Digital Commons Network^™

Clustering 24-Hour Ambulatory Blood Pressure Time Series With Dynamic Time Warping And Time Warp Edit Distance, John Knight

Theses and Dissertations

Ambulatory blood pressure monitoring (ABPM) captures dynamic circadian changes in blood pressure (BP) that are not reflected in static clinic readings. This study applied time-series clustering with two elastic distance measures—Dynamic Time Warping (DTW) and Time Warp Edit Distance (TWED)—to identify distinct phenotypes in 2,155 24-hour ABPM time series from participants in the Maracaibo Aging Study. DTW and TWED both yielded three clusters corresponding to non-dipping, moderate-dipping, and strong-dipping patterns. The non-dipping group showed elevated nighttime BP, associated with greater cardiovascular and cognitive risk, while the strong-dipping group was associated with higher education and younger age in baseline clinic measurements. …

Seagrass Preference Among Pinfish In The Lower Laguna Madre, Nathaniel Garza

Theses and Dissertations

Pinfish (Lagodon rhomboides) is a common estuarine fish species found from Massachusetts to the Yucatan, Mexico. As juveniles, pinfish spend a significant portion of their life in coastal seagrasses which provide both shelter from predators and food. Along the Texas coast, there are three major species of seagrass- turtle grass (Thalassia testudinum), manatee grass (Syringodium filiforme) and shoal grass (Halodule wrightii) that differ in structural complexity. The goal of this study was to determine if pinfish associate more with one seagrass species than the others. A year-long field study was completed using twelve sample sites in the Lower Laguna Madre, …

Population Structure Of Red Drum (Sciaenops Ocellatus (Linnaeus, 1766)) In Two Systems In The Northwestern Gulf Of Mexico, Sandra Antonia Leal

Theses and Dissertations

Red drum (Sciaenops ocellatus) are an economically significant species of fish inhabiting the Gulf of Mexico. There are limited studies assessing S. ocellatus population structure focused on the southern coast of Texas. A total of 1,008 fish were collected over one year on a quarterly basis at South Bay (SB) and Holly Beach (HB) in the Lower Laguna Madre (LLM) of Texas to assess population structure. Juvenile S. ocellatus utilize the water systems of the LLM as a nursery ground and were more abundant at SB (n = 718) than HB (n = 290). The most abundant age classes were …

Investigating Mariculture-Associated Ecosystem Services Across The Northern Gulf Of Alaska, Josianne Haag

Oceanography

The rapid expansion of mariculture in Alaska can drive physical and chemical alterations to the marine environment by introducing non-native organisms or artificially increasing the biomass of a native species. Currently, the main mariculture products grown in Alaska include the Pacific oyster (Crassostrea gigas), the Pacific blue mussel (Mytilus trosuslus), and three macroalgae species: ribbon kelp (Alaria marginata), sugar kelp (Saccharina latissima), and bull kelp (Nereocystis luetkeana). This dissertation examines how these species can impact their surrounding environment to better inform management practices for this growing industry. This research characterized the resource use of C. gigas and M. trossulus seasonally …

A Mixed Methods Study Of The Weather And Climate Science Curriculum Pilot In South Carolina K-12 Schools, 4-H, And Agricultural Education Programs, Emily B. Hood

All Dissertations

Weather and climate science topics in K-12 education are more important now than ever due to extreme weather and climate events happening worldwide. Most U.S. science teachers included climate science in their courses, but they may not have a sufficient background in the topic which can hinder their efforts, or there is no explicit curriculum for the teacher to utilize. Research indicates that there is a need for innovation in the curriculum to help prepare children to become the next generation of leaders and address complex problems, such as issues related to weather and climate science. There are a few …

Taxonomy Of Endophytic Fungi Associated With Vallisneria Neotropicalis, Md. Arafat Rashid

Graduate Theses and Dissertations (2019 - present)

