Digital Commons Network^™

Artificial Intelligence In Enzyme Engineering, Margret Pagare

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Review Of Protein-Protein Interaction Prediction Using Artificial Intelligence, Brian Ng

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Artificial Intelligence In Aptamer Design: Current Research In Machine Learning, Jennifer L. Matthews

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

How Ai Has Improved And Built Upon Previous Methods In Determining Protein Structures And Folding, Alexander J. Bulsiewicz

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

A Metadata Analysis Of Unionid Mussels Of The Greenup Pool Of The Ohio River Using Occupancy Modeling And Species Area Curves, Tyler Mitchell Annarino

Theses, Dissertations and Capstones

Although North America contains the largest diversity of freshwater mussels in the world, only ~24% of species in the United States and Canada have stable populations. This group provides unique hurdles for surveying, and current unionid survey protocols include neither longitudinal studies nor randomization of sites. This project conducts a metadata analysis of freshwater mussels in the Greenup Pool of the Ohio River (GPOR) to answer three questions: 1. Does a combination of longitudinal scope, randomization of sites, and historic methodology of surveying result in useful occupancy/detection models (ODMs) of unionids in large streams at the family level? 2. Does …

Biological And Chemical Evaluation Of Amide-Based Cjoc42 Derivatives As Potential Gankyrin-Inhibitors For The Treatment Of Breast, Lung, And Liver Cancer, Benita Britton-George

Theses and Dissertations

Gankyrin is an ankyrin-repeat protein overexpressed in certain cancers and is responsible for cell growth and proliferation. Gankyrin is important to the development of many types of cancer, including breast, lung, and liver cancer. Consequently, gankyrin and its various protein-protein interactions, are prospective therapeutic targets for inhibiting the progression of certain cancers. In 2016, the first small molecule inhibitor of gankyrin, cjoc42, was discovered and subsequently demonstrated modest antiproliferative activity against liver cancer cells. Previous work from our lab demonstrated that replacing the sulfonate ester of cjoc42 with an amide group significantly improved gankyrin binding while enhancing antiproliferative activity against …

Neural Congruency Contrastive Learning Framework Validation Using Artificially Created Eeg Data For Dyslexia Research, Jacqueline M. Torres

Theses and Dissertations

Analysis of electroencephalogram (EEG) recordings in children with dyslexia has been commonly used to explore the neural mechanisms underlying reading disorders. Yet, challenges such as low signal-to-noise ratio (SNR), high inter-subject and inter-trial variability, and the inherently multivariate nature of EEG signals hinder the isolation of neural components elicited during reading diagnostic tests. To mitigate these challenges, the neural-congruency analysis framework was recently proposed, leveraging traditional machine learning optimization methods to incorporate domain knowledge about the congruency of neural responses across participants (i.e., consistent neural responses among proficient readers). However, the application of deep learning techniques, specifically contrastive learning, remains …

Qualitative Analysis Via Network Models Of Human Dynamin-1 Throughout Gtp Hydrolysis, Kevin Brian Schulman

Theses and Dissertations

This thesis aims to elucidate the molecular mechanisms by which nucleotide binding dictates the intrinsic dynamics and to understand the functional conformational changes of Human Dynamin-1 during the GTP hydrolysis cycle through the use of Elastic Network Models (ENM). A comprehensive understanding of this process is crucial given dynamin's role in clathrin-mediated endocytosis (CME). The research utilized both experimentally derived crystal structures and AlphaFold-predicted structures of dynamin, specifically examining the GTPase and Bundle Signaling Element (BSE) domains across nucleotide-free, GTP-bound, GDP-bound, and transition states. The essential features of the research methodology involved a multi-scale computational approach. Qualitative analyses were performed …

Human Recreation Influences Activity Of A Large Carnivore In An Urban Landscape, E. C. Bolas, J. F. Benson, R. V. Blakey

School of Natural Resources: Faculty Publications

No abstract provided.

