Digital Commons Network^™

Characterization Of Phytoplankton-Excreted Metabolites Mediating Carbon Flux Through The Surface Ocean, Yuting Zhu, Hanna S. Anderson, Eli Salcedo, Samuel E. Miller, Krista Longnecker, Melissa C. Kido Soule, Sheean T. Haley, Gretchen J. Swarr, Rogier Braakman, Sonya T. Dyhrman, Elizabeth B. Kujawinski

Chemistry & Biochemistry Faculty Publications

The marine labile dissolved organic carbon (DOC) pool is a dynamic reservoir of thousands of molecules that cycles approximately one-quarter of Earth’s primary production within days to weeks. After excretion by phytoplankton and other microbes, metabolites are rapidly consumed, resulting in low standing concentrations (picomolar to low nanomolar). Despite the decades-long search for labile DOC sources and molecular identities, marine phytoplankton exometabolomes are not well characterized, largely due to difficulties in measuring small polar molecules in saline water. Here, we profiled the exometabolomes of six axenic phytoplankton species representing key functional groups including a diatom (Thalassiosira pseudonana CCMP1335), a …

Mitochondrial Genome Of The Indo-Pacific Mesophotic Coral Leptoseris Columna (Scleractinia: Agariciidae) Assembled Using Pacbio Long-Read Sequencing, Nomita Rani Adhikary, Daniel J. Barshis, J. Antonio Baeza

Biological Sciences Faculty Publications

Leptoseris columna, a mesophotic coral species belonging to the family Agariciidae, is distributed throughout the Indo-Pacific region. This species is considered as of "Least concern" by the IUCN, yet, faces multiple local and global stressors. To support conservation plans, this study sequenced and characterized the complete mitochondrial genome of L. columna. The complete mitochondrial genome of Leptoseris columna was assembled using PacBio long-reads with a coverage of 459× per bp. The AT-rich mitochondrial genome of Leptoseris columna is 18,546 bp long and comprises 13 protein-coding genes (PCGs), 2 transfer RNA genes (trnM and trnW), and 2 ribosomal RNA …

Land Use Influences Dissolved Organic Matter Composition In The U.S. Coastal Critical Zone Network, Aleksandar I. Goranov, Elizabeth V. Whitney, Brian R. Moyer, Katherine L. Tully, Patrick G. Hatcher, Yu-Ping Chhin

Chemistry & Biochemistry Faculty Publications

Coastal watersheds are highly productive biogeochemical systems supporting robust coastal fisheries and contributing significantly to the marine gross primary production flux. These ecosystems are comprised of civil infrastructure, farms, forests, and marshes, and their diversity is reflected in the quantity and quality of dissolved organic matter (DOM). Here, we assess the role of farming in influencing DOM from surface waters of six coastal tidal creeks adjacent to forest and farm sites in the US Critical Zone Network. Molecular fingerprinting using electrospray ionization - Fourier transform - ion cyclotron resonance - mass spectrometry revealed that farm-influenced DOM was enriched in nitrogen-, …

Agricultural Productivity Under Energy Development: Insights From California, Wai Yan Siu, Sherzod B. Akhundjanov

ODU Articles

This paper examines how agricultural productivity patterns in Kern County, California, a leading region for both agricultural production and oil and gas development, co-vary with the spatial and temporal expansion of hydraulic fracturing and associated energy infrastructure. Using parcel- and county-level analyses, we characterize how agricultural productivity differs across proximity to energy development and across spatial scales. The results reveal spatially heterogeneous and scale-dependent patterns: parcel-level evidence indicates lower Enhanced Vegetation Index-based vegetation productivity within the 20-mile proximity zone around fracking wells, while county-level results show heterogeneous crop-specific yield changes during the post-expansion period. Together, these findings highlight the importance …

Wearable Sensor-Based Phase Segmentation Analysis Of Front Crawl Swimming: A Scoping Review, Jonathan Simoes, Samuel Aylward, Daniel Hamze, Daniel James Goble, Daniel M. Russell, Joshua Haworth

Exercise Science Faculty Publications

Front crawl swimming stroke phase segmentation has historically relied on video analysis, but the development of wearable sensor technology has created new opportunities for automated phase segmentation. This scoping review mapped the available evidence on wearable sensor-based stroke phase segmentation methods in front crawl swimming, following PRISMA-ScR guidelines. A systematic search of SPORTDiscus, Web of Science, and IEEE Xplore conducted from January to June 2026, identified 15 eligible peer-reviewed studies published between 2000 and 2024. The review revealed an emerging field of research that has converged methodologically around inertial measurement units (IMUs) and the Chollet phase segmentation framework while remaining …