This study presents the first comprehensive taxonomic and ecological investigation of endophytic fungi (EF) associated with the submerged aquatic macrophyte Vallisneria neotropicalis in the southern United States. Over a 12 month period, from April 2023 to March 2024, leaf samples were collected from two distinct sites in Mobile Bay, Alabama a disturbed, brackish Causeway location and a cleaner, less impacted site at Meaher State Park. Using culture dependent methods, a total of 257 fungal endophytes were isolated from 1,200 leaf segments. All isolates belonged to the phylum Ascomycota, distributed across 3 classes, 6 orders, 10 families, and 19 taxa. The …

A Molecular Mechanism Of Epithelial To Mesenchymal Transition (Emt): An Evidence Based Lesson Applying Molecular Biology Through The Lens Of Cancer, Sophie Hasson, Melissa Rowland-Goldsmith

Open Educational Resources

This lesson aims to strengthen students’ critical thinking and molecular biology data analysis skills as well as their understanding of concepts related to the hallmark of cancer: tissue invasion and metastasis. Students begin by learning about the invasion of cancer cells, Epithelial-Mesenchymal Transition (EMT), and an important protein involved in EMT: E-cadherin. They then apply molecular biology knowledge to analyze data from multiple papers to infer the relationship between Snail and E-cadherin in different types of cancers. Next, they continue to interpret data from many papers to determine that a repressor transcription factor is present during EMT in cancer cells …

From Morphology To Machine Learning And Genomics: Understanding Phenotypic Variation In Wild Ducks, Sara Gonzalez

Open Access Theses & Dissertations

Understanding the genetic underpinning and distribution of phenotypic variation within and between divergent groups is core towards shedding light into how populations diverge and adapt, as well as how hybridization breaks or builds on these scenarios; and thus, central to evolutionary biology. In wild organisms, however, quantifying and linking phenotypic traits to underlying genetic processes, like mutation, gene expression, epigenetics and allele interactions, remains challenging. This difficulty arises from the complex interplay between morphology, environment, and gene regulation, as well as the logistical barriers of collecting and standardizing large-scale data across individuals and populations. As a result, researchers are increasingly …

What Limits Dryland Ecosystems? Patterns Of Soil Fertility And Resource Limitation In The Chihuahuan Desert, Dylan Stover

Open Access Theses & Dissertations

Human activities are substantially altering global resource cycles with widespread implications for biogeochemistry and ecosystem functioning globally. Drylands, regions where precipitation is outweighed by water losses, are especially sensitive to these large shifts in resource cycles due to their inherently low and variable resource availability. In these regions, resource availability and biological activity are often concentrated around plants – or fertile islands – and predominantly driven by pulses of water. However, our knowledge of the processes influencing biological productivity in drylands – patterns of soil fertility and resource limitation – remains lacking, and their unique biogeochemical and biological processes create …

Gpu-Based Electromagnetic Microwave Tomography For Brain Imaging And Stroke Detection, Pablo Sotelo Torres

Open Access Theses & Dissertations

Each year, an estimated 795,000 people in the U.S. suffer a stroke, with approximately 610,000 being first-time cases. Of these, 87% are ischemic strokes, while the remaining 13% are hemorrhagic. Current imaging methods, such as Computed Tomography (CT), Positron Emission Tomography (PET), and Magnetic Resonance Imaging (MRI), provide useful information into brain tissue properties; while each technique has its advantages, they remain expensive, non-portable, and often too slow for emergency bedside or in-ambulance use. Electromagnetic Microwave Tomography (EMT) offers a promising alternative: an affordable, portable, rapid, and safe method for stroke detection. By contrasting dielectric properties between healthy and affected …

The Transition Zone Hypothesis On Biodiversity Of The Indian River Lagoon System, Florida, Richard L. Turner

