Digital Commons Network^™

Genetic Analysis Of Triplicated Genes Affecting Sex-Specific Skeletal Deficits In Down Syndrome Model Mice, Kourtney Sloan, Kristina M. Piner, Pathum Randunu Nawarathna Kandedura Arachchige, Charles R. Goodlett, Yann Herault, Gayla R. Olbricht, Joseph M. Wallace, Randall J. Roper

Mathematics and Statistics Faculty Research & Creative Works

Down syndrome (DS) is caused by the triplication of human chromosome 21 (Hsa21), resulting in skeletal insufficiency (low bone mineral density) and altered bone development. DS mouse models recapitulate these deficits, including sexual dimorphism in long bone alterations. Historically, Ts65Dn mice provided much of the insight behind DS-related skeletal deficits with ∼100 trisomic orthologous genes, but there are concerns about the genetic fidelity in this model due to the included triplication of genes not homologous to Hsa21. A new DS model, Ts66Yah, subtracted the non-Hsa21 homologous trisomic genes from Ts65Dn but has not been evaluated for long bone deficits. Comparing …

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …

Asymmetric Synthesis Of Borylated Amines Via Rhodium Catalyzed Hydroboration Of Allylamine Derivatives: Surprising Role Of Counterions And Accelerators, Rukshani Wickrama Arachchilage

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The Catalytic Asymmetric Hydroboration (CAHB) reaction is a valuable method for synthesizing chiral organoboron compounds. Nevertheless, key mechanistic details, including catalyst activation, ligand effects, and rate-determining steps, are difficult to generalize and remain not fully understood. Building on previous research from the Takacs group, this work explores acyclic N-acyl allylamines as substrates in rhodium-catalyzed hydroboration and investigates the formation of active catalysts from various rhodium precursors, the role of counterions (e.g. BF₄, BArF-), ligand-to-metal ratios, and the impact of external fluoride additives (e.g. TBAT). Hydroboration of acyclic N-acyl allylamines achieves up to 90% yield and 99 : 1 …

Standardization Of Coal Ash Testing, Classification, And Harvesting, Benjamin Gallagher, Chris Frishcosy, Eric Hageman

World of Coal Ash Proceedings

Standards such as product specifications, test methods, practices and guides play a crucial role in supporting both commerce and science. Standardization helps build consistency and reliability whether it pertains to the performance of an ingredient in a product or in the measurement of a material characteristic. Coal combustion products, such as coal ash and synthetic gypsum, exhibit unique characteristics and many standard have been developed to characterize these materials and support their beneficial use. ASTM is a voluntary, consensus-based organization, and publishes many standards related to coal combustion products. Currently, there are seven ASTM standards related to chemical analysis of …

Lessons Learned From Managing Ash Pond Closure Waters, Danny Stephens, Tom Geeza, Phil Benson, Ashwin Ranna

World of Coal Ash Proceedings

The water management issues created by ash pond closure are complex and can create technology selection and operational management challenges. Ash dewatering activities produce highly variable effluents, depending on ash composition, aging, and dewatering and stormwater management techniques. Effluent limitations can also be highly variable, depending upon the size of the receiving body and the anticipated composition of the effluent stream. The user often faces competing risks: installing an unnecessarily complex and expensive treatment plant, being limited on closure activities by limitations in water treatment capabilities, or both. This paper presents several lessons learned from assessing ash closure water management …

Herbularyo (Folk Healer): An Herbal Medicine Card Game, Maryjane T. Magsino, Inah Marie Q. Rivera, Armando M. Guidote, Genejane M. Adarlo

Chemistry Faculty Publications

Herbularyo, a card game teaching about herbal plants (HPs), was created and evaluated as a viable educational card game based on Tuomisto and Aksela’s criteria. A quasi-experiment was performed on 81 Grade 8 students from a private high school and 50 Grade 11 from a public high school. Independent t-test revealed that the control group (CG) and experimental group (EG) (p=0.386), and EG1 (played ≤5) and EG2 (played >5) (p=0.681) are not comparable with each other. Paired t-test showed EG performed better (p=0.001) than CG (p=0.901) whereas ANCOVA showed that playing Herbularyo improved students’ information retention (p=0.006). EG1 and EG2 …

Pest Risk Modelling For Climate-Smart Vegetable Production In East Africa, Marc Marin Agbodjan, Komi Mensah Agboka, John Odindi, Elfatih Abdel-Rahman, Onisimo Mutanga, Frank Chidawanyika, Chrysantus Tanga, Daniel Munyao Mutyambai, Sevgan Subramanian, Bonoukpoè Mawuko Sokame

