a misguided, paternalistic understanding of physical transformation as a catalyst for positive social change, resulted in the demolition of significant physical and cultural spaces, fundamentally altering the character and landscape of this community. Furthermore, a reliance on external experts coupled with minimal community consultation further alienated and marginalised Windsor's Black population, depriving them of agency in the renewal process. Through a meticulous examination of redevelopment records, community archives, and oral histories, this study explores the transformative consequences of redevelopment on Windsor's Black community. This paper will demonstrate how the loss of the community’s physical spaces not only disrupted intricate kinship networks, cultural practices, and economic structures, but also obscured their visibility as one of the city's oldest and most resilient communities
Design and Synthesis of New Ligands for the Preparation of Amphiphilic Nanoparticles
No full textThe aim of my thesis is to synthesize new hydrophobic and hydrophilic ligands in preparation of a novel amphiphilic nanoparticle in a feasible and cost effective manner, and to examine their self-organizing properties
Unorthodox Orthodoxy: Why There is no "Right" Way to do Religion
No full textCritical Reflections Submission 2018
"Unorthodox Orthodoxy: Why There is no 'Right' Way to do Religion"
By: Ashley Ruby, B.A. (Religious Studies)
Candidate: Master of Philosophy (Humanities) - Memorial University of Newfoundland
An integral branch of philosophy is that of philosophical theology, a branch both heavily contributed to, and hotly contested by philosophers and clergy for millennia. Many religious leaders have exclaimed that the use of philosophical thinking in theology leads to corrupt beliefs and practices while others, such as Augustine, have argued that a via-media approach to theology and philosophy can be both useful and non-heretical. These arguments themselves have continued for thousands of years, the philosophical side demanding logic while the religious side demanding faith, proclaiming that applying logic to an illogical God would lead to chaos, encourage doubt, and bring about unorthodoxy en masse.
The term "orthodoxy," in Christian theology, refers to "right" or "correct" belief. By this definition, we can assume that a Christian who considers themselves to be orthodox is one who believes, unwaveringly, in the set of beliefs articulated for them by their church or other governing religious body. Orthodoxy and orthopraxy are sometimes convoluted into one, with the former referring solely to belief while the latter defines physical practices such as prayer and ritual. For the purposes of this argument, this paper will focus on orthodoxy alone.
The idea that one belief pertaining to an untouchable, un-seeable, long-silent God can be labelled as "right" while another is wrong is widely held, despite the fact that both scripture and doctrine are scribed by mortal hands. This concept of orthodoxy permeates history to the point that Jesus himself was executed on charges of radical unorthodoxy (blasphemy and sedition). Though a far-reaching and ancient concept, this paper aims to argue that the concept of orthodoxy, of dictated right and wrong beliefs, is completely non-existent.
This research supports its claim using methods of philosophical theology as well as the lack of scriptural support for many Christian rituals and practices (such as the Holy Rosary), lack of coherence among books, verses, authors, and translations of the Holy Bible, and the fact that God himself has had no say in any of these matters to begin with, with the last instance of God directly and verbally interacting with a human occurring in the Old Testament. This paper will attempt to make orthodoxy, as a term to be applied universally, obsolete, and instead solidify the true essence of orthodoxy, which is in reality a personal and unique pattern of belief for each and every human being.
In short, orthodoxy is not something that can be spelled out by one person to be obeyed by all persons, but something that exists only between the individual and God, and that individual, unwritten, doctrine that God has inscribed on the heart of each person is different, for Christians and non-Christians alike. God is universal and yet personal. As such, the concept of orthodoxy is abstract and impossible to define in a universal sense. The concept simply does not exist.
Key Words: Theology, Philosophical theology, Orthodoxy, Biblical studies, Source criticism, Augustine, Justin Marty
Role of Autophagy Inhibition in Development of Alzheimer's Disease: Resumption of Autophagy Leads to Neuronal Survival
No full textViable, Healthy and Safe CommunitiesAlzheimer's Disease (AD) is the most common neurodegenerative disorder associated with impaired memory, affecting 48 million people worldwide. Currently, the only treatments available are for symptomatic relief, rather than inhibiting its progression. The possible biochemical reasons for AD pathologies are inflammation, mitochondrial dysfunction, increased oxidative stress, and inhibition of autophagy. Autophagy is the cell's mechanism for removing defective proteins and organelles; however, the role of autophagy in AD is not well understood. It has been shown that Ubisol-Q10 (water-soluble formulation of coenzyme-Q10) stabilizes mitochondria and reduces oxidative stress. This results in the inhibition of premature aging (senescence) in fibroblasts from Alzheimer's disease (AD) patients with the presenilin-1 (PS-1) mutation. This PS-1 mutation leads to the build-up of defective proteins including amyloid-beta plaques which can induce oxidative stress and mitochondrial destabilization. Since Ubisol-Q10 was shown to reduce these AD pathologies, it was hypothesized that it may lead to the resumption of autophagy in AD fibroblasts. Through gene expression analysis, we observed that Ubisol-Q10 resulted in the upregulation of autophagy related genes at the mRNA level. We have also confirmed the expression of these genes at the protein level using Western Blotting and immunofluorescence. Ubisol-Q10 treatment led to increased expression of autophagy genes in AD fibroblasts compared to untreated AD fibroblasts. The autophagy gene expression profile of Ubisol-Q10 treated AD cells was observed and was comparable to fibroblasts from healthy subjects. Ubisol-Q10 was shown to prevent the formation of amyloid-beta plaques in the brains of transgenic AD mice as well as improve their long term and spatial memory. To confirm the fibroblast model results are transferable to an in-vivo neuronal model, transgenic mouse brains were examined for upregulation of autophagy in Ubisol-Q10 treated mice. Indeed, there was activation of autophagy. Therefore, autophagy seems to play a key role in neuronal health and its inhibition can lead to Alzheimer's Disease. These results indicate that Ubisol-Q10 could be a potential therapeutic to ameliorate the progression of the disease