Ocean Engineering and Marine Sciences Faculty Publications

The Indian River Lagoon System (IRL) is regarded as having a high level of biodiversity. The level of biodiversity is often attributed in part to the 2-degree latitudinal span (251 km) of the IRL and to its position in a transitional zone between tropical and temperate biotic provinces. This hypothesis was tested for submerged aquatic vegetation (SAV) based on a recent treatise (Littler, Littler, and Hanisak, 2008). Five of seven species of seagrass are tropical, and two have either a broad or very narrow latitudinal distribution; the transition-zone hypothesis does not hold for seagrasses. Most macroalgae (131 spp.) are tropical/subtropical; …

Evaluation Of Ramp Instead Of Forage During Grain Adaptation And Different Sorghum Varieties On Enteric Methane Production From Cattle, Jack T. Fort

Department of Animal Science: Dissertations, Theses, and Student Research

Two experiments were conducted to evaluate the use of RAMP (Cargill Corn Milling, Blair, Nebraska) compared with traditional forage-based adaptations on methane (CH₄) and carbon dioxide (CO₂) emissions, performance, and carcass characteristics. Experiment 1, 64 yearling British × Continental steers (initial BW = 423 ± 6 kg) were adapted using 100% RAMP (RAMP) or a traditional forage diet (CON; 43% forage) before transitioning 22 d to a common finishing diet containing 65.6% steam-flaked corn. Emissions were measured in paired replications using a two-chamber indirect calorimetry barn. During adaptation RAMP did not affect CH₄ production (g/d; …

Integrating Innovative Sensing And Ground Measurements For Forage Mass Estimation In Rye Pasture, Pedro Henrique Jota Fernandes

Department of Animal Science: Dissertations, Theses, and Student Research

The United States beef industry relies on forages to provide up to 80% of total lifetime dry matter intake, making accurate forage mass estimation essential for determining stocking rates, improving grazing efficiency, and supporting economic sustainability. Traditional methods to quantify forage mass, however, are time-consuming and labor-intensive. This thesis presents research efforts to achieve accurate forage mass estimation in cereal rye pasture by integrating novel sensing technologies.

Chapter 1 reviews the importance and evolution of forage mass estimation methods, from destructive clipping to indirect approaches based on canopy measurements. It then introduces remote sensing, from proximal tools to drone- and …

Effect Of Planting Date, Insecticide Efficacy, And Hail Injury On Soybean Gall Midge (Resseliella Maxima Gagné) Infestation In Soybean, Natasha Hiromi Umezu

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

Resseliella maxima Gagné (Diptera: Cecidomyiidae) is a recently described and economically significant pest of soybean (Glycine max (L.) Merr.) in the Midwestern United States. Since its identification in 2019, this species has become widespread and is now associated with substantial yield losses in parts of the region. Prior to its formal description, orange larvae were observed in soybean associated with plants damaged by hail, suggesting that plant injury may influence infestation. Given the pest’s economic importance, understanding the role of hail injury and developing effective, integrated management strategies are critical for mitigating its impact.

Field studies were conducted to …

When Thermal Risk Indices Work And When They Don't: A Case Study Of Two Maize Insect Pests, Komi Mensah Agboka, Frank Thomas Ndjomatchoua, Luca Rossini, Ritter A. Guimapi, Elfatih M. Abdel-Rahman

All Peer-Reviewed Publications

The biological life cycle of terrestrial arthropods, using temperature as the primary driving factor has a large interest for insect pests in agriculture, forestry, urban ecosystems, as constitutes the basics for the development of mathematical models for decision making. A recent study proposed a physiologically-based risk index (RI) which finds large applications in the definition of risk maps; however, further case studies are needed to better explore its strengths and limitations. This study aims to extend this knowledge by presenting an application of the RI on two economically significant pests: the fall armyworm Spodoptera frugiperda and the stem borer Busseola …

The Effects Of Green Orientation And Technological Agility On Sustainable Competitive Advantage Under Environmental Uncertainty: Organizational Agility As A Pathway, Sahilali Saiyed, Vimal Kumar, Abdul Waaje, Adi Prasetyo Tedjakusuma

