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Gradient Based Optimization Methods For Robust Learning And Biomedical Signal Modeling, Jarrod Mau

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation explores how modern artificial intelligence techniques can be used to better understand complex biological data. Specifically, it develops new machine learning based methods and applies them to two important biomedical problems: analyzing brain signals and studying protein behavior.

The first part of the work introduces a new machine learning approach designed to improve how computers classify structured data. Traditional neural networks are powerful but can sometimes generalize poorly. This research proposes a method that combines the flexibility of neural networks with the reliability of ensemble techniques, leading to more robust and accurate predictions across different types of datasets. …

Ecological Insights And Management Implications Of The Global Migratory Connectivity Of Green Turtles, Jaime Restrepo, Dina Nisthar, Harris Wei-Khang Heng, Lily K. Bentley, Corrie Curtice, Sarah Deland, Ei Fujioka, Patrick N. Halpin, Sarah K. Poulin, Roldán A. Valverde

School of Earth, Environmental, & Marine Sciences Faculty Publications

Aim

Green turtles are a widely distributed and highly migratory species; despite extensive data on their movement, there is no species-specific global synthesis on the subject. Based on three decades of published literature and building on previous global analyses, we developed a global network model of migratory connectivity for green turtles to better understand their spatial biology.

Location

Global.

Time Period

1990–2022.

Major Taxa Studied

Green Sea Turtle (Chelonia mydas).

Methods

We conducted a structured literature review extracting georeferenced information on the movement of green turtles from 1990 to 2022, aggregating this information into a single connectivity model, …

Low Climate Benefit Of Nordic Coastal Marshes: Site Conditions Outweigh Grazing Effects And Shape Trade-Offs Between Carbon Storage And Its Stability, Carmen Leiva-Dueñas, T. Banta, Christoffer Boström, Franziska Eller, Johan Eklöf, Line Holm Andersen, Kai Jensen, Marianna Lanari, Ella Logemann, Pere Masque, Thomas Ostertag, Christoph Reisdorff, Anaïs Richard, Anu Vehmaa, Jukka Alm, Mikael Von Numers, Dorte Krause-Jensen

Research outputs 2022 to 2026

Coastal marshes, recognized as effective organic carbon (OC) sinks, have gained attention for their potential contribution to climate mitigation through protection and restoration. However, the climate mitigation potential of Nordic coastal marshes remains understudied, likely due to their heterogeneous and often non-tidal nature. To fill this gap, we examined soil OC storage and accumulation rates, and the effects of grazing, a common management practice, across eight Nordic coastal marsh areas spanning broad climate and environmental gradients. We also assessed soil methane emissions in selected areas. The Nordic marshes studied store a median of 7 kg OC m⁻² (interquartile range, …

Beyond Morphology: Testing Molecular Assessment Of Macroinvertebrate Communities In Alpine Streams Of The Teton Range, Usa, Joshua Vollmer

All Graduate Theses and Dissertations, Fall 2023 to Present

Alpine streams and the macroinvertebrate communities that reside within them are threatened by the rapidly changing climate. Long-term monitoring of these communities is required to understand how they are changing and to predict their future trajectories. Historically, stream monitoring and assessment has been performed by collecting and identifying individuals using their morphological traits. However, in alpine aquatic ecosystems, distinct macroinvertebrate species often lack the morphological differences that allow them to be distinguished. DNA metabarcoding, an alternative method for identification which uses genetics instead of morphological differences, is not impacted by this issue, and therefore, may be better suited for alpine …

Sequential Products Of Anaerobic Denitrification In Calcareous And Noncalcareous Soils By Use Of The Gas Chromatograph, Grant S. Cooper

All Graduate Theses and Dissertations, Fall 2023 to Present

The sequential products of anaerobic denitrification were determined on seven Western soils (four alkaline, two acid, and one neutral) by soil and gas analysis. The soils with 1% alfalfa and added KNO3 were incubated at moistures slightly greater than field capacity and with an atmosphere of He. The soils and gases were periodically analyzed and balance sheets prepared. The sequence of NO3-->NO2-->N2O-->N2 operated in all soils. The rates of nitrogen interchanges and maximal amounts of nitrate, N2O2 and N2 were determined. From this data it was postulated that the rate-limiting process for denitrification in acid soils is …