Role Of Estrogen Receptor Alpha In Modulating The Circadian System In Female Mice, Victoria Alvord

Theses and Dissertations--Biology

Circadian rhythms are approximately 24-hour cycles of physiology and behavior. Circadian rhythms of eating, or meal timing, are linked to cardiometabolic dysfunction in humans. Mistimed eating, such as breakfast skipping and eating late at night, increases the risk of obesity, diabetes, and cardiovascular disease in humans. Likewise, disrupted eating rhythms cause obesity in mice. This dissertation investigates how estrogens regulate eating behavior rhythms and tissue clock timing in female mice. Chapter 1 reviews three key components critical to this work. The first is an overview of the field of chronobiology and the function of the circadian system. The second is …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

Exploring The Limitations Of Substrate Scope In Dimethylallyltryptophan Synthases, Evan T. Miller

Theses and Dissertations--Pharmacy

Natural products (NPs), are the largest source of bioactive compounds in Nature, and are essential to the treatment of human disease. Nearly 50% of drugs approved for use from 1981 to 2019 owe some aspect of their development to NPs, either in terms of their structure, pharmacophore, or mechanism of action. However, NPs are difficult to structurally optimize. Chemoenzymatic methods for NP derivatization have been increasingly seen as practical alternatives to traditional synthetic methods. Prenyltransferases (PTs) are involved in the primary and secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically …

Using Camera-Based Unmarked Spatial Capture-Recapture Modeling To Estimate Reintroduced Elk (Cervus Canadensis) Population Parameters And Distribution In Southeastern Kentucky, Claire Marie Muia

Theses and Dissertations--Forestry and Natural Resources

Estimation of population parameters is important for wildlife management decisions. Elk reintroduced to southeastern Kentucky experienced early irruptive population growth and are currently monitored using a statewide harvest-based statistical population reconstruction model (SPR) across the Kentucky Elk Restoration Zone (KERZ). Because the SPR model is spatially coarse and difficult to scale to the smaller management units comprising the KERZ, we conducted a spatially explicit capture-recapture study using a clustered camera-trapping array deployed for 10 weeks from June–August 2024 to estimate elk population parameters within Management Unit 4. Due to a lack of resights of GPS-marked elk, population parameters were estimated …

Understanding Knowledge And Perceptions Of The Beef Industry On A Land-Grant University Campus, Allison E. Reaves

Theses and Dissertations--Community & Leadership Development

A well-researched phenomenon in the agricultural industry is the effects of constant innovation coupled with an increasing divide between producer and consumer. This issue has been presented as especially prevalent within animal agriculture and the beef industry, a predominant concern considering Kentucky’s agricultural commodities. This study (n = 31) utilized a mixed-methods approach to understand the knowledge, perceptions, and behavior of beef consumers on a land-grant university campus. Methodologies included Python’s DeepFace emotion recognition, semi-structured interviews, and the JMALI agricultural literacy assessment. Findings revealed participants to be below expected agricultural literacy levels of high school graduates (M=11), with no …

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …

Impacts Of Management Practices And Soil Properties On Free-Living Nitrogen Fixation In Eastern South Dakota, Laura Galvan Nuevo

Electronic Theses and Dissertations

Free-living nitrogen (N) fixation (FLNF) may represent a sustainable pathway to supplement crop N demand in agroecosystems, yet edaphic and management factors regulating this process under field conditions remain poorly understood in the Northern Great Plains. Using 15N2 direct method to quantify potential FLNF (pFLNF) and baseline FLNF (bFLNF), this thesis investigates how crop rotations (2-, 3-, and 4-year systems), tillage management (conventional vs. no-till), cover cropping, and soil properties affect the potential of free-living diazotrophs to supply N via FLNF in a long-term no-till corn-based system in Southeastern South Dakota. A two-year field study evaluated pFLNF across four growing …

Design, Syntheses And Biological Applications Of Fluorescent Probes For Nad(P)H, Hsa And Cellular Microenvironment Sensing, Adenike M. Olowolagba