Michigan Tech Publications

Despite the strengthened efforts on sustainability and technological activities by firms, the existing literature lacks a clear picture regarding how green orientation (GO) and technological agility (TAG) can be transformed into sustainable competitive advantage (SCA) and at what time the conversion process may be most efficient. This paper conceptualizes organizational agility (OGA) based on the resource-based view (RBV) and dynamic capabilities theory (DCT) and hypothesizes that GO and TAG indirectly affect SCA with the mediating impact of environmental uncertainty (ELU). A moderated-mediation model was tested based on a sample of 200 managers (HR, marketing, accounting/finance, quality control, R&D) of auto-parts …

Spotted Seal Coastal Haul Out Behavior In Arctic Alaska, Maeghan Connor

Biological Sciences

Hauling out - the act of exiting the water to rest, molt, breed, and pup on solid surfaces - is a key behavior of pinnipeds worldwide. Unlike other ice seals (i.e., ice-associated phocid species), spotted seals (Phoca largha) in Alaska frequently use terrestrial substrates to haul out during the summer and fall open-water period in the Chukchi and Beaufort Seas. Despite being a core aspect of spotted seal ecology, their terrestrial haul out behavior remains understudied. To address this, we analyzed data collected from 2020 - 2022 near two known haul out sites in Dease Inlet, Alaska, including time-lapse camera …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Margalefidinium Polykrikoides Group Iii Va, Usa Strain Growth And Sac-Like Pellicle Cyst Dynamics, Eduardo Pérez Vega

OES Theses and Dissertations

Margalefidinium polykrikoides is a harmful cosmopolitan dinoflagellate that blooms in coastal waters. The effect of temperature and salinity on the growth of M. polykrikoides VA strain was examined using microscopy and growth models. M. polykrikoides Group III VA strain grew better at warmer temperatures and lower salinities than M. polykrikoides Group III NY strain, Group I Korea strain, and Japan strain (unknown group). Modelers need to use the temperature and salinity growth responses from M. polykrikoides Group III VA strain to better simulate and predict M. polykrikoides blooms in the Chesapeake Bay.

Dinoflagellates produce cysts as a strategy to withstand …

Expression, Purification And Characterization Of Full Length Tdp-43, Danya Abouzaid

Honors Theses

TAR DNA-binding protein 43 (TDP-43) is a 43 kDa RNA-binding protein linked to several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. 5-7,28,30,33 Studying full-length TDP-43 has been difficult because of its intrinsic instability and tendency to aggregate.19,25,28,33,36 In this study, we focused on overcoming the difficulties to express full-length TDP-43 in E. coli recombinantly. We focused on expressing full-length TDP-43 as a fusion construct with a maltose-binding protein (MBP) to improve solubility and stability. Our strategy was to purify TDP-43-MBP fusion and make biomolecular condensates with RNA before cleaving the tag with thrombin protease. …

Interactions Between Black, Brown, Blue And Green Carbon From Terrestrial To Marine Ecosystems: A Critical Review, Allison White, Richard Kline, Md. Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Black and brown carbon are byproducts of the incomplete combustion of biomass or fossil fuels. These light-absorbing aerosols influence climate by altering the radiative balance through the absorption and scattering of sunlight, exacerbating global climate change. Their subsequent deposition on terrestrial and marine environments affects surface albedo, snow and ice melt, and biogeochemical processes, leading to further environmental consequences. In contrast, green and blue carbon refer to carbon stored in terrestrial vegetation and marine ecosystems, respectively. These ecosystems play a crucial role in mitigating climate change by sequestering atmospheric carbon; however, they are increasingly threatened by climatic disturbances, anthropogenic activities, …

Leptinotarsa Texana Schaeffer And Gargaphia Arizonica Drake & Carvalho As Potential Biocontrol Agents For The Noxious Weed Solanum Elaeagnifolium Cav, Samikshya Subedi, Stephanie L. Kasper, Alexis Racelis, Greg Lefoe, Rupesh R. Kariyat

