Digital Commons Network^™

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 …

Using Genetic Analysis To Infer Familial Relationships Of Westslope Cutthroat Trout In The Lower Priest River, Idaho, Kolby Emtman

EWU Masters Thesis Collection

The Westslope Cutthroat Trout (Oncorhynchus lewisi) is a native species of salmonid that holds both cultural and ecological significance in the Idaho Panhandle region of the United States. Within this region, the Priest River is a major contributor of migrant Westslope Cutthroat Trout to the Clark Fork Pend Oreille basin. This study aimed to estimate the proportion of juveniles that have at least one migrant parent, illustrate gene flow using juvenile half sibling relationships, and showcase varying levels of spawning success using juvenile full sibling relationships. Sampling of juvenile individuals occurred in 11 tributaries of the Priest River over …

Molecular Detection Of Campylobacter Spp. In Filth Flies Associated With Broiler Breeder Facilities In Oklahoma And Arkansas, Allen Szalanski

Entomology and Plant Pathology Faculty Publications and Presentations

Adult filth flies (Diptera: Muscidae) (non-biting flies that develop in decaying organic matter) are abundant in poultry facilities and may contribute to the dissemination of pathogenic Campylobacter spp. among flocks. We sampled adult house flies, Musca domestica L., and black dump flies, Hydrotaea aenescens (Wiedemann), at five broiler-breeder farms in Oklahoma and Arkansas to determine the prevalence of Campylobacter spp. vectored by filth flies and the effects of farm, fly species, and location (inside vs outside houses) on the rates of Campylobacter spp. occurrence. A total of 1,076 house flies and 1,008 black dump flies were collected inside and outside …

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 …

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 …

The Biology Of Soulmates: Are We Wired For Connection?, Christiane Betfarhad

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Light At The Wrong Time, Alexis Murdock

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Kenyon College Neuroscience Department Faculty And Staff

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Green Hydrogen-Based Decarbonization Approach For Steel Industry With Hybrid Renewable Energy Sources, Raju Kumar Maurya, Dharmbir Prasad, Rudra Pratap Singh

Mansoura Engineering Journal

This work provides a micro-pilot techno-economic and environmental assessment of a green hydrogen-driven decarbonization scenario for low-carbon steel production at the capacity of 1 ton steel produced (i.e., requiring 50 kg of green hydrogen). In this work an integrated renewable energy (RE) scenario for the steel production site at Jamuria, West Bengal, India is planned to utilize solar photovoltaic (PV), wind turbines (WTs), battery storage and a diesel backup generator to meet the hydrogen production load from an electrolyzer using HOMER Pro software. The results show that the proposed micro-pilot system produces excess electricity with respect to the plant's operating …

Intelligent Audio‑To‑Indian Sign‑Language And Sign‑To‑Audio Translation System Using Mediapipe, Tensorflow, Whisper And Google Tts, N. Pothanna, T. Kusuma, S. Haindavi, T. Sreeja, Shaik Shaheem Taj

Mansoura Engineering Journal

Communication barriers between the Deaf community and the general public remain a persistent challenge, particularly in multilingual settings where Indian Sign Language (ISL) is the primary mode of interaction. We propose a real-time bidirectional translation framework integrating MediaPipe for hand landmark extraction, a Convolutional Neural Network (CNN) classifier built with TensorFlow/Keras for gesture recognition, OpenAI Whisper for robust multilingual speech-to-text transcription, and Google TTS for naturalistic speech synthesis. The system achieves 93% classification accuracy across 35 ISL classes (alphabets A–Z and numerals 1–9) on a dataset of 42,700 images, with macro and weighted F1-scores of 0.93. Deployed as a Flask …

A Quantitative Analysis Of Burrowing And Subterranean Locomotion In The Sand Lance Using A Transparent Sediment, Issei Fujita, Makoto Tomiyasu, Jun Yamamoto, Yasuzumi Fujimori

Journal of Marine Science and Technology–Taiwan

Sand lances (Ammodytes spp.) rely on rapid burrowing into sediment for predator avoidance. Although their sediment grain-size preferences are well documented, the biomechanics underlying burrowing success remain unclear because natural substrates are opaque. Using a transparent-sediment system, we directly visualized and quantified burrowing kinematics to: (1) test the effect of body size (total length, TL) on burrowing success; (2) examine entry mechanisms (e.g., swimming speed, entry angle); and (3) describe locomotion within sediment. Logistic regression on the full dataset (N = 28 fish) identified TL as the primary determinant of success, with larger individuals exhibiting significantly higher success …

Enhancing Underwater Imagery And Organism Detection Using Reinforcement Learning, K. Arul Deepa, P. Ramya, Karpaga Vinodha, Dharmaraja C