Drought-Tolerant Plants Of Great Salt Lake: Determining Dormancy Break, Germination, And Seeding Timing Requirements To Improve Restoration Under Hydrologically Extreme Conditions, Montana Horchler

All Graduate Theses and Dissertations, Fall 2023 to Present

Wetlands are declining worldwide, and those in arid regions are especially vulnerable to climate change, drought, water diversions, and other human pressures. As a result, land managers increasingly rely on active revegetation to re-establish native plant communities and their associated ecosystem functions. Restoration that utilizes seeds as the propagule source is often the most cost-effective way to revegetate large areas, but in highly variable environments such as exist at Great Salt Lake, Utah, drought and flooding regularly limit plant establishment. Restoration practitioners require science-informed strategies to reach their goal of establishing diverse native plant communities with high native species cover. …

Social And Institutional Factors Influencing Restoration Decisions In Sagebrush Plant Communities In The Great Basin, Carmen Calzado-Martínez

All Graduate Theses and Dissertations, Fall 2023 to Present

Sagebrush landscapes of the Great Basin in the western United States have changed dramatically over the past century. Invasive grasses, repeated wildfires, and past land-use practices have made it increasingly difficult for native plant communities to recover once they are damaged. Most restoration efforts occur after disturbances such as wildfire, when ecosystems may already be severely degraded. An alternative approach is proactive restoration, which aims to strengthen ecosystems before major damage occurs. 

This dissertation examines whether proactive restoration strategies could realistically be used in sagebrush rangelands and what factors influence their adoption. The research combines three complementary approaches. First, interviews …

Post-Wildfire Erosion And Biogeochemistry: Integrating Aerial Imagery And Soil Testing To Assess Landscape Recovery, Justin A. Allred

All Graduate Theses and Dissertations, Fall 2023 to Present

After a wildfire, land managers are required to monitor large tracts of land with limited time and budgets. Traditionally, tracking landscape recovery is a time intensive process. This research explored the effectiveness of using drones (UAVs), strategic soil sampling, and computer modeling as additional tools for land managers in order to monitor the recovery more efficiently.

By using drones to collect aerial imagery and using machine learning, plant regrowth was monitored in back-to-back years. The machine learning model performed well at telling broad groups apart (trees vs grass) but it struggled to identify differences between plant species. Because many plants …

Comparing Strategies For Wetland Revegetation In An Uncertain Water Future, Hailey M. Machnikowski

All Graduate Theses and Dissertations, Fall 2023 to Present

Wetlands worldwide are expected to experience more frequent and intense droughts and floods due to climate change. These shifting water conditions introduce challenges to restoring wetland plants, especially using direct seeding. Seeding is cost and labor-efficient compared to planting, but seeds and seedlings are highly vulnerable to water stress, so restoration efforts often fail when conditions are too wet or dry. Understanding how to improve seed-based revegetation under these conditions is increasingly important. Therefore, we sought to understand the response, measured by percent canopy cover or dry biomass weights, of native plants to different durations of drought in greenhouse experiments, …

Influence Of Coterie On Utah Prairie Dog Translocation Success, Bonnie Stokes

All Graduate Theses and Dissertations, Fall 2023 to Present

The Utah prairie dog (Cynomys parvidens) is a threatened species found in southwestern Utah. Utah prairie dogs are small, burrowing squirrels that live in family groups called coteries. Translocation, the intentional capture, movement, and release of animals from one location to another, has been widely used to aid in their recovery; however, post-translocation survival remains low. The primary objective of this study was to evaluate the effect of translocating Utah prairie dogs as intact coteries on post-translocation survival.