School of Earth, Environmental, & Marine Sciences Faculty Publications

Silverleaf nightshade (Solanum elaeagnifolium Cav.; SLN) is a perennial forb native to the southern United States, Mexico and South America that has become a serious agricultural weed across the world. Biological control has emerged as a significant alternative for the management of (SLN) due to the challenges and high costs associated with chemical and mechanical controls. In this study, we used a combination of field and laboratory studies to (1) explore the fundamental and realized host ranges of two North American insects, Leptinotarsa texana Schaeffer and Gargaphia arizonica Drake & Carvalho and (2) assess their suitability as potential biological …

Regional Variation And Epidemiological Insights In Malaria Underestimation In Cameroon, Sarafa A. Iyaniwura, Qing Han, Ngem Bede Yong, Ghislain Rutayisire, Agnes Adom-Konadu, Okwen Patrick Mbah, David Poumo Tchouassi, Kingsley Badu, Jude Dzevela Kong

All Peer-Reviewed Publications

Background: Despite significant global effort to control and eradicate malaria, many cases and deaths are still reported yearly. These efforts are hindered by several factors, including the severe underestimation of cases and deaths, especially in Africa. Methods: We used a mathematical model, incorporating the underestimation of cases and seasonality in mosquito biting rate, to study the malaria dynamics in Cameroon. Using a Bayesian inference framework, we calibrated our model to the monthly reported malaria cases in ten regions of Cameroon from 2019 to 2021 to quantify the underestimation of cases and estimate other important epidemiological parameters. We performed Hierarchical Clustering …

The Dissemination Potential Of Microsporidia Mb In Anopheles Arabiensis Mosquitoes Is Modulated By Temperature, Fidel Gabriel Otieno, Priscille Barreaux, Affognon Steeven Belvinos, Edward Edmond Makhulu, Thomas Ogao Onchuru, Anne Wambui Wairimu, Stancy Mandere Omboye, Cynthia Nyambura King’Ori, Bonoukpoè Mawuko Sokame, Anthony Kebira Nyamache, Jeremy Keith Herren

All Peer-Reviewed Publications

Microsporidia MB, a vertically transmitted endosymbiont of Anopheles mosquitoes, shows strong potential as a malaria control agent due to its ability to inhibit Plasmodium development within the mosquito host. To support its deployment in malaria transmission reduction strategies, it is critical to understand how environmental factors, particularly temperature, influence its infection dynamics. In this study, we investigated the impact of four temperature regimes (22 °C, 27 °C, 32 °C, and 37 °C) on Microsporidia MB prevalence and infection intensity by rearing mosquito larvae under controlled laboratory conditions. Our results demonstrate that elevated temperatures, especially 32 °C, significantly enhance both larval …

Large Language Models (Llms) For Clinical Note Generation: International Classification Of Disease (Icd) Code, Knowledge Graph (Kg) And Prompt Evaluation, Ivan P. Makohon

Computer Science Theses & Dissertations

In the past decade, a surge in the amount of electronic health record (EHR) data in the United States occurred, driven by a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients’ assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering them. Manually writing these notes is time-consuming, increasing patient waiting times and potentially delaying diagnoses. Large language models (LLMs), such as GPT-4o, possess the ability …

Normalization Of Temperature Effects For Quality Assurance Of Quantitative Prostate Apparent Diffusion Coefficient Imaging Across Multiple Sites, Ken-Pin Hwang, Joshua Yung, R Jason Stafford, Caroline Chung, Aradhana M Venkatesan

Faculty, Staff and Student Publications

Background: Apparent Diffusion Coefficient (ADC) as measured by diffusion weighted imaging is known to negatively correlate with prostate tumor aggressiveness. Heterogeneity in system and protocol performance causes potential variability in ADC acquired across a large scanner network, prompting a need to evaluate quantitative ADC from a prostate-specific MR diffusion protocol as part of quality assurance (QA). Due to the temperature dependence of ADC, repeatability and reproducibility assessments typically require phantoms to maintain a temperature of 0°C, imposing a considerable burden when assessing large numbers of scanners.

