Life Sciences Commons^™

When Empathy Goes Quiet, Miko Warshaw

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The 400 Millisecond Mind, Adrian Mangine

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

The Effect Of Cover Crop Management Strategies On Nutrient Availability In No-Till Corn, Emily C. Marsh

Theses and Dissertations--Plant and Soil Sciences

Cover crops are reported to have long-term soil health improvements, one of which is reducing erosion. However, popular cereal cover crops, such as rye (Secale cereale L.), have the potential to cause a yield penalty in the following corn (Zea mays L.) crop due to a reduction in available nitrogen. Legumes, such as Austrian winter pea (Pisum sativum L. var. arvense), are thought to reduce this yield penalty due to their capacity to fix nitrogen. Sulfur is another nutrient of interest, especially as rates of atmospheric deposition of sulfur have declined, leading to more deficiencies being …

Soil Solarization As A Sustainable Approach To Manage Weeds And Arthropod Pests, And Its Effects On Soil Nitrate And Lettuce (Lactuca Sativa L.) Yield In Kentucky And Tennessee High Tunnels, Paula Luize Lessmann

Theses and Dissertations--Plant and Soil Sciences

The use of high tunnels (HTs) has increased over the past 15 years, with more than 1,700 and 700 structures currently in Kentucky and Tennessee, respectively. High tunnels are widely used to extend the growing season and protect specialty crops from adverse weather conditions. However, continuous production and limited crop rotation within HTs can lead to the accumulation of soilborne pathogens, plant-parasitic nematodes, arthropod pests, and weeds, ultimately reducing crop yield and quality. Management of these biotic issues is particularly challenging in HTs due to limited pesticide options compared to open field production. Soil solarization, a non-chemical method that uses …

Mineral-Associated Organic Nitrogen Pool Size, Composition, And Accessibility Mediated By Agricultural Management And Soil Geochemical Characteristics, Gabriella M. Griffen, Andrew H. Whitaker, Emma L. Bergh, Marian Carrell, Erik Knatvold, Aniko Konya, A. Stuart Grandy, Andrea Jilling Ph.D., Marco Keiluweit, Rachel Hestrin

Faculty Publications

Mineral-associated organic matter (MAOM) contains a substantial portion of soil nitrogen (N). MAOM-N could serve as an important N source for crops, but its availability and response to agricultural management across different soil types remains largely unknown. We characterized MAOM-N isolated from nine paired soils spanning a range of geochemical characteristics and maintained under two land uses—more intensively managed annual cropping systems or less intensively managed grasslands. On average, we found that MAOM contained approximately two-thirds of total soil N. Across all soil types, more intensive agricultural management resulted in a 50% decline in MAOM-N stocks, as well as a …

Dataset: Participation Versus Points: Examining The Impact Of Grading Conditions On Student Resource Use During An Out-Of-Class Biology Concept Assessment, Tiffany J. Burgess, Crystal Uminski, Brian A. Couch

School of Biological Sciences: Faculty Publications

Instructors use concept assessments to collect diagnostic information regarding student learning and to inform decisions surrounding instructional interventions and course modifications. Administering concept assessments out-of-class helps preserve already limited instructional time, but instructors still must consider whether to apply a lower-stakes (i.e., participation) versus higher-stakes (i.e., correctness) grading scheme. An increase in stakes is likely to prompt additional effort, but it may also increase undesired behaviors and inadvertently prompt external resource use, such as students leveraging their notes, the internet, or their peers. In the present study, we compared student self-reported resource use on a biology concept assessment administered under …

Rapid Urbanization Reduces Genetic Diversity And Increases Genetic Differentiation Of A Lynx Spider Oxyopes Sertatus In Central Taiwan, Ying-Yuan Lo, Chi Wei, Wan-Jyun Chen, Chung-Ping Lin

