Digital Commons Network^™

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Single-Molecule Orientation And Localization Microscopy, Sophie Brasselet, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Single-molecule localization microscopy (SMLM) offers enhanced spatial resolution in optical microscopy, providing detailed insights into the spatial organization of proteins in cells at the nanoscale. Over the past decade, SMLM has progressively incorporated the capability to retrieve the orientations of single molecules using their polarized dipolar emission pattern. Here we explore recent advancements in single-molecule orientation and localization microscopy (SMOLM), which yields super-resolved images of molecular three-dimensional (3D) orientations, wobble and 3D positions. This advancement opens possibilities to explore the nanoscale organization and conformation of biological molecules as well as to monitor and design local 3D optical fields in nanophotonics. …

Long-Term Patterns In The Relative Abundance Of Common Snook As A Factor Of Shifting Environmental Conditions In The Florida Coastal Everglades, Jordan A. Massie, Ryan J. Rezek, Rolando O. Santos, W. Ryan James, Natasha M. Viadero, Ross E. Boucek, Jennifer S. Rehage

Marine Science

Objective Environmental variability as a factor of climate change and water management can result in fluctuations in the abundance and distribution of fish populations from year to year, with either negative or positive effects depending on behavioral and physiological requirements and the ability to adapt to changing conditions. Variability in water levels can also influence prey availability, affecting predator abundance in seasonal foraging areas. In this study, our objective was to better understand how environmental variation has affected the relative abundance of Common Snook Centropomus undecimalis in the freshwater/estuarine habitats of Everglades National Park. Methods Electrofishing data over 17 years …

Linking Hydrology, Temperature, And Energetics: Global Change Implications For The Foraging Ecology Of A Generalist Predator, Mack White, W. Ryan James, Justin S. Lesser, Ryan J. Rezek, Jonathan R. Rodemann, Ross E. Boucek, Rolando O. Santos, Jennifer S. Rehage

Marine Science

Objective: The objective of this study was to quantify the effects of temperature, hydrology, and body size on the diet and energy requirements of a generalist predator, Common Snook Centropomus undecimalis (hereafter, “snook”), to gain a better understanding of predator–prey dynamics in the wake of global change. We first ask how temperature, hydrology, and body size influence the occurrence of fish, invertebrates, and empty stomachs in the diet of snook. Next, we model the energetic requirements of snook as a function of body size and temperature. Last, we use predation simulations to test how changes in prey quality, together with …

Quantification Of Terpenes In Various Commercial Cannabis Products By Gas Chromatography-Flame Ionization Detection And Gas Chromatography-Mass Spectrometry, Kaitlyn M. Ignaszak

Forensic Science Master's Projects

The goal of this research project was to identify and quantify the terpenes in five commercial cannabis products (dried bud, kief, two tinctures, and a pain cream) using gas chromatography-flame ionization detection (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Terpene identification and quantification were conducted using GC-MS and GC-FID, with a standard sample containing 21 terpenes of known concentrations. To determine the most effective extraction conditions, three organic solvents (ethanol, acetonitrile, and ethyl acetate) were employed. Additionally, the effects of extraction time on terpene yield were investigated by analyzing aliquots collected at five different time intervals, ranging from one hour to …

Script-Based Inferences In An Image Schema Story Understander, Jamie C. Macbeth, Boming Zhang, Sharmin Badhan

Computer Science: Faculty Publications

Recent studies of large language models (LLMs) have revealed that they lack human-like cognitive models of reasoning and understanding. An important thread of research merges image schemas into symbolic artificial intelligence systems where their use as conceptual building blocks and primitives shows promise for the study of human cognition through intelligent systems that perform neurosymbolically. The work presented in this paper demonstrates image schema primitives being used in structures of a representation system called conceptual dependency (CD) and in broader commonsense knowledge structures called scripts. We present a story under- standing system that uses image schemas as primitives in scripts …

Resource Assessment Report No. 4: North Coast Demersal Scalefish Resource - Kimberley 2025 Assessment, Fabian Trinnie, Rubie Evans-Powell, Ainslie Denham, Sybrand A. Hesp, Corey Wakefield, Craig L. Skepper, Brett Crisafulli, Stephen J. Newman