Northern Bobwhite Habitat Selection During The Nonbreeding Season In A Riparian Corridor In Colorado, J. M. Wolske, A. C. Behney, L. A. Powell

School of Natural Resources: Faculty Publications

No abstract provided.

Cold Atmospheric Plasma Induced Degradation Of Organophosphate Pesticides On Kevlar Swatches, Ta Chun Lin, Victor Somtochukwu Mbanugo, Boluwatife Stephen Ojo, Yue-Wern Huang, Marek Locmelis, Frank Daoru Han

Biological Sciences Faculty Research & Creative Works

Cold atmospheric plasma (CAP) was evaluated for degrading organophosphate pesticide (OP) residues (acephate, malathion, and dimethoate) from Kevlar fabrics. Fourier transform-Infrared (FTIR) spectroscopy, scanning electron microscope (SEM) imaging and tensile strength testing confirmed that CAP treatment preserved Kevlar's structural integrity and mechanical properties. Results show degradation efficiency increased with higher power, shorter discharge gaps, and longer exposure duration. Hyperspectral imaging supported the detection of plasma-induced spectral changes, reinforcing the presence of reactive species. The strong oxidative potential of CAP facilitated the rapid breakdown of OPs into nontoxic byproducts. These findings demonstrate the potential of CAP as a portable, energy-efficient solution …

Ca-Vqvae: Cortical Folding Aware Numerical Representation Of White-Matter Structure, Yanjun Lyu, Jing Zhang, Lu Zhang, Tong Chen, Xiaowei Yu, Minheng Chen, Yan Zhuang, Chao Cao, Tianming Liu, Dajiang Zhu

Computer Science Faculty Research & Creative Works

White matter (WM) serves as a fundamental component of the brain providing essential structural support and facilitating the brain cognitive processes. Thus, an accurate and efficient description of the brain's white matter structure is essential for understanding brain function connectivity and development. In this work we used the deep model to combine the information of the WM fiber bundle shape and its related cortical folding patterns together representing the WM fiber bundle from diffusion MRI tractography into a pre-defined low-dimensional space and generate the numerical representation vector. This cortical-aware vector-quantized variational encoder (CA-VQVAE) framework leverages cortical locations and folding patterns …

Classiffication Of Mild Cognitive Impairment Based On Dynamic Functional Connectivity Using Spatio-Temporal Transformer, Jing Zhang, Yanjun Lyu, Xiaowei Yu, Lu Zhang, Chao Cao, Tong Chen, Minheng Chen, Yan Zhuang, Tianming Liu, Dajiang Zhu

Computer Science Faculty Research & Creative Works

Dynamic functional connectivity (dFC) using resting-state functional magnetic resonance imaging (rs-fMRI) is an advanced technique for capturing the dynamic changes of neural activities and can be very useful in the studies of brain diseases such as Alzheimer's disease (AD). Yet, existing studies have not fully leveraged the sequential information embedded within dFC that can potentially provide valuable information when identifying brain conditions. In this paper, we propose a novel framework that jointly learns the embedding of both spatial and temporal information within dFC based on the transformer architecture. Specifically, we first construct dFC networks from rs-fMRI data through a sliding …

Thyroid Carcinoma Recurrence Prediction Using Artificial Intelligence On Prognosis Parameter, Supawat Suntornlimsiri

Chulalongkorn University Theses and Dissertations (Chula ETD)

Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid malignancy and is increasingly diagnosed worldwide. Although typically localised, PTC exhibits a notable risk of bilateral involvement, with contralateral disease occurring in up to 44 percent of cases. While completion thyroidectomy is recommended in selected high-risk scenarios, it carries potential complications, making accurate prediction of contralateral involvement essential. This study investigates the utility of classical statistical methods and machine learning (ML) algorithms—Support Vector Machines (SVM), Extreme Gradient Boosting (XGBoost), and Random Forest (RF)—in predicting contralateral PTC using a retrospective dataset of 122 lobectomy patients. ML models, especially RF with …

Immunofluorescence-Based Detection Of Myc–Egr1 Pathway Activity In P53-Deficient Human Colorectal Cancer Cells, Samantha E. Schultheiss, Lyndsea Skojec, Erick Spears Dr.