Dissertations, Master's Theses and Master's Reports

Fluorescent probes have emerged as powerful tools for investigating complex biological processes due to their high sensitivity, selectivity, and capability for real-time, non-invasive imaging. In particular, the detection of key biomolecules such as NAD(P)H, viscosity-related parameters, human serum albumin (HSA), and pH is essential for understanding cellular metabolism, redox homeostasis, and disease progression. In Chapter 2, three coumarin-based fluorescent probes (A–C) were designed, synthesized, and characterized for monitoring NAD(P)H levels in living cells. Probes A and B feature coumarin–cyanine hybrid structures linked via vinyl and thiophene bridges to 3-quinolinium acceptors, respectively, while probe C incorporates a dicyano moiety to replace …

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Applied Forest Restoration And Conservation In Michigan: Advancing American Beech Restoration And Documenting A Historical Insect Collection, Thomas E. Panella

Dissertations, Master's Theses and Master's Reports

Forest restoration and conservation require both practical management approaches and the preservation of biological resources that support future research. This dissertation presents applied research conducted in Michigan that advances American beech (Fagus grandifolia) restoration in response to beech bark disease (BBD) while documenting an important historical entomological resource. Chapters 1–3 focus on overcoming practical barriers to American beech restoration. Restoration protocols were developed and refined for identifying BBD-resistant trees, graft propagation, rootstock collection, container production, and the field establishment of grafted BBD-resistant trees. A greenhouse experiment evaluated the influence of growing media and fertilization on container stock quality, …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

Rate Response Of Curlyleaf Pondweed And Native Plants To Flumioxazin In Minnesota Lakes, Pearl J. Jensen

All Graduate Theses, Dissertations, and Other Capstone Projects

Curlyleaf pondweed (Potamogeton crispus L.) is an invasive aquatic plant present across the United States that causes significant recreational issues, outcompetes native plant species, and depletes water quality. Before senescing in mid-summer, curlyleaf pondweed forms a large number of turions that can lay dormant in the sediment for several years. Typical herbicide management of this species occurs in early spring to target the plant before turion production occurs and while native plants are dormant. Flumioxazin has shown potential in curlyleaf pondweed management in small scale studies, but its effects have not been assessed in operational management. In this study, treatments …

The Forensic Implications Of Hydrochloric Acid (Hcl) Exposure On Dna Preservation In Human Teeth, Shaelyn Lee Zimmerman

Graduate Student Theses, Dissertations, & Professional Papers

Identity is a human right, and forensic anthropological methods are often aimed at returning identity to decedents. Three main pathways are used for the identification of human remains: fingerprints, dental records, and DNA analysis. Identification efforts may be hindered when perpetrators attempt to obscure the victim’s identity. In cases where corrosive substances, such as hydrochloric acid (HCl) are used, dental comparison and fingerprinting often fail and genetic analysis becomes the best chance of achieving personal identification.

Previous studies have shown teeth are an excellent source of DNA. Large, multi-rooted teeth, such as molars, are often preferred because they contain the …

Labor Savings From Mechanical Rice Transplanting In Bangladesh, India, Nepal, And The Philippines: A Systematic Review And Meta-Analysis, Rodrigo S. David

ASEAN Journal on Science and Technology for Development

Rice production in South and Southeast Asia faces serious challenges, including acute labor shortages and rising wages, which threaten regional food security. Mechanical rice transplanting offers a promising solution; however, evidence on labor savings, especially region-specific data, remains inconsistent. This systematic review and meta-analysis aimed to quantify labor savings from mechanical versus manual transplanting across Bangladesh, India, Nepal, and the Philippines.

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a systematic search was conducted across four major scientific databases (2000–2026) using Boolean search terms for mechanical transplanting and labor outcomes. Of 284 initial records, 52 met eligibility …

Climate And Seasonal Influences On Indo-Pacific Sea Level: Insights From 30 Years Of Satellite And Tide Gauge Data, Karlina Triana

ASEAN Journal on Science and Technology for Development

We analyze Indo-Pacific sea-level variability using monthly satellite altimetry (1993–2025) validated against records from 16 tide-gauge stations. Cross-comparisons show strong agreement, especially in the western Pacific, confirming the reliability of altimetry for regional assessments. Seasonal SLA variability is largest in the Bay of Bengal and South China Sea and reflects monsoonal forcing, whereas interannual fluctuations in the eastern Indian and western Pacific oceans are dominated by ENSO and modulated by PDO. Harmonic decomposition isolates annual and semi-annual cycles, and an EOF/PCA framework identifies the leading modes: EOF1 (30.8%) captures basin-scale interannual variability and EOF2 (20.9%) reflects the seasonal cycle. Spectral …