All Peer-Reviewed Publications

Agricultural productivity in East Africa is increasingly threatened by climate-sensitive insect pests. This study investigates the occurrence of key vegetable pests: Brevicoryne brassicae, Plutella xylostella, Maruca vitrata, and Liriomyza mik. A comparative species distribution modelling evaluated pest risk projections under climate change. Four variable selection strategies were tested: case 1 (correlation and variance inflation factor [VIF] filtering across all predictors), case 2 (correlation and VIF filtering of bioclimatic variables merged with other predictors), case 3 (filtering based on environmental values at species occurrence point to approximate realized niches), and case 4 (dimensionality reduction using principal component analysis). These strategies were …

Leveraging Information Theory And Ecological Network Analysis To Monitor Communication Networks In A Student Aerospace Team, Christine Sessions

Doctoral Dissertations and Master's Theses

Effective communication is a critical component of successful collaboration in group projects and team settings. However, systematically tracking and analyzing team communications can be challenging, especially in complex, multi-member teams such as those found in the aerospace industry. This paper explores an information-theoretic approach that leverages encoding techniques and graph theory to analyze communication networks within a university’s multi-year, student-led cubesat design project (Project COMET). By utilizing Shannon Entropy as a measure of information flow, encoding communication patterns, and analyzing Ecological Network Analysis parameters, this research aims to understand how an Embry-Riddle Aeronautical University student project team evolves over the …

Should I Stay Or Should I Go?: Evaluating The Role Of Climate And Weather Stressors On Moving Decisions In Southeast Florida, Arielle Perry

Electronic Theses and Dissertations

As climate and weather hazards intensify, Southeast Florida communities face mounting pressures that increasingly influence patterns of migration and immobility. This research examines evidence of climate migration in high flood-risk neighborhoods in Fort Lauderdale by exploring why some populations choose to stay, while others leave, in the context of a changing climate. Using focus group discussions, I investigate how climate and non-climate related factors shape mobility outcomes among residents in the city. Migration outcomes were primarily influenced by negative climate and weather hazard experiences, discontent with existing public in-situ adaptations, and non-climate disamenities, which eroded participants’ sense of place. Voluntary …

Phenological Overlap In Obligate Plant-Pollinator Mutualism, Austin J. Carlson

2026 Spring Honors Capstones Projects

Plant-pollinator mutualisms require temporal overlap between flowering and pollinator activity, so climate-driven timing shifts can weaken the interaction and, in severe cases, destabilize the system. This work investigates how reduced overlap affects persistence in an obligate plant-pollinator pair using a coupled differential equation model in which a phenological overlap factor scales the saturating mutualistic benefit. Simplification with a constant overlap enables closed-form equilibrium and stability analysis, revealing that below a critical overlap threshold, coexistence is no longer maintained. Rescaling reduces the parameter space from ten quantities to seven dimensionless groups, and sensitivity analysis identifies the degree of species dependence and …

Red Lines, Green Blooms: Assessing The Effects Of Historical Environmental Disparity On Algal Communities In The Twin Cities, Mn, Georgia C. Akins

Environmental Studies Honors Projects

Redlining, a discriminatory housing policy from the 1930s, shaped lastng urban inequalites that may extend to environmental conditons. This study examines links between redlining and urban water quality in the Twin Cites using algal communites as indicators. Across 28 water bodies sampled in 2022 and 2024, physical, chemical, and biological metrics were compared by redlining grade. Results show limited relatonships between redlining and most variables, with only surface water temperature differing significantly. Nutrients and algal diversity were unrelated to redlining, instead reflectng present-day conditons. These findings suggest contemporary factors play a stronger role than redlining in shaping urban freshwater ecosystems.