Science University Research Symposium (SURS)

Immunofluorescence-Based Detection of MYC–EGR1 Pathway Activity in p53-Deficient Human Colorectal Cancer Cells

The Wnt signaling pathway drives proliferation in the intestinal epithelium and maintains those cells in an undifferentiated state. Dysregulation of this pathway results in uncontrolled proliferation of the intestinal epithelium which can lead to colorectal cancer. These effects are driven by the expression of a common Wnt target gene, MYC. Upregulation of MYC expression by the Wnt signaling pathway, either during normal Wnt signaling or dysregulated Wnt signaling, canonically drives intestinal epithelial cells into a proliferative state. Under a specific cellular context, the loss of functional p53, MYC …

Exploring The Myc-Egr1 Pathway In Human Colorectal Cancer Cells, Jacob L. Dykstra Iii, Bishoy S. Sami, Dr. Erick Spears

Science University Research Symposium (SURS)

The WNT signaling pathway plays a crucial role in the regulation of cell growth and death in the intestinal epithelium and during colorectal carcinogenesis. In the presence of Wnt, MYC is upregulated, which leads to the proliferation of intestinal epithelial cells. Under certain cellular conditions, namely the loss of p53 function common to colorectal tumors, MYC upregulates the expression of the tumor suppressor EGR1, leading to apoptosis. This MYC-EGR1 pathway has been observed in p53-knockout mouse embryonic fibroblasts but has yet to be observed in human cells. These studies aim to assess the activity of the MYC-EGR1 pathway in human …

Restored Wetlands Show Rapid Vegetation Recovery And Substantial Surface-Water Expansion, Thilina D. Surasinghe, Yin-Hsuen Chen, Kunwar K. Singh

Center for Geospatial Science, Education & Analytics Faculty Publications

Ecological restoration is essential for improving the ecological integrity of degraded ecosystems to enhance ecosystem services and biodiversity. In this study, we assessed the effectiveness of wetland restoration on retired cranberry farms by analyzing vegetation recovery and surface-water dynamics using the enhanced vegetation index (EVI) and normalized difference water index (NDWI) derived from Sentinel-2 satellite imagery. To quantify temporal dynamics of both vegetation recovery and surface-water cover, we identified the spectral distinctions among restored wetland plant communities. Our results indicated the emergence of distinct plant communities upon restoration. Restored wetlands in general showed significant and progressive vegetation recovery and expanding …

Syntheses And Characterization Of Isomeric 3-Bromopropanol Capped Oligoviologens, Marcus Anthony White

Theses, Dissertations and Capstones

The work described in this thesis has generated new oligoviologen structures designed to facilitate the formation of supermolecules that incorporate photoactive and redox-active groups. These viologens have several potential uses; for example, the 4+ oligoviologen (viologen 5) exhibits solvatochromic properties in various polar protic and polar aprotic solvents, indicating suitability for use as a solvatochromic dye. The syntheses of bis(4,4’-bipyridine)ortho-xylene, bis(4,4’-bipyridine)meta-xylene, and bis(4,4’-bipyridine)para-xylene were demonstrated through ¹H NMR characterization and confirmed through literature. Bis(4,4’-bipyridine)ortho-xylene, bis(4,4’-bipyridine)meta-xylene, and bis(4,4’-bipyridine)para-xylene were produced in 68%, 72%, and 54% yields, respectively. 4,4’-Bipyridine-1-[4-(bromomethyl)phenylmethyl]-1’- …

Joanne Stubbe And The Mechanistic Study Of Ribonucleotide Reductases, Madysen York

Natural Sciences Student Research Presentations

To catalyze the formation of deoxyribonucleotides from ribonucleotides, the enzyme has to remove an hydroxyl from the ribose sugar part of the molecule (circled in in green) (“Ribonucleotide Reductase”).

The problem is that hydroxyl doesn’t naturally want to break from the base it is attached to, leaving many researchers unable to discern the chemical process going on inside these enzymes that make the bond break possible (Strauss).