Resource Assessment Reports

The North Coast Demersal Scalefish Resource (NCDSR) comprises ecological suites of tropical demersal fish species that occur predominantly in inshore waters (20–250 m deep) and offshore waters ( > 250 m deep) of the North Coast Bioregion (NCB). More than 60 demersal species are landed by fisheries operating in the Kimberley and Pilbara regions of the NCB each year, including high-value snappers (Lutjanidae), groupers (Epinephelidae), and emperors (Lethrinidae). As outlined in the NCDSR Harvest Strategy (DPIRD, 2017), the Kimberley resource is currently monitored through annual reviews of total removals and catch rate trends of indicator species, as well as periodic (every …

(Si15-068) Advanced Numerical Methods For The Solution Of Nonlinear Fisher Equation, Vikash Vimal, Richa Kumari, Ashish Awasthi

Applications and Applied Mathematics: An International Journal (AAM)

This paper examines the use of advanced numerical techniques to approximate solutions of the Fisher equation with higher-order accuracy. This technique integrates the method of lines with a strong stability-preserving Runge–Kutta scheme of orders four and five stages (SSPRK-54) for the numerical formulation. This scheme is then tested on two examples and the results show that it is more efficient than existing methods and requires less computing power. These equations are widely used across scientific and engineering disciplines, with particular relevance in biomedical studies, such as estimating the boundary size of tumors. The difficulties arising from their nonlinear nature are …

Evaluating Early Successional Habitat Selection By Herpetofauna And Pygmy Rattlesnakes In Tennessee, Carlin Frost

Tennessee State University Alumni Theses and Dissertations

Coupled with climate change, global biodiversity declines are exacerbated by increasing anthropogenic pressures and ecosystem destruction. Amphibians and reptiles are particularly vulnerable due to their specific and narrow habitat requirements. In Tennessee, the Western Pygmy Rattlesnake (Sistrurus miliarius streckeri) is classified as Threatened and is primarily associated with floodplains adjacent to early successional habitats (ESH) in the western Interior Plateau ecoregion. These ESH support unique flora and fauna but have declined in recent decades, largely due to urban encroachment and disturbance suppression. Studying snakes is challenging because of their limited activity periods, small home ranges, and low detectability from cryptic …

The Role Of Water In Peptide Behavior And Peptide-Based Water-Responsive Crystals, Janel Jannette Rivera Cancel

Dissertations, Theses, and Capstone Projects

Water plays a crucial role in shaping the behavior and function of biomolecules across the liquid, supercooled, and glassy states. This thesis presents a dual approach combining computational simulations and experimental investigations to explore the influence of water on biomolecular systems, particularly peptide-based materials. We employ molecular dynamics simulations to study the hydration-dependent structural dynamics of homopolymer peptides. Simulations were carried out across a range of temperatures and pressures to analyze changes in hydration and structural stability, shedding light on the behavior of peptides under supercooled and glassy conditions. These studies are especially relevant for understanding biomolecular stability in cryopreservation. …

Nonlinear Optics Through Femtosecond Light-Matter Interactions, Shah Faisal B. Mazhar

Dissertations, Theses, and Capstone Projects

This dissertation offers experimental and theoretical insights into nonlinear light-matter interactions induced by intense femtosecond (fs) laser pulses. It investigates key phenomena, including stimulated Raman scattering (SRS) from phonon and magnon quasiparticles, supercontinuum (SC) generation via self-phase modulation (SPM), conical emission (CE) arising from four-wave mixing (4WM), and modulation instability (MI) driven by cross-phase modulation (XPM) between SRS and SC processes. These effects are studied in diverse media using state-of-the-art femtosecond lasers.

The interplay among SRS, SC, 4WM, and MI is examined to probe vibrational modes and temperature-dependent magnetic excitations in condensed-matter systems. Experiments are conducted on anisotropic uniaxial calcite …

Miscanthus × Giganteus Increases Soil Maximum Water Holding Capacity Compared To Maize, Jessica T. Nelson, Maoz Dor, Andy D. Vanloocke, Jacob E. Studt, Perla K. Schrock, Marshall D. Mcdaniel

School of Earth, Environmental, & Marine Sciences Faculty Publications

Soil ecosystem services, like the ability to store water, have been depleted after a century of conventional, annual cropping, and perennial crops offer a solution to this and other agricultural environmental issues. We assessed the impact of Miscanthus × giganteus (miscanthus), a perennial biomass crop, on soil water holding capacity and structure compared to continuous maize (Zea mays L.) at two sites in Iowa. After three growing seasons, we measured the following: (1) maximum water holding capacity (MWHC) with and without soil structure, and (2) total porosity and pore size distribution (PSD) via micro-computed tomography (microCT). Miscanthus increased MWHC …