Journal of Marine Science and Technology–Taiwan

Underwater environments pose significant challenges in assessing image quality and organism detection due to light scattering and absorption, which limits visibility and color fidelity. Existing solutions often fail to effectively address these challenges, resulting in suboptimal image quality and hindering organism identification. This paper examines the problem through a dual-focused approach: enhancing underwater images and detecting organisms using the Underwater Image Enhancement Benchmark (UIEB) dataset. The first step introduces a state-of-the-art method for image enhancement by applying reinforcement learning (RL) principles. By formulating the enhancement process as a Markov Decision Process (MDP)—where states are represented by image features and actions …

Dna Barcoding Complements Citizen Science Identifications In An Arthropod Survey At Governors Island, New York, Malky Gestetner

Dissertations and Theses

Arthropods are declining worldwide, threatened by habitat loss, climate change, and growing urbanization. Efforts to monitor arthropod biodiversity are crucial for conservation policies and for maintaining the ecosystem services provided by these animals in urban environments. Surveys of arthropods have been attempted in many New York neighborhoods, but no formal assessment has been conducted on Governors Island, which harbors 72-acres of parkland within a short boat ride away from Manhattan. This is a deficiency which this study helps to address. Following student-led collection efforts within four Governors Island sites, DNA barcoding was employed to complement specimen identification based on morphology …

Assessment Of The Antimicrobial Properties And Skin Microbiota Of Unisexual (Ambystoma) Salamanders Within Defensive Toxins, Sydney Stanton

Senior Honors Theses and Projects

As antibiotic resistance continues to pose a significant threat to public health, discovery of novel antibiotics could provide tools to combat this threat. Amphibian skin exhibits complex pathogen defense physiology and diverse skin microbiota, which suggests that it could be a potential source of novel antibiotics. A critical feature of amphibian skin is mucus, which is secreted as a defense mechanism and contains many immune system components such as symbiotic microbiota and antimicrobial peptides. To test the antibacterial properties of amphibian mucus, this study assesses whether mucus secretions from unisexual Ambystoma salamanders are effective at inhibiting the growth of safe …

Data From: Mass Mortality Of Avian Migrants In New Mexico, Usa, That Coincided With An Extreme Weather Event, Dylan M. Osterhaus, Allison J. Salas, Patricia L. Cutler, Mara E. Weisenberger, Kerry Mower, Abigail J. Lawon, Timothy F. Wright, Jeanne M. Fair, Martha J. Desmond

Fish, Wildlife, & Conservation Ecology: Datasets

No abstract provided.

Data And Code From: Migration Speed, Timing, And Long-Term Shifts In Age Structure In North American Passerines During Fall Migration, Dylan M. Osterhaus, Martha J. Desmond, Timothy F. Wright

Biology: Datasets

No abstract provided.

“Shaking The Ladder” Reveals How Analytic Choices Can Influence Associations In Nutrition Epidemiology: Beef Intake And Coronary Heart Disease As A Case Study, Colby J Vorland, Lauren E O'Connor, Beate Henschel, Cuiqiong Huo, James M Shikany, Carlos A Serrano, Robert Henschel, Stephanie L Dickinson, Keisuke Ejima, Aurelian Bidulescu, David B Allison, Andrew W Brown

Children’s Nutrition Research Center Staff Publications

Nutrition epidemiological models involve many analytic decisions, such as defining exposures, selecting which covariates to include, or configuring variables in different ways. We explored the impact of analytical decisions on conclusions in nutrition epidemiology using self-reported beef intake and incident coronary heart disease as a case study. We used REasons for Geographic and Racial Differences in Stroke (REGARDS) data, and selected covariates and their configurations from published literature to recapitulate common models used to assess associations between meat intake and health outcomes. Three model sets were designed: sets one and two used continuous and quintile-defined beef intakes, respectively, each with …

Examining Widely Held Propositions On Human Dietary Protein Needs And Benefits: A Critical Review Of The Science That Shapes Both The Data And Our Understanding Of An Essential Macronutrient, Mitchell M Kanter, Sally Aaron, Steven N Austad, Andrew W Brown, Nicholas A Burd, Wayne W Campbell, Mark Cope, Teresa A Davis, John W Erdman, Miguel Freitas, Kristen Hicks-Roof, Samuel Klein, Wantanee Kriengsinyos, Dudley W Lamming, Donald K Layman, Heather J Leidy, Kevin C Maki, Richard D Mattes, Shalene Mcneill, Daniel R Moore, Stefan M Pasiakos, Stuart M Phillips, David Raubenheimer, Wendy Reinhardt, Nancy R Rodriguez, Stephen Simpson, Hans H Stein, Luc J C Van Loon, Connie M Weaver, David B Allison