A Simple Statistical Tool To Correct The Daily Temperature Effect On Dielectric Soil Matric Potential Sensor Readings, Sebastián Bravo Peña, Meindert Commelin, Ole O. Wendroth

Plant and Soil Sciences Faculty Publications

High-resolution time series recorded by soil water dielectric sensors are often affected by other processes. Dielectric soil matric potential sensors, such as the TEROS 21, exhibit temperature sensitivity, resulting in deviations of readings from the true value due to soil temperature fluctuations. However, methods for correcting this effect remain limited. The objective of this study was to create a straightforward, scale-based statistical approach to mitigate the influence of daily temperature oscillations on matric potential dielectric readings. The temperature sensitivity correction function (TSCF) identifies, quantifies, and smooths diurnal fluctuations caused by soil temperature dynamics. We provide a detailed description of the …

Adversarial Robustness In Biomedical Time-Series Models, Rohan Tiwari

Bioengineering Theses

This study investigates adversarial vulnerabilities in deep learning models for biomedical time-series classification across two clinically important modalities: electrocardiography (ECG) and electroencephalography (EEG). Using the MIT-BIH Arrhythmia and CHB-MIT seizure datasets, I evaluate time-domain attacks (FGSM, PGD), Fourier-domain constrained attacks, and learned spectral perturbations designed to reveal modality-specific sensitivity patterns. Across both tasks, a consistent trend emerges low-frequency components (0–5 Hz) constitute a dominant axis of adversarial vulnerability, with perturbations in this range producing the steepest degradation in classification performance. In ECG models, protecting the physiologically relevant QRS band (5–20 Hz) significantly improves robustness, whereas EEG models remain highly sensitive …

Impacts Of Offshore Wind Energy Development On The Commercial Sea Scallop Fishery, Sarah Borsetti, Daphne M. Munroe, John M. Klinck, Andrew M. Scheld, Eileen E. Hofmann, Eric N. Powell, David B. Rudders

CCPO Publications

The Atlantic sea scallop (Placopecten magellanicus) fishery on the Northeast U.S. continental shelf generates approximately USD 500 million ex-vessel revenues annually, making it one of the most valuable single species fisheries in the United States. Wind energy development is planned for key areas on the U.S. Mid-Atlantic shelf where the Atlantic sea scallop fishery operates, creating novel challenges in managing trade-offs between traditional users like fisheries and new users like offshore wind energy. An agent-based modeling framework that integrates spatial dynamics in Atlantic sea scallop stock biology, fishing fleet behavior, and federal management decisions, was implemented to investigate …

The Shoreline Protection Potential Of Oyster Reefs: A Systematic Review And Meta-Analysis, Jessica R. Fergel, Robert E. Isdell, Gabriella Dipetto, Karinna Nunnez, Sean T. Gregory, Evan Hill, Donna Marie Bilkovic

Biological Sciences Faculty Publications

Nature-based solutions for erosion control that incorporate oyster reefs, alone or in combination with other habitats, are an increasingly popular approach due to their potential to protect shorelines and enhance oyster production. However, the extent to which natural or constructed oyster reefs provide shoreline protection remains unclear. We conducted a global systematic literature review and meta-analysis to summarize and evaluate the potential of oyster reefs in attenuating waves, promoting sediment accretion, and/or reducing shoreline erosion. Factors extracted from studies included shoreline protective measures examined, oyster reef structure type, and oyster reef tidal location. The results of the meta-analysis showed generally …

Investigating The Impact Of Cyanobacterial Harmful Algal Blooms On Freshwater Bivalves, Destiny Devlin

Theses, Dissertations and Culminating Projects

Harmful algal blooms (HABs) threaten freshwater ecosystems by producing toxins that disrupt aquatic organism functions and pose risks to human health. This study investigated how exposure to toxin-producing cyanobacteria affects the behavior and toxin accumulation of Asian clams (Corbicula fluminea) under controlled laboratory conditions. Asian clams were collected from a freshwater site in New Jersey, maintained in greenhouse bins, and fed either Microcystis novacekii (non-toxin-forming, control N=3) or Microcystis aeruginosa (toxin-forming, experimental N=3) at 100,000 cells/mL for 28 days. Weekly behavioral assays were conducted to track shell opening, burying, clustering, valve closure, foot extension, and time to first opening. Toxin …