This study was conducted within the West Desert Recovery Unit in Iron and Beaver Counties, Utah, during July–October 2023 and …

Visualizing Probabilistic Model Checking: An Interactive Framework For Exploring Ctmc Models, Ishara Mawelle Kankanamge

All Graduate Theses and Dissertations, Fall 2023 to Present

Probabilistic model checking is a critical method for analyzing systems characterized by uncertainty, such as communication protocols, randomized algorithms, and biochemical networks. While formal verification tools provide precise numerical data about these systems, interpreting these results is often limited by large state space, high-dimensional state space and time dependent evolution. Current tools typically output raw numerical data, offering limited support for intuitively understanding the time-dependent behavior of a model. This research presents an interactive visualization framework designed to bridge the gap between complex numerical analysis and human intuition. The framework integrates coordinated visual interfaces, including lower-dimensional state-space projections and synchronized …

Impacts Of Climate-Smart Agriculture On Greenhouse Gas Emissions In Southeast Arkansas Cotton, Cassandra Seuferling

Graduate Theses and Dissertations

Increasing concerns of climate change have led to the evaluation of greenhouse gas (GHG) emissions [i.e., carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)] from agroecosystems, particularly cotton (Gossypium hirsutum) production. Technology improvement and conservation agriculture methods [i.e., reduced-tillage (RT) instead of conventional tillage (CT) and the use of cover crops (CC)] require further evaluation regarding GHG emissions from Arkansas cotton production. The first objective of the study was to evaluate four gas-flux-determination methods [i.e., linear or exponential regression models, with negative fluxes (WNF) included in the dataset or replacing negative fluxes (RNF)] on CO2, CH4, and N2O fluxes …

Low Methane Emissions From Nutrient-Rich Former River Channels In A Hydrologically Managed Dryland Delta, Siena Stassi, Jude A. Benavides, Chu-Lin Cheng, Marcelo Gomes Da Silva, Nicholas E. Ray, Nathan O. Barros, Rafael M. Almeida

School of Earth, Environmental, & Marine Sciences Faculty Publications

Anthropogenic stresses in dryland regions can alter hydrology, salinization, and biogeochemical processes. How these pressures influence methane (CH4) cycling and emissions from aquatic ecosystems remains poorly understood. Over the course of 1 year, we measured diffusive and ebullitive CH4 emissions from resacas—shallow, hydrologically managed distributary channels prevalent throughout the Lower Rio Grande Valley along the US–Mexico border. Despite warm, nutrient-rich waters, CH4 emissions from resacas were low, and more comparable to rates observed in estuarine systems. CH4 fluxes were positively related to temperature but negatively related to salinity and rainfall. Elevated salinity, driven by evaporation and source water from the …

Landscape Connectivity And Wildlife Access To Water Across An International Border: Barriers And Opportunities For Facilitating Transboundary Movement, Bogdan Chivoiu, Erin L. Koen, Michael J. Osland, Christopher A. Gabler, Jerald T. Garrett, Ernesto Reyes, Stephanie A. Bilodeau, Mitch A. Sternberg, Jude A. Benavides, James Martinez

School of Earth, Environmental, & Marine Sciences Faculty Publications

Rapid global acceleration in the construction of physical barriers along international borders has greatly influenced biodiversity and animal movement. Physical barriers can fragment landscapes, hinder access to essential resources, impact long-distance migrations, and inhibit dispersal and gene flow. The effects of physical barriers on animal movement and landscape connectivity can be exacerbated in dryland environments where access to water is a limiting factor. In recent decades, the construction of border barrier infrastructure has accelerated along the international boundary between the United States and Mexico. Here, we used a landscape connectivity model to investigate the effects of barriers on wildlife access …

Assessing Geomorphic Change From Large Wood Additions In An Intensively Monitored Watershed, Alexander Walt

All Graduate Theses and Dissertations, Fall 2023 to Present

Rivers across the American West are under stress. Over time, human activities have decreased riparian vegetation and removed naturally occurring large wood from fallen trees and beaver dams. Overgrazing, wetland drainage, and artificial barriers like levees and berms have further changed these ecosystems, leaving behind simple channels that lack varied habitat for aquatic species.