Water’S Effect On The Decomposition Of Baptisia Australis, Jackson Whiteside, Adeline Beckham, Jeremy Little, Reese Cobb, Darlene Panvini

Science University Research Symposium (SURS)

Detritus, dead organic matter, is an essential part of nutrient cycling in Earth’s ecosystems. If dead organic matter could not be decomposed, dead matter would be amassed everywhere, and its nutrients could not be returned to the soil to nourish living species. Detritivores decompose this dead matter and return its nutrients to the soil. How quickly matter decomposes is influenced by a variety of abiotic factors. One abiotic factor which is of interest to decomposition is water quantity and frequency. This study aimed to test if Baptisia australis decomposes faster in dry or wet conditions. The expected results are that …

Potential Impacts Of Construction On Bat Populations In Warner Parks, Nashville, Tennessee, Jackson Whiteside, Wyatt Fooks, Jeremy Little

Science University Research Symposium (SURS)

Human development continues to alter natural landscapes, often with significant consequences for wildlife populations. Among the most sensitive taxa to such disturbances are bats, which serve vital ecological roles as insect predators, pollinators, and seed dispersers. Because bats depend on specific roosting and foraging habitats, even minor environmental changes can strongly influence their activity and diversity. A new road is proposed through an area of Warner Parks, Nashville, Tennessee which is otherwise untouched. This may affect the biodiversity and the populations of bats as a result. Wildlife Acoustic MiniBat 2 acoustic monitoring equipment was used to gather echolocation calls of …

Functionalizing Silver Nanoparticles With Histamine, Noah J. Deblanco

Science University Research Symposium (SURS)

Silver nanoparticles (AgNPs) are of increasing interest in biomedical research due to their antimicrobial properties, biocompatibility, and high surface-area-to-volume ratio. A major challenge, however, lies in stabilizing AgNPs under physiological conditions and understanding how their surface interactions influence potential medical applications. This project explores the synthesis of AgNPs using the Turkevich method and investigates their behavior when exposed to varying biological conditions, including changes in pH and temperature. In addition, preliminary efforts are being made to functionalize AgNPs with small biological signaling molecules to evaluate their effects on nanoparticle stability and surface interactions. Characterization is performed primarily through UV-Vis spectrophotometry, …

Effects Of In-Stream Large Woody Debris Management On Riparian Salamander Population Dynamics, Sydney Hermann

Theses, Dissertations and Capstones

The addition of large woody debris (LWD) into streams is an increasingly common habitat restoration method used to support brook trout populations and other sensitive freshwater species. Wood jams create localized reductions of water velocity, increase organic matter retention, intensify overbank flows, and promote habitat heterogeneity. These changes enhance interaction between the floodplain and the stream which can influence forest habitat variables such as leaf litter, soil pH, moisture, and invertebrate abundance. Salamander demographics reflect the stability of these forest habitat variables, and population declines can be indicative of environmental disturbance, stress, or change. Evaluating how this trout-targeted management effects …

Structural Impacts Of Canonical And Non-Canonical Oligonucleotide Modifications, Deepak Shrestha

Wayne State University Dissertations

Nucleic acids, including DNA (deoxyribonucleic acid) and RNA (ribonucleic acids), are the fundamental building blocks of living organisms. The events that cause modification of DNA/RNA are of interest because they impact the nucleic acid function. Targeting DNA is important for treating diseases such as cancer. Cisplatin (cisPt) is a well-studied drug that targets DNA and blocks replication, but its use is limited by adverse side effects and cellular resistance. Prevoius research addressed some of these challenges through development of platinum analogues such as carboplatin and oxaliplatin. Amino acid-linked platinum analogues (AAPt) are the focus of this thesis work. AAPt complexes …

Mass Spectrometry Combined With Chemical Biology To Study Human Ailments, Eric Thomas Jacquerio Davis