Biological Sciences Faculty Publications

Urbanization is a dominant force driving destructive and irreversible changes of natural habitats in modern times. While the effects of urbanization on community composition and phenotypic responses are well-documented, its influence on genetic diversity and population structure remains understudied, particularly for invertebrates in subtropical regions. This study tested the hypothesis that urbanization reduces genetic diversity and increases population differentiation in the lynx spider Oxyopes sertatus, a common foliage-dwelling spider in Taiwan. We sampled 245 individuals from 17 sites distributed along an urban-rural gradient and quantified urbanization intensity using land-use composition at both landscape (4 km²) and local (0.25 km²) …

Evaluating Species At Risk In Data-Limited Fisheries: A Productivity-Susceptibility Analysis For Marine Aquarium Fish, Gabrielle A. Baillargeon, Alice A. Wynn, Jemelyn Grace P. Baldisimo, Michael F. Tlusty, Andrew L. Rhyne

Biological Sciences Faculty Publications

The marine aquarium trade (MAT) is a significant global industry harvesting millions of wild-caught, live coral reef fishes for public and private aquaria markets in the United States and Europe annually, while supporting fisher livelihoods in the Indo-Pacific. This diverse and species-rich trade is considered data-limited, creating barriers to quantifying the current and future socio-ecological sustainability of the fishery. We present a revised and expanded productivity–susceptibility analysis (PSA) that serves as a holistic risk assessment to estimate the vulnerability of marine aquarium fish to overfishing. Our global analysis includes 306 species that are actively in trade. Improvements to the PSA …

Challenging And Diagnosing Structured Population Models By Testing Predictions From Stochastic Demography, Stephen P. Ellner, Robin E. Snyder, Daniel T. Blumstein, Dylan Z. Childs, Joshua C. Fowler, Christina M. Hernández, Julien G. A. Martin, María Paniw, Yngvild Vindenes

Biological Sciences Faculty Publications

1. Structured population models are parameterized to accurately project expected population sizes, stage/state distributions and population growth rates, but they also predict the variation in outcomes among individuals, such as the variance and skewness of lifetime reproductive output (LRO) and lifespan, the probability of never reproducing, and many other life-history metrics.

2. Testing such predictions about individual outcomes can be very useful model 'stress tests', because they depend on how components of the model (e.g. submodels for survival and fecundity) interact over multiple time steps, not just on the accuracy of the submodels. Because data on among-individual variation is rarely …

Letter From The Faculty Editor, Beth Kegley

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Featured Faculty Mentor/Student Team, Lauren Rogers, Danielle Reeves

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Intelligent Dual-Energy X-Ray Absorptiometry (Idxa) And Small Animal Scanning As A Useful Tool To Measure Appendicular Bird Bone Mineral Density, Frank J. Dirrigl Jr., Samuel R. Buchanan

School of Integrative Biological & Chemical Sciences Faculty Publications

Accurately assessing the bone mineralization status of birds is crucial for poultry production and wild bird studies. We investigated the use of dual-energy x-ray absorptiometry (DXA) using Small Animal Measurement software to measure bone mineral content (BMC) and areal bone mineral density (aBMD) in excised radii of the willow ptarmigan (Lagopus lagopus) as a bird model. Our exploratory tests involved 117 scans to evaluate scanning parameters, scanning board types, bone stabilization, scan mode and size, and region of interest placement. Results indicated that mean BMC or aBMD were each significantly different when scanned on a forearm positioner board …

A Preliminary Investigation Of Research Collaboration Through Scientific Paper Co-Authorship In The Gulf Of Mexico, Juliet Vallejo, Evelyn Roozee, Dongkyu Kim, Andrew M. Song, Christopher A. Gabler, Jasper R. De Vries, Antonia Sohns, Gordon M. Hickey, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

It is well known that publications with collaborators from external institutions increase citations. This effect scales with spatial distance. There are also many barriers to long-distance collaborations, including linguistic differences, funding constraints, and the incremental costs of remote collaboration. This paper uses the Gulf of Mexico as a case study to examine long-distance research collaboration because it consists of three countries with diverse development levels and two prominent diplomatic languages, within a singular regional ecosystem of tremendous natural and economic value. This paper uses bibliometric network analysis to examine scientific research article co-authorship in the Gulf of Mexico from 2000 …