Efforts to restore rivers have made some progress, but many projects are small in scale and focus more on reshaping the river rather than restoring the natural processes that keep it healthy. This study evaluates a different approach—Low-Tech Process-Based Restoration (LTPBR)—which works with nature to rebuild …

Fractsynth: Exploring Glitch Timbres With Chaos Theory, Aidan Roach

The Transdisciplinary STEAM+ Journal

In this paper, I explore how chaos theory can be used to design a new kind of synthesizer with the primary focus of producing glitchy, unpredictable sounds. Glitch music embraces abstract sound design, malfunctioning electronics, and randomness as the main compositional elements. However, most synthesizers rely on stable, repetitive oscillators that often sound too controlled. To challenge this, I developed FractSynth, a real-time synthesizer that uses chaotic attractors–including the Logistic Map, Henon Map, and Lorenz System–as modulation sources for frequency, amplitude, and tone. The software also features real-time Lyapunov Exponent Tracking, which gives users a direct visual of how …

Dementia Detection In Low-Resource Languages: Evaluating Translation-Assisted Transfer Learning For Multilingual Clinical Assessment, Kylar A. Deloach

Honors Theses

Alzheimer's disease (AD) is a growing global health concern, with millions of people affected worldwide and cases expected to rise significantly in the coming decades. Early detection is critical for patient treatment and care, and recent advances in natural language processing (NLP) have shown promise in identifying linguistic markers associated with AD. However, most existing work has focused on English, leaving speakers of other languages with limited access to such tools. This study investigates how effective AD detection models trained on English data are at transferring to Greek, a low-resource language with limited dementia-related speech data available. We propose a …

Climate Change-Related Effects On Carbon Emissions And Net Ammonification Across Lowland To Upland Soils From A High-Latitude Coastal Ecosystem, Jenna M. Ross, Karen H. Beard, Katharine C. Kelsey, Matteo Petit Bon, A. Joshua Leffler

Wildland Resources Faculty Publications

Warming, sea-level rise, and changing herbivory patterns are affecting ecosystem processes in northern coastal soils, including carbon and nitrogen cycling, although their combined effects are poorly understood. We studied the impact of these changes in a full-factorial microcosm experiment using four distinct soil types from the Yukon-Kuskokwim Delta of western Alaska. Soil was collected from three coastal wetlands, which differ in flooding frequency and use by migratory geese, and one rarely-flooded upland tundra used by geese in late summer. Microcosms containing these soils were incubated for 16 weeks at 10°C or 18°C, with or without three short-term floods, and with …

Ai-Driven Multispectral Drone Monitoring For Afforestation In Arid Environments, Hesham Morgan, Ali Elgendy, Brandon Tran, Tamer Ismail, Mohamed M. Moursy, Yehya Kh. Shehadeh, Ahmed Elgharib, Ahmed Abdullah Al-Dughairi, Ali El Mubarak, Khaled Allam Harhash, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Monitoring large-scale afforestation projects in arid and semi-arid environments requires accurate, high-resolution, and repeatable methods to assess tree survival and growth. In this study, we integrated unmanned aerial vehicle (UAV) multispectral imaging with an advanced object detection framework to evaluate vegetation establishment in the Shuayb Al-Budai afforestation site, part of the Imam Turki bin Abdullah Royal Natural Reserve, Kingdom of Saudi Arabia (KSA). Multispectral datasets were acquired using a MicaSense Altum-PT sensor and processed through a masked Region-based Convolutional Neural Network (RCNN) with two backbone architectures: ResNet-101 and VGG19-BN. The Mask R-CNN–ResNet-101 model achieved superior performance, with an overall accuracy …

Vulnerability Of Bass Populations To Our Changing Climate In The Mississippi River, Cameron Schreifels

Celebrating Scholarship and Creativity Day (2018-)

Climate change is altering habitats and damaging bass populations throughout the Mississippi. The main factors of climate change affecting bass are shifts in water quality and significant weather events, which have increased bass vulnerability. With rising temperatures and eutrophication changing the way these bass hunt for their prey, it has made it easier for other non-native species to encroach on their habitat, which has led to bass further encroaching on other species due to climate change.  Given their economic importance and cultural significance, better management practices are needed to find new ways to protect them and ensure they remain a …