Purpose: To develop a QA procedure at room temperature for assessing the reproducibility of …

Smags-Lasso: A Novel Feature Selection Method For Sensitivity Maximization In Early Cancer Detection, Hamid Khoshfekr Rudsari, Sara Khorami-Sarvestani, Johannes F Fahrmann, James P Long, Samir Hanash, Kim-Anh Do, Ehsan Irajizad

Faculty, Staff and Student Publications

Background: Sensitivity and specificity are foundational metrics for cancer detection tools. However, most machine learning algorithms prioritize overall accuracy during optimization, which fails to align with clinical priorities of early detection. We aim to develop a feature selection machine learning algorithm while maximizing sensitivity at a given specificity.

Methods: We developed SMAGS-LASSO, a machine learning algorithm that combines our developed Sensitivity Maximization at a Given Specificity (SMAGS) framework with L1 regularization for feature selection. This approach simultaneously optimizes sensitivity at user-defined specificity thresholds while performing feature selection. SMAGS-LASSO utilizes a custom loss function with L1 regularization and multiple parallel optimization …

Forecasting Chemoradiation Response Midtreatment For High-Grade Gliomas Through Patient-Specific Biology-Based Modeling, David A Hormuth, Maguy Farhat, Bikash Panthi, Holly Langshaw, Mihir D Shanker, Wasif Talpur, Sara Thrower, Jodi Goldman, Sophia Ty, Calliope Custer, Jeanne Kowalski, Thomas E Yankeelov, Caroline Chung

Faculty, Staff and Student Publications

Purpose: The entire course of radiation therapy (RT) for high-grade glioma (HGG) is currently derived from pre-RT magnetic resonance imaging (MRI). Although it is possible to adapt RT during the course of treatment, it is often guided only by anatomical changes to the tumor. This study seeks to determine if a biology-based mathematical model, parameterized by patient-specific, multiparametric MRI (mpMRI) data, can accurately forecast HGG response during RT.

Methods and materials: Twenty one patients with HGG planned for 6 weeks of concurrent RT and chemotherapy were imaged weekly with mpMRI during RT and at 1, 2, and 3 months post-RT. …

Personalized Risk Prediction For Cancer Survivors: A Generalized Bayesian Semi-Parametric Model Of Recurrent Events With Competing Outcomes, Nam Hoai Nguyen, Seung Jun Shin, Elissa Dodd-Eaton, Jing Ning, Wenyi Wang

Faculty, Staff and Student Publications

Multiple primary cancers are increasingly more frequent due to improved survival of cancer patients. Characteristics of the first primary cancer largely impact the risk of developing subsequent primary cancers. Hence, model-based risk characterization of cancer survivors that captures patient-specific variables is needed for healthcare policy making. We propose a Bayesian semi-parametric framework, where the occurrence processes of the competing cancer types follow independent non-homogeneous Poisson processes and adjust for covariates including the type and age at diagnosis of the first primary. Applying this framework to a historically collected cohort with families presenting a highly enriched history of multiple primary tumors …

Knowledge Mapping And Visualized Analysis Of Research Progress In Onconephrology: A Bibliometric Analysis, Yiwei Wang, Shuling Fan, Wei Wang

Faculty, Staff and Student Publications

Objectives: Onconephrology is an expanding subspecialty focused on the management of cancer patients with renal injury. This study used a comprehensive bibliometric analysis to emphasize the need for cooperation between oncologists and nephrologists, exploring current trends and future research areas in onconephrology.

Methods: Relevant literature on onconephrology published between 1 January 2000 and 27 April 2024 was retrieved from the Science Citation Index Expanded of the Web of Science Core Collection, followed by manual screening. Bibliometric analyses were performed using CiteSpace, VOSviewer, and Bibliometrix software.

Results: A total of 1,853 publications, including 1,647 articles and 206 reviews, by 11,606 authors …