Wayne State University Dissertations

Post-translational modifications (PTMs) are essential as chemical changes that regulate protein function, activity, stability, interactions, and localization after protein synthesis. PTMs, such as phosphorylation, acetylation, and ubiquitination, can activate or deactivate proteins, influence their interactions with other molecules, and determine their cellular location. This regulation is vital for numerous biological processes, such as cell cycle control, signal transduction, and gene expression. Abnormal PTMs are linked to various diseases in humans, including parasitic infection, blood disorders, cancers, and neurodegenerative diseases, making their study crucial for understanding disease mechanisms and developing targeted therapies. In the Pflum lab, we are interested in the …

Data For Research Collaboration And Co-Authorship In The Gulf Of Mexico, 2000–2018, Owen Temby, Dongkyu Kim, Juliet Vallejo

Datasets

This dataset documents research collaboration and co-authorship among organizations engaged in environmental science in the Gulf of Mexico from 2000 to 2018. The data were compiled through bibliometric analysis of scientific articles, with each record containing publication-level and author affiliation information, as well as institutional and country codes. The dataset provides the basis for network analysis of collaborative patterns among institutions in the United States, Mexico, and Cuba. Variable definitions and data structure are described in the accompanying README file.

Centrality Algorithms For Weighted Homogeneous Multilayer Networks, Ayomide Ayowole-Obi

Computer Science and Engineering Theses - Archive

Applications need to be modeled for analyses. With the availability of many alternate data Models, choosing one needs to be done carefully by considering the complexity of data to be modeled and its analyses requirements. Social networks and other newer applications are primarily relationship-oriented and also have multiple types of entities and relationships. Although simple and attributed graphs have been used historically for modeling these applications, recently, multilayer networks (or MLNs) have been shown to be more effective in preserving the semantics of the application better and further provide flexibility of analyses. However, choice of MLN as a data model …

Gaps In Knowledge: Topological Insights Into The Structure Of Science, Gavin Engelstad

Mathematics, Statistics, and Computer Science Honors Projects

Understanding scientific development is essential to ascertaining the mechanisms leading us into the future. Building this understanding requires both methodological developments and empirical research. This thesis contributes in both aspects using a topological approach to examine scientific knowledge. The first section presents a new algorithm to find optimal cycle representatives for homological features in complex networks, a context for which we demonstrate existing algorithms can be inadequate. The second section applies a number of topological methods, including our cycle optimization algorithm, to data on individual scientific fields, demonstrating the value of topological approaches and highlighting new insights about how science …

Quantifying Multidimensional Effects Of Physicochemical Parameters On Pfas Adsorption Using A Hybrid Response Surface Methodology-Machine Learning Approach, Harsh V. Patel, Jazmin Green, John Park, Stephanie Luster-Teasley Pass, Renzun Zhao

Engineering Management & Systems Engineering Faculty Publications

Per- and polyfluoroalkyl substances (PFAS) contamination has posed a significant environmental and public health challenge due to their ubiquitous nature. Adsorption has emerged as a promising remediation technique, yet optimizing adsorption efficiency remains complex due to the diverse physicochemical properties of PFAS and the wide range of adsorbent materials. Traditional modeling approaches, such as response surface methodology (RSM), struggled to capture nonlinear interactions, while standalone machine learning (ML) models required extensive datasets. This study addressed these limitations by developing hybrid RSM-ML models to improve the prediction and optimization of PFAS adsorption. A comprehensive dataset was constructed using experimental adsorption data, …

Optimization Of Free-Time Controlled Constrained Sweeping Processes And Applications, Thi Dai Trang Nguyen

Wayne State University Dissertations

Optimization and optimal control have a wide range of applications across fields like engineering, biology, data science, and economics. This dissertation is devoted to advanced optimal control problems discontinuous constrained differential inclusions of the sweeping type involving the duration of the dynamic process into optimization, which are truly challenging and underinvestigated in control theory while being highly important for various applications. To attack such problems, we use the method of discrete approximation while establishing its well-posedness and strong convergence to optimal solutions of the controlled sweeping process. This approach, married to advanced tools of variational analysis, enables this research to …