Pd-Catalyzed Microwave Irradiated Cross-Coupling Of Carboxylic Acids And Amino Alcohols., Md Shahin Reza

Tennessee State University Alumni Theses and Dissertations

Amino esters are valuable pharmaceutical intermediates with anesthetic properties and applications as prodrugs. In this study, we have developed a new microwave-assisted method for the cross-coupling of aromatic carboxylic acids with amino alcohol using a palladium catalyst. This approach has enabled an efficient synthesis of amino esters, overcoming challenges such as side reactions and product separation.

Effects Of Tillage On Wheat Canopy, Stephanie Adanna Anyanwu

Tennessee State University Alumni Theses and Dissertations

Abstract Wheat canopy cover and greenness are useful crop performance indicators that provide significant insight into the performance of wheat crops. Understanding the effects of no-till and conventional tillage practices on winter wheat canopy cover and greenness will help inform agronomic decision making in wheat production. Therefore, the aim of this study was to assess the effects of no-till and conventional tillage practices on wheat canopy cover and greenness using drones. Wheat canopy cover mapping was carried out using deep learning supervised classification. The normalized difference vegetation index (NDVI), green normalized difference vegetation index (GNDVI) and optimized soil adjusted vegetation …

Distribution And Occurrence Of Cyanohabs, Nutrients, And Water-Quality Data In The Tennessee State University Wetland, Kristi Hill

Tennessee State University Alumni Theses and Dissertations

Toxic algal blooms are an expanding issue for aquatic ecosystems because they are hazardous to human and environmental health. Algal blooms naturally occur from the combination of warm temperatures, sunlight, and abundant nutrients in water, but what triggers them to become harmful algal blooms (HABs) and begin synthesizing toxin is not well understood, and their threat to freshwater sources was not heavily researched until recently. Microcystin (MC), a freshwater algal toxin, is a HABs toxin which targets the liver and causes sickness and death in humans and animals (pets, livestock, and wildlife). Urban freshwater wetlands are among the most HAB …

Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu

Engineering Management and Systems Engineering Faculty Research & Creative Works

Cancer is mainly caused by a relatively small portion of somatic genome alterations (SGAs), called cancer drivers. Despite success in identifying a good number of cancer drivers, many more remain to be discovered to explain various cancers. Moreover, limited tools are available to identify potential interactions among cancer drivers for a better understanding of oncogenesis. To tackle these challenges, we have developed a novel approach called individualized Bayesian inference using a decision tree (IBI-DT). IBI-DT recognizes the genetic heterogeneity among cancer patients, where different individuals or patient subgroups of distinct genomic makeup may have different drivers. IBI-DT works by constructing …

Nonlinear Diffusion, Hydrodynamic Cascades And Jamming In Kinetically Constrained Systems: Insights From Lattice Gas Models, Abhishek Raj

Dissertations, Theses, and Capstone Projects

This dissertation investigates non-linear diffusion processes and emergent dynamical phenomena in kinetically constrained lattice gases. Two central models are considered: a one-dimensional lattice gas exhibiting a diffusion cascade triggered by hydrodynamic nonlinearities and a triangular ladder exclusion model that undergoes a jamming transition. The former demonstrates stretched exponential decay consistent with non-perturbative long-time tails, while the latter illustrates how classical-quantum mappings yield insight into glassy dynamics and mobility constraints. Through a combination of numerical simulations, analytical perturbation theory, and mean-field approximations, the work uncovers mechanisms underlying anomalous transport, jamming transitions, and the breakdown of perturbative hydrodynamics.

Memory-Efficient Graph Processing On Gpus: Reducing Intermediate Data Structure Overhead, Chang Ye

Dissertations and Theses Collection (Open Access)

The increasing scale of real-world graphs in domains such as fraud detection, community detection, and biological analysis demands high-throughput, memory-efficient graph processing solutions. GPUs offer massive parallelism for accelerating such workloads, and numerous frameworks have been developed to leverage their computational power. These frameworks primarily focus on optimizing scheduling to better align graph processing with GPU architectures. It performs well for algorithms with low memory demands, such as BFS, SSSP, and PageRank. However, for algorithms that require substantial memory, such as label propagation, and subgraph counting, the limited memory capacity of GPUs often becomes a significant bottleneck.