Standardization Of Neuromuscular Reflex Analysis—Role Of Fine-Tuned Vision-Language Model Consortium And Openai Gpt-Oss Reasoning Llm-Enabled Decision Support System, Eranga Bandara, Ross Gore, Sachin Shetty, Ravi Mukkamala, Christopher K. Rhea, Brittany S. Samulski, Amin Hass, Atmaram Yarlagadda, Shaifali Kaushik, Malith De Silva, Andriy Maznychenko, Inna Sokolowska, Kasun De Zoysa

VMASC Publications

Background/Objectives: Accurate assessment of neuromuscular reflexes, such as the Hoffmann reflex (H-reflex), plays a critical role in sports science, rehabilitation, and clinical neurology. Conventional interpretation of H-reflex electromyography (EMG) waveforms is subject to inter-rater variability and interpretive bias, limiting reliability and standardization. This study aims to develop an automated, interpretable, and robust agentic AI–driven framework for H-reflex waveform analysis. Methods: We propose a fine-tuned Vision–Language Model (VLM) consortium combined with a reasoning Large Language Model (LLM)–enabled decision support system for automated H-reflex interpretation. Multiple VLMs were fine-tuned on curated datasets of H-reflex EMG waveform images annotated with expert clinical observations, …

Electronic Bills Of Lading And Blockchain Technology: A Regulatory Perspective, Hsin-Hua Tsai

Journal of Marine Science and Technology–Taiwan

Information and communications technology (ICT) systems are increasingly relevant to the maritime sector. Regarding the revolution of the bill of lading, many shipping lines and other technology startups have been looking into developing viable electronic transport documents that have the same functions as paper bills of lading to reduce supply chain risks. The limitations of the paper-based process have become increasingly visible in the COVID-19 crisis. The main purpose of the article is to analyze the application of blockchain bills of lading, which utilizes computational logic to create the digital ledger, and users can set up algorithms and rules to …

Intelligent Formation Control Using Orfbls And Adaptive Backstepping Sliding-Mode Control To Address Uncertain Tilting In Multi-Quadrotors During Wind Gusts, Ching-Chih Tsai, Chun-Fu Mao, Kumail Hussain

Journal of Marine Science and Technology–Taiwan

In terms of aerial robotics, stable and precise formation control is a significant challenge for tilting multi-quadrotors during disturbances. This paper proposes a fixed-time formation control strategy for tilting multi-quadrotors to address the effect of external wind gusts. The observer accurately predicts environmental disturbances and an adaptive backstepping sliding-mode control (ABSMC) method with an output recurrent fuzzy broad learning system (ORFBLS) addresses these disturbances within a finite time. ORFBLS dynamically adjusts its structure through a growing ORFBLS structure to allow nodes to be added as needed. The method's stability is validated using Lyapunov stability theory and ensures the convergence of …

Visually Guided Landing System On Ship Deck For Multicopter, Dong-Lin Li, Shih-Kai Lee, Tzu-Hsiang Chou

Journal of Marine Science and Technology–Taiwan

Traditionally, high-value fish have been located at sea using helicopters. However, with advancements in technology, maritime drones have become increasingly important in recent years. Compared to traditional helicopter-based methods, drones offer significantly lower operational costs, making them cost-effective. However, the challenging sea conditions, including strong winds and the swaying motion of vessels, pose significant challenges for drone landings.

This paper proposes a stable approach for multicopter landing on ships at sea, incorporating improved marker detection, enhanced wind resistance control, and more accurate deck motion prediction. In the marker detection phase, we introduce a method to improve the accuracy of ArUco …

Evaluating Matching Frontier Methods For Crash Modification Factor Estimation, Usama Elrawy Shahdah, Eman K . Ali, Sania Reyad Elagamy

Mansoura Engineering Journal

This study evaluates "matching frontier" methods against conventional approaches for estimating Crash Modification Factors (CMFs). Thirty-four method-model combinations were tested, including 16 frontier variants, 8 propensity-score-matching algorithms with negative binomial and mixed-effects models, and two benchmarks (empirical Bayes and cross-sectional), across multiple sample sizes and three true CMF values (0.80, 1.00, and 1.30). Of these, 30 converged successfully; 4 mixed-effects models with replacement-based matching failed due to duplicate control observations. Each scenario was evaluated across 10 Monte Carlo replications to quantify performance uncertainty.

Synthetic crash data were generated with known treatment effects, examining scenarios ranging from ideal (386 treated, 21,000 …