Fossil-Fuels In A Decarbonized Country? Modeling The Drivers Of Icelandic Oil Sales, Inbal Armony

Environmental Studies Honors Projects

Although 100% of Iceland’s electricity comes from renewable energy sources, it still relies on fossil fuels for land transportation, marine transportation, aviation, and some industry. Understanding geographic nuances in oil use is critical to achieving Iceland’s goals of carbon neutrality by 2040. As the island has one primary urban center with two thirds of the population, information is lacking about oil use in non-Capital areas and a gap between state and municipal climate plans. Using newly available data of oil sales at the municipality-level in a Small Area Estimation model, we analyze drivers of oil sales across Icelandic municipalities. We …

Ais26s: Ai In Biomedicine, Shiqian Shen

Paul English Applied Artificial Intelligence (AI) Institute Publications

This presentation explores the role of artificial intelligence in advancing biomedical research and clinical practice from the perspective of a physician-scientist. Dr. Shiqian Shen discusses current challenges in neuroscience and medicine, including limitations in human observation, data analysis, and decision-making across complex biological systems. The talk highlights how AI-driven approaches such as computer vision, neural signal processing, and large-scale data modeling can improve the understanding of disease mechanisms, enhance experimental workflows, and enable more precise, patient-centered care. Specific applications include automated classification of neural activity, behavioral analysis in animal models, and multimodal data integration. A key concept introduced is “shadow …

Tissue-Specific Heavy Metal Accumulation And Sediment–Mangrove Dynamics In Port Everglades, Florida, Dimitrios Giarikos, Amy Hirons, Jason Gershman, Sophie Welch

SECLER Data

Coastal wetlands near industrialized waterways face increasing heavy metal contamination, yet the role of mangroves as biogeochemical buffers remains poorly understood. This study quantified 16 heavy metals in sediments and red mangrove (Rhizophora mangle) tissues (roots, branches, and leaves) across four sites near Port Everglades, Florida, examining tissue-specific partitioning, contamination patterns, and sediment-to-plant transfer. The South Turning Basin (STB) was the principal contamination hotspot, with geometric mean (GM) concentrations of arsenic (As; 27.8 µg/g) and zinc (Zn; 203 µg/g) exceeding threshold effect levels, while Cu exceeded its probable effect level (PEL; 193 µg/g). Mercury (Hg) exceeded its PEL …

Chemometric Analysis Of Dissolved Organic Matter Using Fluorescence, Dani Fellner, Ken Overway

Honors Projects

Univariate spectroscopic techniques have been utilized to measure dissolved organic matter (DOM), but challenges arise in the separation and characterization due to similarities in chemical structures and spectral overlap. Multivariate techniques utilize a combination of known analytes with their unique excitation and emission spectra from fluorescence measurements to quantify amount of each analyte present in the mixture using parallel factor analysis. Tryptophan, tyrosine, and phenylalanine are common amino acids found in environmental samples and can be quantified due to their intrinsic fluorescence qualities. These amino acids can be utilized to estimate the amount of DOM in a sample since proteins …

Ai Need Not Make One Slothful, Roy A. Kaelin Jr

Faculty Publications

As National Louis University seeks to plan and advance its way amid the potential perils and pitfalls of so-named artificial intelligence, one finds that with reasonable workflows and guard rails, the use of AI proposes both potential promise and prospect, to assist and augment the natural intelligence that students and teachers bring to the classroom, encouraging them to pursue STEM-related activities with the preparation and deployment of focused and directed AI-bots. This paper presents examples and a case study of that directed and focused approach, the incremental lessons learned to date, and a proposed path to advance worthwhile AI …

Designing Enhanced Nonlinearity In Plasmonic Devices With Epsilon-Near-Zero Films, Kevin Tran Le

Electrical Engineering and Computer Science (MS) Theses

The growing demand for energy-efficient optical information processing motivates compact nonlinear photonic devices that can operate at low power. Silicon photonics is a mature platform for linear optical functions, but nonlinear operation remains challenging because of its weak Kerr response, two-photon absorption at telecommunication wavelengths, and limited compatibility with deeply subwavelength plasmonic confinement. This thesis computationally investigates epsilon-near-zero thin films integrated into plasmonic waveguide architectures as a route toward stronger light–matter interaction in compact nonlinear devices.

Two waveguide geometries are examined: a hybrid metal-insulator-metal plasmonic slab waveguide incorporating an ultrathin indium tin oxide epsilon-near-zero layer (5–50 nm), and a dielectric-loaded …

Applications Of Cyrene For Pharmaceutical Synthesis, Anjali Mae Rabindran

Undergraduate Honors Thesis Collection

Cyrene is a cellulose-derived molecule that has gained interest in green chemistry as both a solvent and precursor for pharmaceutical intermediates. In this study, biocatalytic and chemical strategies were evaluated for converting Cyrene into these intermediates. Cyrene was carried through variations of a five-step sequence: reduction, reductive amination, esterification, tosylate salt formation, and Lewis-acid mediated acetal opening to generate ring-opened pyranose products (“deoxy sugars” and “deoxy amino sugars”). We successfully synthesized deoxy sugar intermediates; however, the production of stereochemically pure deoxy amino sugar intermediates was limited by unresolved diastereomeric mixtures. These findings highlight the promise of Cyrene as a renewable …

Isolation, Purification, And Characterization Of Α-Galactosidase From Watermelon (Citrullus Lanatus), Christopher Henley Jr.

Chemistry & Biochemistry Undergraduate Honors Theses

The enzyme α-galactosidase is a type of glycosidase that removes galactose sugar units from larger molecules in cells. Compounds that inhibit glycosidases have been useful for understanding the structure and function of the enzymes they inhibit, and some have been used to treat certain diseases. Using inhibitors of α-galactosidase to study its characteristics and mechanisms may provide insights into its role in disease and its general utility. Advances in fields such as agriculture, sustainable fuels, and biomedicine may be facilitated by inhibition studies of α-galactosidase, but the current library of known inhibitors is relatively lacking. Obtaining α-galactosidase enzymes from chemical …

Course Insight Portfolio: Math 1060 Calculus Of One Variable I, Minh Ha, Dinaniaina Florence Rafidimanantsoa, Preston Sessoms, Rishabh Shukla

Publications

The following portfolio is a representation of the course MATH 1060, Calculus I, taught at Clemson University. The contents can be broken down into 3 major components.

• The first being an analysis of the students who may typically be in the course, the prerequisites required to take the course, and what paths students have after completing the course. This analysis is based upon the course curriculum at Clemson, and as a result will likely not align with that of other universities

. • The second major component is a map of the concepts discussed in MATH 1060 as well …

Course Insight Portfolio Math 1040: Precalculus And Introductory Differential Calculus, Jessica Ayers, Morgan Hayes, Meghan Kerrick, Uthman Rasaq, Drishty Singh

Publications

This portfolio includes four primary elements. First is a document titled “Where did they come from? Where are they going?” that provides a description of the types of students who are likely to take the course, followed by the “Course Concept Map” that visually depicts the flow of topics and possible misconceptions in MATH 1040. Additionally, the “Misconceptions Overlay” document lists articles that offer interesting discussion and further insight into the ideas students may bring to MATH 1040 or develop throughout the course. Two lesson plans are included that cover “Continuity and Introduction to Classifying Discontinuities” as well as an …

Course Insight Portfolio: Math 1080, A Gentle Introduction To Infinite Series, Igor Luis Aureliano, Leyanis Falcon Hernandez, Ross George, Fnu Monika

Publications

This lesson aims to introduce the concept of an infinite series through geometric representations and partial sums to help students develop an intuitive understanding of convergence. A common misconception students may have when first encountering infinite series is the belief that “a sum of infinitely many things must be infinite”. Through the study of a convergent geometric series, students will investigate how the limit of partial sums can produce a finite value, thereby addressing this misconception and developing a more accurate understanding of infinite series.

Environmental Sustainability Assessment Of Field Phosphate Monitoring Methods For Creeks, Quintino Medi

All Theses

Creeks serve as conduits for water, nutrients, and contaminants to larger water bodies such as rivers and lakes, and their health is a key indicator of overall watershed water quality condition. Unlike rivers, creeks are under-monitored due to their small size, hydrological variability, and limited accessibility. Many technologies exist for monitoring phosphorus in surface waters. Technologies may be classified into two general categories: i) proxy real-time sensors, which record generic water quality parameters, and ii) chemical reagent-based assays, which quantify soluble reactive phosphorus (SRP) in batch samples. There is a lack of studies that compare the features and benefits of …

Estimating Body Size And Biogeography In The Genus Alligator, Madelyn M. Turala

Electronic Theses and Dissertations

Several studies have examined correlations between total body length (TL) and skeletal measurements in the American alligator (Alligator mississippiensis), with some measurements serving as stronger predictors of TL than others. Femur length (FL) has been found to be tightly correlated with TL in A. mississippiensis, and this relationship has been used to estimate body size of extinct crocodilians. This thesis demonstrates that the humerus, radius, ulna, and tibia are also strongly correlated with TL and useful for body size estimation in A. mississippiensis, and thus, can be applied to related extinct crocodilians. Additionally, species distribution modeling …

Adsorption Of Pfas On Bridged Functionalized Organosilica Materials, Elisha Lawerh Kabutey

Electronic Theses and Dissertations

PFAS are hazardous contaminants that have a devastating impact on human health and the environment. Their hazardous nature has led to the development of various adsorption methods for removing these contaminants from water sources. In this study, functionalized organosilica materials were synthesized from bis[3-(trimethoxysilyl)propyl] amine using the sol-gel method. The surface amino groups of the organosilica were converted into amine hydrochloride groups. Their adsorption properties were evaluated using salts of perfluorooctanoic acid, perfluorooctanesulfonic acid, and perfluorobutanesulfonic acid. Results showed excellent adsorption capacity of the materials. Adsorption of PFAS leads to particle agglomeration and flotation of the spent material. A column …

Decomposition In Urban Forest Patches Across A New York-New Jersey Urbanization Gradient, Cailee Sprouse

Theses, Dissertations and Culminating Projects

"Urbanization causes habitat fragmentation, pollution, homogenization of soil profiles, and replacement of native flora and fauna, which can alter vital ecological processes like decomposition. It is essential to investigate the impacts urbanization may have on ecosystem functioning to better inform urban land management. Studies have shown conflicting results on the impacts of urbanization on soil decomposition rates, with some showing higher, lower, or similar decomposition rates in urban soils compared to rural soils. This study aims to investigate the effects of urbanization and soil characteristics on decomposition rates in three urban forest patches in New Jersey and New York using …

Cyanine Dyes As Next-Generation Fluorophores: Applications In Cell Sorting And Fingerprinting Technologies, Super-Multiplexed Spectroscopy, Biomedical Imaging, And Beyond, Lucas Allen Davis

Undergraduate Honors Thesis Collection

As biochemical, pharmaceutical, and medical sciences advance, the demand for technologies capable of probing multiple cellular targets simultaneously continues to increase. Super-multiplexed spectroscopic techniques offer a pathway toward comprehensive cellular fingerprinting by overcoming the spectral limitations of conventional fluorescence labeling. By circumventing the traditional “color barrier,” cyanine-based Raman tags enable the simultaneous discrimination of numerous cellular morphologies, allowing spectroscopy and imaging to be integrated for high-dimensional cellular analysis. Technologies developed in Goda Lab—including high-throughput flow cytometry, virtual freezing fluorescence imaging (VIFFI), Fourier-transform coherent anti-Stokes Raman spectroscopy (FT-CARS), and MERdot nanoparticles—address longstanding trade-offs between throughput, resolution, sensitivity, and multiplexing capacity. Central …

Shark Immunology And Its Biomedical Potential: Evolution, Innovation, And The Imperative Of Conservation, Reesha Bhagat

Undergraduate Honors Thesis Collection

This review aims to shed light on a significant ecological deficit and its implications for the future of science and medicine. Sharks possess a uniquely adaptive, cancer-resistant, and evolutionarily refined immune system with transformative biomedical potential, making their conservation a scientific and medical imperative. We are losing something medically irreplaceable, and we don’t even fully understand it yet. Shark conservation is a pressing scientific imperative because sharks are ecologically essential and represent an irreplaceable biomedical resource.

The Impact Of Quantum Computing On Ransomware, Byron Denham

Graduate Theses and Dissertations

Ransomware is one of the most pervasive and dangerous threats to cybersecurity today. Attacks involving ransomware have been responsible for the disruption of critical services in many fields including healthcare, education, and government. In the current paradigm, crypto ransomware relies on asymmetric cryptography to perform its operations in a way that ensure the victim’s only chance for file recovery is by paying the attacker’s requested ransom payment. However, advancements in quantum computing threaten the asymmetric cryptography that ransomware relies on. It has been shown that, once developed, a sufficiently powerful quantum computer will have the ability to break asymmetric cryptography …

Soil Moisture Regime Effects On Near-Surface Soil Chemical Properties In Alfisols Under Native Tallgrass Prairie In Arkansas, Sydney M. Talley

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

Tallgrass prairie ecosystems provide many crucial ecosystem services, including nutrient cycling and storage, organism habitat, and soil and water conservation. However, tallgrass prairies are considered an endangered ecosystem, particularly in the Ozark Highlands and Grand Prairie regions of Arkansas, where less than 0.05% of Arkansas’ original prairie land area remains. Understanding soil nutrient supplies over time in native tallgrass prairie ecosystems is critical for quantifying the success of restoration and rehabilitation activities. The objective of this study was to evaluate the effects of soil moisture regime (SMR) (i.e., aquic and udic), region (i.e., Ozark Highlands and Grand Prairie), and their …