This dissertation addresses …

Role Of Axial Ligation In The Conformational And Redox Properties Of Cytochromes, Morgan Elisabeth Reik

Dartmouth College Ph.D Dissertations

Heme proteins are crucial for many biological processes including respiration, transport, and catalysis. As electron carriers containing redox active metal centers, their electron transfer (ET) properties are tuned by the protein environment, wherein the reduction potential can be influenced by factors such as heme solvent accessibility, charge, the presence of neighboring redox centers, as well as the identity of the axial ligand. The axial ligand in heme proteins is especially crucial for tuning the electronic properties of the metal center, as it affects the driving force of the reaction. However, the redox properties of heme proteins are further modulated by …

Tetrigidae Of Ethiopia: First Species Delimitation Via Dna Barcoding And Description Of Three New Species †, Tarekegn Fite, Hendrik Devriese, Dustin Kulanek, Josip Skejo, Niko Kasalo, Manaye Misganaw, Tadele Tefera, Jandouwe Villinger, Martin Husemann

All Peer-Reviewed Publications

Tetrigidae is a caeliferan family of Orthoptera constituting a diverse and relatively ancient lineage of small Orthopterans, which has its greatest diversity in tropical and subtropical areas. However, to date, few studies have been conducted on the identification and description of Tetrigidae species in Ethiopia, and even fewer molecular data are available. Hence, we performed the first species delimitation study via DNA barcoding of species belonging to the genera Paratettix, Leptacrydium, Dasyleurotettix, and Morphopoides from Ethiopia. We provide 35 new sequences of the COI gene belonging to six species of these genera. We show that Ethiopian Tetrigidae can be successfully …

Linking Core Concepts And Competencies In General Chemistry Via Gowin’S Theory Of Learning And Vee Heuristic, Vijay Vyas, Scott A. Reid

Chemistry Faculty Research and Publications

The content in introductory science courses has often been criticized as “miles wide and inches deep”. In general chemistry, several revisions have focused on framing around a set of core or anchoring concepts, and we recently adapted the anchoring concepts content map (ACCM) of the American Chemical Society (ACS) to develop an anchoring concept-based curriculum for our general chemistry courses. In this article, we describe efforts to connect this curriculum with laboratory learning using Gowin’s theory of learning and the associated knowledge Vee heuristic. Within this framework, the laboratories themselves become events connecting the conceptual and methodological domains, …

Patterns Of Ecological Quality In Portuguese Transitional Waters Over The Last Five Decades: A Framework Based On Benthic Foraminifera For The Sado Estuary, J. Moreno, F. Moreno, F. Fatela, E. Leorri, M. Leira, P. Masqué, M. C. Freitas

Research outputs 2022 to 2026

This study aimed to examine the validity of benthic foraminifera-based indices – Foraminiferal Stress Index (FSI), diversity index Exp(H'bc), and Ecological Quality Ratio (EQR) – for evaluating estuarine environmental conditions and supporting palaeoecological reconstructions, focusing on the Sado estuary (southwest Portugal). Located near heavily industrialized urban areas and designated as a Nature Reserve, this estuary faces human pressures and high natural values, leading to management conflicts. Foraminiferal assemblages were analysed in surface sediment samples, with known concentrations of several metal(loid)s, and in dated core samples. Correlations were found between metal(loid)s, organic matter, grain size, and salinity (as a proxy for …

Coupling Category Alignment For Graph Domain Adaptation, Nan Yin, Xiao Teng, Zhiguang Cao, Mengzhu Wang

Research Collection School Of Computing and Information Systems

Graph domain adaptation (GDA), which transfers knowledge from a labeled source domain to an unlabeled target graph domain, attracts considerable attention in numerous fields. However, existing methods commonly employ message-passing neural networks (MPNNs) to learn domain-invariant representations by aligning the entire domain distribution, inadvertently neglecting category-level distribution alignment and potentially causing category confusion. To address the problem, we propose an effective framework named Coupling Category Alignment (CoCA) for GDA, which effectively addresses the category alignment issue with theoretical guarantees. CoCA incorporates a graph convolutional network branch and a graph kernel network branch, which explore graph topology in implicit and explicit …

Robust Ai Solutions For Financial Markets Through Generative Modeling, Dynamic Graph Learning, And Reinforcement-Based Portfolio Optimization, Jingyi Gu

Dissertations

Financial markets are inherently uncertain and dynamic, driven by complex factors such as macroeconomic signals, investor sentiment, and evolving inter-asset relationships. While machine learning has advanced financial modeling, existing approaches often fall short in addressing the real-world intricacies of finance. This dissertation confronts two critical challenges, human-driven stochasticity and risk-intensive decision-making under real-world trading constraints, while seizing a pivotal opportunity, the structural dynamics of evolving financial systems. These elements are foundational to advancing robust and practical financial intelligence.