Histochemical Alteration, Protein Nitration, And Antioxidant Expression In Oysters As Early Warning Indicators For Microplastic Contamination In The Texas Gulf Coast, Rebecca Muñiz, Md Faisal Amin, Md. Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Microplastics are widely distributed in aquatic environments and have been detected in numerous organisms. Marine bivalves are among the most affected aquatic organisms by microplastics due to their filter-feeding behavior. In this study, 60 oysters were collected from two sites along the Texas Gulf Coast. Fourier transform infrared (FTIR) spectroscopy and Nile red staining were used to detect microplastics in oyster (Crassostrea virginica) tissues. We compared field and laboratory samples collected after a two-week depuration period to identify differences in the shape and size of microplastics in oyster tissues. Results from the field sites showed a large number of microplastics, …

A Note On The Novel Passive Sampling In Environmental Dna (Edna) Collection Technique To Detect Yellow Mud Turtle (Kinosternon Flavescens): Field And Laboratory Approaches In Turtle Edna, Sakib Tahmid Rishan, Richard J. Kline, Md. Saydur Rahman

School of Integrative Biological & Chemical Sciences Faculty Publications

Environmental DNA (eDNA) is a powerful and sensitive method for monitoring aquatic and terrestrial organisms, offering insights into their distribution. Usually, eDNA is collected using a filter membrane through water filtration. However, the passive eDNA method can simplify sampling and broaden its scope, offering new insights for ecological surveillance. This study examined the efficacy of six different membrane filters in detecting the yellow mud turtle (Kinosternon flavescens) through a novel passive eDNA method. After being immersed in water for 12 h, only the mixed cellulose ester (MCE) membrane filter consistently demonstrated specific polymerase chain reaction (PCR) amplification using …

Varying Dna Methylation Patterns In The Florida Sand Skink (Plestiodon Reynoldsi) In Relation To Fire Histories, Victoire Hj Litre

College of Graduate Studies: Theses & Dissertations

Epigenetics is the study of changes in phenotype not caused by changes in DNA sequence. DNA methylation is the most well-studied epigenetic mechanism in an ecological context. Reptiles use DNA methylation to respond to environmental stressors and differences among habitats. The Florida Sand Skink (Plastidome reynoldsi) is federally listed as a threatened species. They are endemic to the threatened, fire-dependent Florida scrub habitat. As they persist in burned habitats, the Florida Sand Skink must be able to rapidly respond to wildfires. To better understand how the Florida Sand Skink adjusts to fire-driven habitat changes, it is important to …

Cogram: A Computational Pipeline For Genome Assembly And Reconstruction Using Graph Neural Networks, William Coggins

College of Graduate Studies: Theses & Dissertations

Genome assembly — the reconstruction of a complete DNA sequence from short, overlapping reads — remains a fundamental challenge in computational biology. A central difficulty is distinguishing true genomic overlaps from spurious connections arising from repetitive sequences, a task that traditional assemblers address through hand-tuned heuristic rules applied to de Bruijn or overlap graphs. This thesis introduces COGRAM (Coggins–Ramasamy Assembly Method), a genome assembly pipeline that reframes sequence reconstruction as an edge classification task on a k-mer overlap graph, replacing heuristic graph cleaning with a learned model.

COGRAM constructs a directed overlap graph from raw sequencing reads using a k-mer …

Evaluating Benthic Macroinvertebrate Communities In Streamside Management Zones In Private, Working Forests, Haley Vaglienti

College of Graduate Studies: Theses & Dissertations

Forestry operations can alter riparian vegetation and increase sediment and nutrient inputs to streams, affecting water quality and aquatic biota. Forestry best management practices (BMPs) including streamside management zones (SMZs) are designed to mitigate those effects by reducing sediment delivery and moderating temperature, flow, and nutrient regimes. We assessed ecological integrity at 24 intermittent stream sites with SMZs in private, working forests across the Piedmont and Southeastern plains of Georgia. At each site, we conducted physical habitat evaluations and characterized benthic macroinvertebrate assemblages. Sites represented a gradient of habitat conditions, SMZ widths, and pine stand ages, allowing for comparisons of …

Monograph Available: Best Practices For Managing Human–Beaver Conflicts In North America: Balancing Ecological Benefits And Human Interests

Human–Wildlife Interactions

This is an announcement about the published monograph titled "Best Practices for Managing Human–Beaver Conflicts in North America: Balancing Ecological Benefits and Human Interests." This publication, part of the HWI Monograph Series, is online and open access.

Characterization Of Microrna Expression In Neuron-Enriched Extracellular Vesicles During Early Life, Allison Molen

Theses and Dissertations

Extracellular vesicles (EVs) are membrane-bound sacs released by cells that carry molecular cargo reflective of their cell of origin. EVs enriched using L1 cell adhesion molecule (L1CAM) as a marker of putative neuronal origin can cross the blood–brain barrier and provide a minimally invasive window into brain-related processes. Exosomal microRNA (miRNA) regulate gene expression and have been implicated in psychiatric disorders, including major depressive disorder (MDD). However, measuring and analyzing miRNA from L1CAM-positive EVs presents substantial analytical challenges due to low abundance and sparse detection across samples.

Plasma samples from participants recruited through the Mid-Atlantic Twin Registry (MATR) were used …

A Mathematical Frameworks For Singular, Nonlinear Phenomena: Applications To Nematocyst Firing And Inhomogeneous Nls With Coulomb Potential, Abdulrahman Alharbi

Theses and Dissertations

Nematocysts are specialized cellular organelles found in all cnidarians, including corals and jellyfish, as well as in some single-celled protists such as dinoflagellates. These organelles display remarkable diversity in morphology and function, playing roles in prey capture and defense. The firing of a nematocyst is one of the fastest accelerations in nature, yet the underlying physical mechanisms remain not fully understood. In this work, we address key questions: how sufficient force is generated to overcome the fluid boundary layer, whether fluid–structure interaction models can reproduce observed dynamics, and what mechanisms trigger discharge.

Our research investigates models based on osmotic pressure …

Machine Learning-Based Spatio-Temporal Modeling Of Climate Dynamics And Desertification In The Sahara–Sahel Region, Stephen M. Tivenan

Theses and Dissertations

Arid climate classifications are threshold-dependent and easily interpretable mappings that are widely used in ecological, agricultural, and climate-related studies. These classifications inform scientific understanding, support policy and land management decisions, and provide an intuitive summary of environmental conditions. Despite their usefulness, traditional arid climate classifications often fail to quantify uncertainty, incorporate spatial context, or account for complex relationships among relevant environmental variables. Existing approaches to uncertainty assessment have largely relied on comparing classifications across multiple datasets or alternative formulas, but these methods generally overlook important spatial dependence and latent structure in the data.

This dissertation develops three machine learning-based statistical …

Climate, Biogeography, And Dispersal: A Unifying Framework For Ameri-Caribbean Dry Forests, Pablo Lopez Bustamante

Theses and Dissertations

Seed dispersal is a crucial ecological function that enables plants to alter their distributional range, avoid intense competition and natural enemies near the parent plant, and recover from disturbances. These processes shape species and functional composition of forests. Wind has traditionally been considered the dominant dispersal mechanism in Ameri-Caribbean dry forests, yet growing evidence suggests that other dispersal mechanisms also play significant roles in this ecosystem, responding differently to biotic and abiotic conditions. Still, how dispersal syndrome composition influences plant communities, the ecological drivers underlying these patterns, and the effects of climate change on dispersal syndrome dominance remain poorly understood. …

Modeling Inherited Retinal Disease In Zebrafish, Meet Patel

Theses and Dissertations--Biology

Inherited retinal diseases (IRDs) affect millions of people worldwide. Majority of IRDs are caused by degeneration of rod and cone photoreceptor cells (PRCs) due to gene mutations. The overarching goal of my dissertation is to model and evaluate the molecular role of various gene candidates involved in IRDs such as cone rod dystrophy (CRD) and retinitis pigmentosa (RP).

Mutations in CDHR1, a photoreceptor specific cadherin have been associated with CRD and recapitulated in mouse CDHR1 knockouts. However, the molecular function of CDHR1 remains unknown. CDHR1 has been shown to localize at the leading edge of murine rod nascent outer segment …

Kentucky Bluegrass (Poa Pratensis L.) As A Perennial Groundcover: Establishment And Weed Management In Corn, Kiera S. Searcy

Theses and Dissertations--Plant and Soil Sciences

Perennial groundcover (PGC) systems offer a cost-effective alternative to annual cover crops, by providing continuous soil cover, reducing soil erosion, and contributing to integrated weed management (IWM) in corn (Zea mays L.) production systems. Kentucky bluegrass (Poa pratensis L.) has been proposed as a perennial groundcover for corn due to its low growth habit and seasonal dormancy; however, successful adoption is limited by challenges associated with establishment-phase weed competition and compatibility with weed management programs during corn production. The objectives of this research were to (1) evaluate weed management strategies that support Kentucky bluegrass establishment and (2) assess …

Integrated Crop Management For Hemp (Cannabis Sativa L.) Grain Production In Kentucky, Maria M. Ricciardi

Theses and Dissertations--Plant and Soil Sciences

Cannabis sativa L. is legally defined (U.S.) as hemp if the total tetrahydrocannabinol (THC) concentration remains less than 0.3% on a dry weight basis. Hemp can be produced for cannabinoid extraction, fiber, or grain. Hempseed meal and hempseed oil were approved as feed ingredients for chickens and performance horses in Kentucky. To leverage this opportunity, production requires improvement through an integrated crop management approach. This dissertation (1) reports the main arthropod and disease pests impacting hemp grain; (2) identifies grain yield components and their relationship with corn earworm, Helicoverpa zea (Boddie) (CEW); (3) evaluates Fusarium head blight (FHB) development across …

Breeding For Fhb Resistance And Post-Harvest Quality In Soft Red Winter Wheat, Margaret E. Gillum

Theses and Dissertations--Plant and Soil Sciences

Soft red winter wheat (Triticum aestivum L.) is both an economically and nutritionally important crop in the global food supply. Despite its global importance, wheat is continually threatened by fungal diseases. Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating fungal disease affecting wheat worldwide, resulting in low yields, reduced test weight and mycotoxin production. The mycotoxin deoxynivalenol (DON) is toxic to humans, results in feed rejection in livestock, and is heavily monitored in the food supply. Because of wheat’s importance in the food system, post-harvest quality (milling, baking, and flavor) has been a growing area of …

Evaluating Spatial Variability Of Corn Yield Response To Phosphorus Fertilizer For Improved Precision Phosphorus Management, Jennifer Fridgen

Theses and Dissertations--Plant and Soil Sciences

Soil scientists did not develop soil test-based fertilizer recommendations to support precision nutrient management. Knowledge of crop responses to applied essential nutrients, such as phosphorus (P), and the processes governing these responses at high spatial resolution are necessary to improve precision agronomic recommendations. This dissertation investigates the limitations of current soil sampling methodologies and recommendation frameworks for crop response to fertilizer, with particular emphasis on P fertility in Kentucky (KY) corn production. The first study examined the relationship between the resolution of systematic grid sampling and the spatial structure of soil test variables (Mehlich-3 P (M3P), Mehlich-3 potassium (M3K), and …

Table Of Contents

Scientific Kenyon: The Neuroscience Edition

No abstract provided.