Inhibition Of The Pi3k/Akt/Mtor Pathway In Non-Small Cell Lung Cancer, Gretchen Gunderzik

Celebrating Scholarship and Creativity Day (2018-)

The phosphatidylinositol 3-Kinase (PI3K)/protein kinase B (Akt)/mechanistic target of rapamycin (mTOR) signaling pathway is a cell survival pathway that is commonly unregulated in non-small cell lung cancer (NSCLC). Current inhibitors of this pathway often face the challenge of inherent and developed resistance. There is the need to further develop a targeted treatment therapy focused on inhibition of this signaling pathway. This could synergistically enhance commonly used cancer therapies such as chemotherapy, which NSCLC patients often develop resistance to. Due to the complexity of the pathway, dual inhibition is an intriguing avenue of research as it helps to mitigate resistance from …

Investigating The Synthesis And Antibacterial Activity Of A Main-Chain Cationic Polymer, Emily Smith

Honors Theses

Antibiotic resistance is a growing threat to public health. Due to the overuse of antibiotics in agriculture, the overprescription of antibiotics, and the misuse of antibiotics by patients, antibiotic resistance is spreading at an alarming rate. As antibiotic resistance spreads, the antibiotics we depend on to treat common infections become ineffective. Therefore, it is imperative to develop novel treatments for infections that do not increase the prevalence of antibiotic resistance. One treatment being explored is the use of synthetic polymers with antibacterial properties. Synthetic polymers are advantageous because they can be synthesized from widely available precursors and their structure is …

An Improved Logarithmic Ratio-Product Type Estimator For Mean Modeling And Estimation Under Neutrosophic Uncertainty, Anchal Yadav, Mukesh Kumar

Neutrosophic Systems with Applications

In classical statistics, population mean estimation generally assumes precise and determinate data along with known auxiliary information. However, in real-world situations where observations are imprecise or expressed in interval form, such as temperature variations or financial market data, classical approaches become less effective. To address this limitation, neutrosophic statistics provide a more flexible framework for handling uncertainty and indeterminacy. This study proposes a neutrosophic logarithmic ratio-product type estimator for estimating the finite population mean using auxiliary information. The bias and mean squared error (MSE) of the proposed estimator are derived using a first-order approximation. Furthermore, performance evaluation is carried out …

Warming Climate Amplifies Vapor Pressure Deficit Limits On Gross Primary Productivity, Shiqin Xu, Nate G. Mcdowell, Tim R. Mcvicar, Diego G. Miralles, Stephen Sitch, Pablo Sanchez-Martinez, Joshua B. Fisher, Pierre Friedlingstein, Hylke E. Beck, Matthew F. Mccabe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ongoing climate warming may profoundly impact terrestrial gross primary productivity (GPP), a key component of the global carbon cycle. However, uncertainty in the relative roles of atmospheric water demand (vapor pressure deficit, VPD) and root-zone soil moisture (SM) limits predictions of drought impacts on GPP. Here, we show that growing-season GPP was more strongly constrained by VPD than SM globally, based on observation-constrained model estimates, satellite retrievals and Dynamic Global Vegetation Model simulations. The importance of VPD increased with higher temperatures and more severe and prolonged droughts. This pattern reflects VPD’s critical role in regulating stomatal conductance and plant hydraulic …

Analysis Of The Flavonoid Composition Of Honey Using High-Performance Liquid Chromatography, Bryce Phillips

Honors Theses

Honey is a naturally occurring substance that has a complex composition including compounds such as flavonoids, that contribute to potential health benefits. Quantitative analysis of flavonoids in honey can be challenging due to their similar structural characteristics, matrix effects, and chromatographic peak separation issues. This study aimed to establish calibration curves for five flavonoids–kaempferol, luteolin, chrysin, myricetin, and quercetin– to estimate their concentrations in five honey samples from varying geographic origins. Liquid-liquid extraction was used to isolate the flavonoids from honey. High Performance Liquid Chromatography was utilized to establish calibration curves and analyze honey samples. The calibration curves assembled demonstrated …

Creating A Unique Hemoglobin-Based Oxygen Carrier, Clayton Fuller

Celebrating Scholarship and Creativity Day (2018-)

The purpose of this thesis is to explain the current state of alternative oxygen carriers and propose a new hemoglobin-based oxygen carrier (HBOC) as a blood substitute/ blood therapeutic. Blood donation has drawbacks: risk of spread of infection, short storage time, and blood typing, and the current shortage. There are several possible modifications for hemoglobin to create a carrier (HBOC) which address specific issues related to allowing free hemoglobin to exist extra cellularly. One issue to address is vasoconstriction caused by nitric oxide scavenging, which has been solved by increasing the molecular weight of the HBOC via (co)polymerization, or by …

Assessment Of Morphological Differences And Genetic Variation In Head Shape Of Florida Pompano Trachinotus Carolinus, Neriah Nicholas

Electronic Theses and Dissertations

Genomics research can inform selective breeding programs to improve broodstock and seedstock quality for the U.S. warmwater marine finfish aquaculture industry. Florida pompano Trachinotus carolinus serves as a model species for the industry due to its commercial value and ability to spawn in captivity. This study examined a growth abnormality observed in commercially produced juveniles in partnership with Aquaco Farms LLC. Twenty fish were collected, culled, and euthanized by Aquaco staff, then classified into two head types: “normal” and “concaved”. Eleven morphological measurements were recorded before and after freezing to assess head variation and storage effects. DNA from pectoral fin …

Optimization Of Physalis Angulata L. Callus Induction And Salinity-Induced Antioxidant Production, Firstian Naufal Sistyananda, Erni Suminar, Anne Nuraini, Muhamad Kadapi, Murgayanti, Syariful Mubarok, Rahmat Budiarto, Eddy Renaldi, Kusumiyati

Jurnal Kultivasi

Groundcherry (Physalis angulata L.) is a plant with many medicinal potentials due to its rich secondary metabolites such as phenolic and flavonoid. However, conventional agriculture practices are still limited, especially in Indonesia. This study was divided into two stages. The first stage was conducted to determine optimal 6-BAP and 2,4-D combination for callus induction, while the second stage was conducted to determine callus phenolic, flavonoid, and antioxidant response to salinity stress. The first stage was arranged in factorial completely randomized design with two factors: 6-BAP (0, 2, and 4 mg/L) and 2,4-D (0, 0.5, 1, and 1.5 mg/L). The second …

Growth Of Vanilla Cuttings Under Modified Acid Soil Media And Application Of Several Plant Growth Regulators, Rifqi Raditya Kurniawan, Yugi Rahayu Ahadiyat, Etik Wukir Tini

Jurnal Kultivasi

This research aimed to optimize the growth of vanilla (Vanilla planifolia) cuttings in acid soils by modifying the growing media and applying several types of plant growth regulators (PGRs). Several types of PGRs, including synthetic compounds such as indole-3-acetic acid (IAA) and 6-benzylaminopurine (BAP), as well as natural extracts from shallot (Allium ascalonicum L.) and moringa leaves (Moringa oleifera), were tested to enhance plant performance in acid-growing conditions. The primary objectives were to determine the optimal soil amendment formula and the most effective PGR type for promoting vanilla growth, and to develop a measurable, easy-to-use PGR formulation accessible to farmers. …

Response Of Chlorophyll, Morphology, And Yield Of Several East Java Superior Soybean (Glycine Max L.) Varieties To Levels Of Salinity, Puji Lestari Tarigan, Ida Retno Moeljani, Fadila Suryandika, Hadi Munarko

Jurnal Kultivasi

Soybean production has been extended to saline areas. This development is a strategy to expand planting areas to suboptimal land to increase worldwide production. To support cultivation in these locations, it is necessary to develop superior varieties that are resistant to salinity and provide supporting technological inputs. In saline conditions, soybeans may face stress that leads to morphological, physiological, and yield disturbances. Consequently, the response of several soybeans in East Java should be observed. This study is a pot experiment and arranged in a Factorial Completely Randomized Design (CRD) consisting of two factors, soybean varieties and NaCl concentrations. The treatments …