To this end, this dissertation develops a unified framework for robust financial modeling and decision-making. The framework is architected as a progressive, …

Large-Scale Graph Algorithms And Applications With An Emphasis On Fintech Data, Fuhuan Li

Dissertations

Graph algorithms are essential analytical tools with applications spanning cybersecurity, biology, social media, and increasingly, financial technology (FinTech). The complex and interconnected nature of financial data, particularly in cryptocurrency networks, presents unique opportunities for graph-based analysis in fraud detection and anomaly identification.

This dissertation presents the design and implementation of scalable graph algorithms tailored for large-scale networks, with particular emphasis on FinTech applications. The primary contributions include: (1) novel cover-edge based triangle counting algorithms that significantly reduce computational overhead through breadth-first search preprocessing, achieving substantial speedups over traditional methods and dramatic communication reduction in distributed settings, (2) optimized parallel implementations …

Bodipy-Based Photocages For The Controlled Release Of Hydrogen Sulfide And Persulfides, Yanmei Li

Dissertations

Reactive sulfur species (RSS) such as hydrogen sulfide (H2S) and hydropersulfides (RSSH) are crucial mediators in a variety of physiological and pathological processes. Their regulatory roles span from maintaining cellular redox balance to influencing signaling pathways critical for homeostasis and stress responses. This dissertation investigates H2S and RSSH as biologically important molecules and explores the development of boron-dipyrromethene (BODIPY)-based photocages for its controlled, light-triggered release. Given H2S and RSSH's critical role in redox regulation and cellular protection, achieving spatiotemporal control over its delivery is essential for both therapeutic and research applications. BODIPY scaffolds offer favorable photophysical properties, including visible-light activation …

Reduced Order Models Of Hydrodynamically Interacting Flapping Wings, Jose Pabon

Dissertations

Fish schools exhibit a collective behavior and self-organization that is mediated by hydrodynamic interactions between individual fish. However, the long-time evolution of hydrodynamically interacting collectives is challenging to investigate due to the persistent influence of long-lived vortical structures, and the high-resolution requirements of direct numerical simulation at large Reynolds numbers. Reduced-order models have therefore played an important role in theoretical investigations of collectives of swimming bodies. The main results detailed herein are several new reduced-order models of swimmers that self-propel by flapping, i.e., by executing a prescribed periodic rigid body motion. The models are extensions of a discrete-time dynamical system …

Optimizing Hip And Knee Assistance For Walking And Sit-To-Stand Transitions: An Intrinsic Muscle Mechanics Based Predictive Approach, Neethan Ratnakumar

Dissertations

As the global population ages, the demand for wearable assistive technologies continues to rise, driven by their potential to enhance mobility and independence in older adults. Effectively designed controllers for lower-limb exoskeletons to assist sit-to-stand (STS) and walking are crucial for delivering efficient, safe, and comfortable assistance during daily activities. Traditionally, controller optimization involves biomechanical modeling and user-specific customization. Musculoskeletal simulations play a central role in this process by providing insights into human-exoskeleton interaction dynamics, thereby informing and refining control strategies.

This work presents a simulation-driven approach for developing exoskeleton controllers for walking and STS using two distinct methods: optimal …

Development And Implementation Of Novel Mass Spectrometric Methods For Metabolism Studies In Drug Discoveries, Huifang Yao

Dissertations

The field of drug discovery has evolved significantly over the past few decades, with a growing emphasis on understanding the metabolic pathways and biotransformation processes that influence the pharmacokinetics and pharmacodynamics of drug candidates. Novel mass spectrometric methods have emerged as powerful tools in this domain, facilitating the comprehensive analysis of metabolic profiles and enabling the identification of metabolites with implications for safety, efficacy, and overall drug development. However, challenges remain in quantifying metabolic flux—an essential aspect of understanding drug action—particularly due to the limitations of traditional isotope kinetic assays, which often involve lengthy sample preparation and the use of …

Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel

Graduate Masters Theses

Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …