Digital Commons Network^™

Evaluating Sampling Strategies To Monitor Southern Fox Squirrel (Sciurus Niger Niger) Populations, Casey Robin Hitchens

Theses, Dissertations and Capstones

Reliable population monitoring is essential for evaluating wildlife translocations and informing conservation management, yet traditional monitoring approaches are often labor intensive and require prolonged sampling. This study evaluated marking techniques, survey methods, and population estimation approaches for monitoring a translocated population of southern fox squirrels (Sciurus niger niger) at Marine Corps Recruit Depot Parris Island, South Carolina, USA (MCRDPI). From January-June 2023, I conducted six live trapping and camera trapping sessions across five survey sites. I compared the performance of color-coded collars and tail shaves for individual identification and the recapture probability between live traps and camera traps. Logistic mixed-effects …

Impact Of Cross-Client Heterogeneity In Federated Learning For Real-World Plant Disease Classification, Ritesh Janga

All Graduate Theses, Dissertations, and Other Capstone Projects

Deep learning applications are being adopted in agricultural image analysis that include challenges of data privacy and limited institutional data and heterogeneity of different types of architectures. However, Federated Learning is a model that allows collaborative training on data that does not have to be shared among parties. Therefore, Federated Learning is an effective method of collaborative training; however, its comparative effectiveness as compared to individual (local) training on diverse architectures has never been examined in an agricultural context. The objective of this study was to examine Federated Learning for the purpose of crop disease classification on extreme non-IID distributed …

Soil Organic Carbon And Soil Health Property Responses To Land Management Across Topographic Positions, Mia D. Makovsky

All Graduate Theses, Dissertations, and Other Capstone Projects

uring the last ice age, ice sheets advanced and retreated across the upper Midwest, leaving behind a landscape characterized by poorly drained hummocky topography. Well-aerated soils have formed on uplands and lowlands are dominated by hydric soils. These wetlands and hydric soils have potential to store large quantities of carbon, particularly compared to the well-aerated uplands, but many have been drained and cultivated for decades. Conservation agriculture methods have emerged to protect and conserve soil health from negative effects due to cultivation.The purpose of this study is to determine how agricultural management practices and landscape properties (e.g, topographic position) affect …

Inferring Genes And Biological Systems Under Selective Pressure In The Secondarily Temperate Cryonotothenioids, Esteban Cabrera

Theses, Dissertations and Culminating Projects

Notothenioid fishes represent one of the most compelling examples of adaptive radiation driven by extreme environmental change, having diversified in the chronically cold waters of the Southern Ocean. While most cryonotothenioids evolved highly specialized cold-adapted characteristics, several secondarily temperate species later re-invaded warmer environments. These lineages provide a rare opportunity to examine evolutionary reversibility and the genomic mechanisms enabling escape from extreme specialization. In this study, we investigate two secondarily temperate species, Dissostichus eleginoides and Champsocephalus esox, comparing their protein-coding orthogroups to background sets from Antarctic cryonotothenioids and basal temperate teleosts. Using phylogeny based evolutionary models (BUSTED, aBSREL, and RELAX) …

A Trajectory Of Zostera Marina (Eelgrass) Ecosystem Recovery: Pre- And Post-Hurricane Sandy Degradation In Barnegat Bay, New Jersey, Edgar A. Medina

Theses, Dissertations and Culminating Projects

Hurricane Sandy struck Barnegat Bay, New Jersey in 2012 and obliterated the benthic marine ecosystem with extensive damage to Zostera marina meadows. Previous genetic assessments of Barnegat Bay Z. marina in 2008 revealed low heterozygosity and low connectivity between populations. The great disruption caused by Hurricane Sandy motivated us to investigate the long-term effects of the storm on the genetic condition of the eelgrass populations in the year 2021. The investigation revealed improvements in heterozygosity, inbreeding, and connectivity. These findings drove us to investigate the genetics of Barnegat Bay eelgrass populations in the intervening years of 2013 and 2017 with …

Toward Interpretable Multi-Omics Multimodal Biomedical Artificial Intelligence, Yanjun Lyu

Computer Science and Engineering Dissertations

The complexity of human disease arises from biological processes that unfold across multiple scales, from molecular variation through cellular function, tissue organisation, brain phenotypes, each of which is associated with distinct measurement modalities, regularities, and characteristic. Contemporary biomedical artificial intelligence has brought the opportunity to reveal the complexity with in; however, its methodological default, in which models are trained on most readily available modality, does not adequately engage with the multi-scale connected structure by which biological meaning is constituted. The research area of multi-omics and multi-modal AI for biomedicine remains at an early exploratory stage, and the work presented in …

Limitations Of Reproductive Manipulation By Bacterial Endosymbionts In A Spider Host, Jordyn D. Proctor

Theses and Dissertations--Entomology

Maternally inherited bacterial endosymbionts are common in arthropods. Many of these bacteria manipulate host reproduction to favor the production of infected females, thereby increasing bacterial prevalence in the host population, even if cost is incurred to the host. However, there are also many factors that may inhibit symbionts’ ability to spread in host populations, including environmental constraints, symbiont-imposed costs on the host, interactions with co-infecting bacteria, or host biology. I explored two aspects of symbiont biology within a spider host, Mermessus fradeorum (Linyphiidae), which has varying combinations of up to five different bacterial endosymbionts in local populations: Rickettsiella, Tisiphia …

Patenting Ai Discoveries In Life Sciences: Overcoming Eligibility, Disclosure, And Inventorship Challenges, Dhohyung Kim, Ryan P. Hiler

IP Theory

The pharmaceutical and biotechnology industries face transformative opportunities through artificial intelligence and machine learning integration. However, these technological advances create distinct patent law complications that traditional drug development does not encounter. This article analyzes three interconnected obstacles: establishing eligible subject matter under 35 U.S.C. § 101, meeting disclosure standards under § 112(a), and determining proper inventorship when AI systems contribute substantially to claimed inventions. Drawing from recent USPTO guidance and Federal Circuit precedent, this analysis offers evidence-based strategies for patent practitioners, research scientists, and business leaders seeking robust intellectual property protection for AI-integrated pharmaceutical innovations.

A Conserved Ethylene-Triggered Cell Death Mechanism May Underlie Hollow Stem Formation Across Plant Species, Mengxiao Yan, Weijuan Fan, Yinghui Meng, Jiamin Zhao, Wei Yang, Ziyin Xu, Yusen Gao, Haiyan Zhuang, Wuyu Zhou, Yuqin Wang, Qingjun Huang, Ling Yuan, Hongxia Wang, Jun Yang

Plant and Soil Sciences Faculty Publications

Hollow stems have independently evolved multiple times across the plant kingdom and play crucial roles in plant development and various environmental adaptations. However, the mechanisms underlying stem hollowness remain poorly understood. Water spinach (Ipomoea aquatica) is one of the few hollow-stemmed plants in the Convolvulaceae family (eudicot: asterid), and its hollow stems are essential for thriving in aquatic environments. Using histochemical staining and transcriptome analysis, we found that programmed cell death (PCD) is involved in cavity formation at water spinach shoot tips. Single-cell and spatial transcriptome analyses further revealed that ethylene and reactive oxygen species (ROS) likely drive …

Supplemental Bibliographic Details. From 2001 Mars Odyssey To Earth’S Climate Crisis: Integrating Gamma Spectroscopy, Martian Soil Simulants, And Plant Genomes For Agroecology, Anchored In Sri Lanka’S Mars-Context Serpentinites, Suniti Karunatillake, Maheshi Dassanayake, Carlos Gary Bicas

Planetary Science Lab

Bibliographic details follow to supplement hyperlinked citations in the multinational GANGOTRI-supporting project conceived by Karunatillake, Dassanayake, and Gary-Bicas

Rna-Sequence-Driven Identification Of Differentially Expressed Genes In Α-Crystallin-Deficient Zebrafish, Kehlie Hopper

SPARK Symposium Presentations

Fetal Alcohol Syndrome (FAS) is a condition that develops in infants when exposed to alcohol in utero, leading to physical impairments such as reduced eye size and disrupted retinal function. Alpha-crystallin A is a key structural protein required for proper lens development and maintenance of transparency, while Alpha-crystallin B plays a protective role against cellular stress during eye development. In this study, I compared AB wild-type (ABWT), αA-crystallin knockout (cryaa), and αB-crystallin knockout (cryaba) zebrafish to investigate how the loss of these proteins influences eye development under ethanol exposure. The cryaa mutants exhibited reduced eye size even under control conditions, …

A Sweet Spot For Chemotherapy: The Influence Of Insulin And Glucagon On Oxaliplatin Sensitivity In Colorectal Cancer Cells, Daniella Cohen, Andrea Florian

SPARK Symposium Presentations

There is a well-established relationship between cellular metabolism, cancer progression, and treatment response. Metabolic hormones such as insulin and glucagon regulate pathways involved in cell growth, survival, and stress responses and have been linked to tumor development and chemotherapy sensitivity. Understanding how metabolic signaling influences cancer treatment may provide insight into factors that affect therapeutic outcomes. This study aims to investigate how insulin and glucagon affect the susceptibility of colorectal cancer cells (CRC) to the chemotherapeutic agent oxaliplatin. CRC cells were treated with insulin or glucagon and exposed to varying concentrations of oxaliplatin. Cell viability was measured to evaluate treatment …

Murder On The Menu, Andrea Florian, Leslie Deleon, Angela Simpkins, Anamika Chhetri

SPARK Symposium Presentations

You're invited to a birthday party in Maryland! There will be many guests and even...seafood cuisine at a fancy restaurant! All is well until one of our guests comes down with a peculiar sickness. Do you think you can figure out what happened?

Honeymoon Horror Story, Andrea Florian, Aunalise Terreri, Kiley St. John, Sienna White

SPARK Symposium Presentations

On what was supposed to be a romantic honeymoon getaway, a newly married couple’s paradise quickly turns dark. The wife, Julia Harper, is found dead under mysterious circumstances, and suspicion falls on her neuroscientist husband. As lies unravel, investigators discover that this honeymoon was never about love, but revenge. In the end, all that’s left is betrayal and secrets…Can you solve this murder mystery?

The Last Ball, Andrea Florian, Lili M. Wrenne, Mehrael Adly, Jia Howell

SPARK Symposium Presentations

Sixty-year old, billionaire, Walter Spencer has been found dead at his annual birthday celebration. Guests reported odd behavior before he passed with wild mood swings, speaking gibberish, and experiencing hallucinations. Close friends of Walter say his young 25-year-old wife was the last to see him. Are you able to solve his mystery?

A Sweet Deception, Andrea Florian, Ellis Stafford, Bridget Mcloud, Awi Siam

SPARK Symposium Presentations

Have you ever wanted to be a detective and solve a murder? Well, here is your chance! Bradley Thompson, an investment banker at JP Morgan, was murdered in his home, and we are relying on you to piece together the toxicological clues and find his killer! This murder-mystery activity will involve selecting different toxicological tests and evaluating evidence to determine who committed this heinous crime.

Potential Environmental Triggers Of Goodpasture's Disease And The Role Of The Sulfimine Crosslink, Colton S. Miller, Andrea Florian, Elena Pokidysheva

SPARK Symposium Presentations

Goodpasture’s syndrome (GP) is an autoimmune disorder that primarily affects kidneys and lungs. The main issue for patients with Goodpasture's syndrome is the binding of autoantibodies to the glomerular basement membrane (GBM), which hinders the filtration of blood. A key characteristic of Goodpasture's syndrome is the presence of autoantibodies that target the NC1 domain of the α345 isoform of type IV collagen, a crucial component of the GBM that provides structural support and is critical for filtration function. Sulfilimine bonds crosslink the collagen IV NC1 hexamers, contributing to the stabilization of these structures. A recent clinical case of recurring Goodpasture's …

Radial And Carotid Arterial Pulse Signals For Assessing Cardiovascular Function At Rest And During Post-Exercise Recovery In A Heart Transplant Patient: A Case Study, Md Mahfuzur Rahman, Mamun Hasan, Jennifer F. May, John M. Herre, Leryn Reynolds, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

Aim: This study investigates the feasibility of using radial and carotid arterial pulse signals to assess cardiovascular (CV) function at rest and during post-exercise recovery in a heart transplant (HTx) patient. Method: Two micro-fabricated tactile sensors were used to simultaneously acquire arterial pulse signals at the radial artery (RA) and carotid artery (CA). Measurements were taken at rest and at multiple time points post-exercise on three subjects: an HTx patient, a percutaneous coronary intervention (PCI; coronary stent) patient and a healthy control. An SDOF-TF-based time-frequency analysis algorithm was applied to extract a comprehensive set of CV parameters, including heart rate …

Ecological Feedbacks In The Earth System, Eugene J. Murphy, Jessica J. Williams, Isla H. Myers-Smith, Vivienne P. Groner, David M. P. Jacoby, Lester Kwiatkowski, Jess Melbourne-Thomas, Emma Ransome, Cristina Banks-Leite, Laurent Bopp, Marion Gehlen, Eileen E. Hofmann, Babette Hoogakker, Nadine M. Johnston, Yadvinder Malhi, Emma L. Cavan

CCPO Publications

Ecological feedbacks are fundamental features of the Earth system, affecting physical processes and chemical cycles. Our understanding of the interactions underlying these feedbacks at different spatial and temporal scales and the extent to which feedbacks affect Earth system functioning remains limited. Climate change and other anthropogenic pressures are already negatively affecting ecological processes in marine, freshwater, and terrestrial ecosystems. These will most likely be amplified in the coming decades under our current warming and socioeconomic pathways. The knock-on impacts on ecological feedbacks have the potential to cause rapid perturbations to the Earth system, and may significantly impact the structure and …

End-To-End Modeling For The Ross Sea Region Marine Protected Area: A Review Of Available Tools For Conservation Objectives, James R. Lovvorn, Cara Nissen, Alexis A. Bahl, Erik Behrens, Cassandra M. Brooks, Katy Christensen, Michael S. Dinniman, Lilian A. Dove, Alice K. Duvivier, Eileen E. Hofmann, Hayley Kwasniewski, Young Shin Kwon, Sharon E. Stammerjohn, Lei Xing

CCPO Publications

The challenge of protecting marine ecosystems, including biodiversity and manifold interactions in changing environments, has encouraged development of end-to-end models linking physical drivers through entire food webs to upper-level predators. Ideally such models should have temporal and spatial resolution adequate to capture important small-scale processes, while including scales large enough to encompass local food webs and movements of wide-ranging consumers. The need for component submodels to be manipulated and upgraded independently by scientists from different disciplines, and used selectively depending on questions addressed, favors modular structure allowing linkage of different submodels with varying strengths and weaknesses. As an example, this …

Regional Oceanographic Controls On Water Column Nitrogen Fixation In Northern Australian Waters, Douglas G. Capone, Ajit Subramaniam, Yubin Raut, Joseph P. Montoya, Margaret R. Mulholland, Rachel Ann Foster, Miles Furnas, Edward J. Carpenter

OES Faculty Publications

Large blooms of the diazotrophic cyanobacteria, Trichodesmium, have been re-ported along the north coast of Australia and are readily evident in remote sensing images. During a research cruise in November 1999, we sampled from Townsville to Broome, examined Trichodesmium population densities and their rates of carbon and N₂ fixation alongside microscopy-based cell counts of them and other cyanobacte-rial diazotrophs. Additionally, we also enumerated the picophytoplankton community using flow-cytometry, measured bulk chlorophyll concentrations, carbon and N₂ fixation rates, and water column hydrography, enabling comparison of diazotrophic and picophytoplankton functional groups across the system. Agglomerative hierarchical clustering analysis of physicochemical oceanographic …

Differential Growth Dynamics Of Common Salt Marsh Species Spartina Alterniflora And Juncus Roemerianus Under Varied Sediment Amendments, Caitlin Hemphill, Richard P. Hale, Erik S. Yando

Biological Sciences Faculty Publications

Introduction

Many coastal wetlands are at high risk of degradation or loss due to sea‐level rise. Restoration techniques for maintaining coastal marshes are paramount, with thin‐layer placement (TLP) emerging as one feasible solution. Despite TLP's utilization, additional research is needed on species‐ and sediment‐specific responses.

Objectives

Our research combines greenhouse and field experimentation to test species and sediment composition responses aimed at maximizing vegetation while maintaining increased elevation.

Methods

The greenhouse experiment used two common marsh plants, Spartina alterniflora and Juncus roemarianus. Five centimeters of sediment (mud, sand, and sand/mud mix) was added, and subsequent sediment and vegetation metrics …

Murder Of The Magic Mushroom Man, Andrea Florian, Alexa Cabral, Olivia Fawkes, Emily Gomez

SPARK Symposium Presentations

Rowan Tucker is an heirloom vegetable farmer that lives in Newbury, VT on an 80-acre farm. Most of the money in Rowan’s name was from selling psilocybin mushrooms that he disguised as payments under “crop-selling”. He was found dead presenting symptoms early that morning of confusion, hallucinations, vomiting, sweating, and extreme salivation. How did he get murdered? Who did it?

Floodwater Salinity And Flood Duration Regulate Greenhouse Gas Production In High- Latitude Coastal Wetland And Tundra Soils, Mia J. Dicianna

Electronic Theses and Dissertations

Coastal high-latitude ecosystems are increasingly flooded from storm surges associated with climate change, exposing soils that were historically infrequently inundated to higher-salinity waters for longer durations. Sub-Arctic wetlands and tundra store large amounts of carbon, yet how flooding characteristics, particularly flood duration, influence microbial mineralization and, consequently, greenhouse gas (GHG) production in these soils remains poorly understood. We conducted a full-factorial microcosm incubation experiment in which coastal wetland and tundra soils were subjected to simulated flooding with three durations (1, 3, and 10 days) and four salinity treatments (unflooded, freshwater, 3 ppt, and 12 ppt) and measured carbon dioxide (CO2) …

Winter-Feeding High Forage Vs. High Concentrate Diets To Beef Cows: Effects On Placental Transcriptomics, Lactation Capacity, And Enteric Methane Emissions, Megan Ann Wehrbein

Electronic Theses and Dissertations

Nutritional management and lactation performance are critical factors influencing productivity in cattle. This research includes two complementary studies. The first study was a meta-analysis to develop a lactation curve for Bos taurus cattle in North America using data from machine or hand milked cows. Data from 7 studies were used resulting in 1340 cow-day observations. Milk yield was analyzed by parity (primiparous or multiparous) and feeding management (non-nutrient restricted or nutrient restricted), revealing that primiparous cattle peaked earlier and at lower yields than multiparous cattle, and nutrient restriction reduced peak milk yield. Overall, Bos taurus cattle followed lactation trends similar …

The Critical Role Of Near-Surface Dynamics In Identifying Spawning Areas Of Atlantic Bluefin Tuna In The Gulf Of Mexico, Donald R. Johnson, William J. Teague, Harriet Perry, James S. Franks

Gulf and Caribbean Research

Atlantic Bluefin Tuna, Thunnus thynnus (ABFT), migrate long distances to broadcast spawn in the Gulf of Mexico (GOM) basin, the Mediterranean Sea and the Slope Sea (NW Atlantic). These areas have commonalities including a highly dynamic upper ocean eddy environment that draws nutrients from shallow thermoclines and adjacent continental shelves and can provide temporal sanctuaries from some larval predators. In the GOM basin, the Loop Current (LC) and its energetic spin—off eddies sweep weak swimming predators such as jellyfish (Pelagia noctiluca) into lines and aggregations, leaving relatively open areas as temporal sanctuaries for ABFT larvae during the vulnerable …

Bayesian Multivariate Modelling Of Lone Star (Amblyomma Americanum) Tick Life Stage Abundance And Temporal Trends To Inform Public Health Risk In Virginia, Thabo Lephoto, Henry Mwambi, Oliver Bodhlyera, Holly Gaff

Biological Sciences Faculty Publications

The increasing abundance of ticks poses a growing public health concern due to heightened human exposure to tick bites. The lone star tick (Amblyomma americanum: Ixodida: Ixodidae), a common human-biting species in the United States, has expanded its range in recent years. However, how its different life stages vary across time, habitats, and locations remains insufficiently understood. We analyzed tick abundance data collected in southeastern Virginia between 2009 and 2018, focusing on larval, nymphal, and adult life stages. A Bayesian multivariate modelling framework was used to examine seasonal patterns, habitat effects, spatial variation, and biological links between life stages. Two …

An Ensemble Classifier For Ordinal Outcomes In High-Dimensional Genomics Data, Heranga K. Rathnasekara, Sinjini Sikdar

Mathematics & Statistics Faculty Publications

Analysis of genomics data for predicting disease outcomes is a fast-growing field in medical research. There often exist categorical, specifically, ordinal outcomes that need to be predicted based on genomic profiles. This has led to recent development of some high-dimensional ordinal classification methods that can address the large dimensionality of the genomic covariate set. These high-dimensional ordinal models tend to vary widely in their performance depending on the data they are applied to and the evaluation criteria used. In this article, we outline an ensemble ordinal classifier that integrates different ordinal modeling approaches through bootstrap-based model evaluation, multi-metric performance assessment, …

Does Fishery Management For Groupers (Teleostei: Epinephelidae) Protect Them Effectively? Context From The Iucn's Red List Of Threatened Species, Sean T. Fennessy, Christi Linardich, Kevin Rhodes, Joao P. Barreiros, David Pollard, Eloy Sosa-Cordero, Felicia Coleman, Alfonso Aguilar-Perera, Christopher R. Malinowski, Thierry Brulé, Pedro Afonso, Kayan Ma, Min Liu, Muktha Menon, Colin Wen, Stanley K. H. Shea, Sean N. Porter, Matthew Craig, Yvonne Sadovy De Mitcheson

Biological Sciences Faculty Publications

Worldwide, groupers (Epinephelidae) are commercially valued fishes, which also play key ecological roles on tropical and subtropical reefs. In 2007 and 2016, the IUCN's Groupers and Wrasses Specialist Group assessed all 160+ grouper species, with 17 of these being identified as threatened in 2016 and the major threat factor being overexploitation. Our present study aimed to identify whether management measures (MMs) for previously assessed groupers were established, whether these measures aligned with IUCN's Red List categories, and whether they effectively protect grouper populations. Experts in grouper biology and management assigned scores per grouper species based on the extent to which …

Three Decades Of Classifying Threatened Species: Lessons Learned From And About The Iucn Red List Criteria For Quantifying Extinction Risk, H. Resit Akçakaya, E. J. Milner-Gulland, Mike Hoffmann, Helen M. Regan, Ilona Naujokaitis-Lewis, Andre E. Punt, Kevin J. Gaston, David A. Keith, Stuart H. M. Butchart, Simon N. Stuart, Nigel J. Collar, Moreno Di Marco, Monika Bohm, Alex J. Berryman, David P. Mallon, Axel Hochkirch, Nicholas K. Dulvy, Malin Rivers, Thomas M. Brooks, James R. S. Westrip, Jonathan Paul Rodriguez, Craig Hilton-Taylor, Janet Scott, Simon Tarr, Sophie H. Ledger, Christi Linardich

Biological Sciences Faculty Publications

The IUCN Red List of Threatened Species, the most widely used global system for assessing species' extinction risk, has become a foundational source of information for conservation management, policy and research. Since the adoption of quantitative extinction risk criteria more than three decades ago, the Red List has expanded substantially in scope and influence, informing decisions ranging from species conservation and protected area designation to international agreements, corporate risk assessments and global biodiversity indicators. Given its central role, maintaining scientific rigour, transparency and trust in the Red List system is essential. Feedback from users, emerging from evolving applications and scientific …