Children’s Nutrition Research Center Staff Publications

The essentiality of protein in the human diet is unequivocal. Yet researchers, clinicians, and lay people often believe numerous propositions about dietary protein despite insufficient supporting or refuting data in some instances. To address this disconnect, and to "pressure-test" current beliefs about dietary protein, the Indiana University School of Public Health-Bloomington convened a workshop in February 2025 titled "Human Dietary Protein Needs and Benefits: A Critical Assessment of Postulated Propositions." More than 20 international experts discussed (1) methodologic issues affecting data acquisition and interpretation; (2) "optimal" dietary protein intakes and effects on muscle protein synthesis rates, muscle protein accretion, …

Cross-Sectional And Longitudinal Relationships Between Abdominal Fat Depots And Cardiometabolic Risk In A Sample Of Mexican Adolescents, Luis Ortíz-Hernández, Erica G Soltero, Miguel Camejo, Jesús Valdes

Children’s Nutrition Research Center Staff Publications

Background: The relationship between abdominal fat depots and cardiometabolic risk among youth is inconclusive due to the cross-sectional nature of existing studies and limitations in assessment methods. In this study, we examined cross-sectional and longitudinal associations of subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) with cardiometabolic risk indicators among Mexican adolescents.

Methods: Participants (n = 169 at baseline and 134 at follow-up) were assessed for diastolic or systolic blood pressure (DBP or SBP), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides, glucose, and insulin. VAT and SAT were measured using magnetic resonance imaging. Measures …

Ultra-Processed Foods And The Cardiovascular-Kidney-Metabolic Continuum: Integrating Epidemiological, Multi-Omics, And Translational Evidence, Saiful Singar, Amirhossein Ataei Kachouei, Leandro Lantigua-Somoano, David Manley, Anthony Cardinale, Muhammad Zulfiqah Sadikan, Saurabh Kadyan, Donya Shahamati, Lorena Dias, Amber Wood, Cinthia Chavarria, Sara K. Rosenkranz, Neda S. Akhavan

Department of Medicine Faculty Publications

Cardiovascular-kidney-metabolic (CKM) syndrome integrates excess adiposity, metabolic dysfunction, kidney impairment, subclinical cardiovascular diseases, and clinical events along a staged continuum that invites unified prevention and treatment. Ultra-processed foods (UPFs) are a complex, high-prevalence exposure that may influence risk across CKM stages through nutrient profiles, additives, processing-induced compounds, and packaging-related contaminants. This review synthesizes epidemiologic, mechanistic, and translational evidence with attention to exposure definition and analytic rigor. We summarize NOVA-based UPF operationalization across dietary assessment tools, highlighting misclassification of mixed dishes, brand heterogeneity, and energy under-reporting, and we propose further examination of energy-adjusted models, calibration, and harmonized metrics. Observational studies consistently …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

Population Genomics And Evolution Of Pseudomonas Aeruginosa, Samara T. Choudhury

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is a Gram-negative bacterium ubiquitous in diverse environments and an opportunistic pathogen in humans. It is a leading cause of chronic lung infections in cystic fibrosis patients and of hospital-acquired pneumonia and sepsis. With a large flexible genome and abundant mobile genetic elements, P. aeruginosa exhibits high levels of antimicrobial resistance (AMR), making it a significant public health threat. Evolutionary processes such as homologous recombination, and horizontal gene transfer generate extensive genomic diversity in this species and facilitate the spread of resistance genes. In this dissertation, I investigate the genetic and evolutionary factors shaping P. aeruginosa population structure …

Viral Diversification And Host-Specific Fitness Of Powassan, Heartland, And Bourbon Viruses In New York State, Rachel E. Lange

Electronic Theses & Dissertations (2024 - present)

This dissertation reports important progress for our understanding of emerging and re-emerging tick-borne viruses circulating in North America including Powassan, Deer Tick, Heartland, and Bourbon viruses. Chapter 2 describes important tools for these viruses including multiplex assays for viral and bacterial pathogens in field-collected ticks and mammals, development of full genome sequencing assays and bioinformatic pipelines for evolutionary analysis, and establishment of tick-specific tools for viral isolation and characterization. Chapter 3 focuses on the disease focality of Deer Tick virus, reporting transovarial transmission in nature in Ixodes scapularis for the first time, further evidence to incriminate shrews as potential Deer …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Multifunctional And Adaptive: Tracking How Fibroblasts Respond To Tissue Injury And Facilitate Tissue Remodeling, Joey R. Tavarez

Electronic Theses & Dissertations (2024 - present)

Fibrosis is characterized by an accumulation of proteins in the extracellular matrix (ECM) that results in altered tissue architecture and reduced organ function. In the salivary glands, fibrosis leads to loss of saliva, dysbiosis of the oral microbiome, an increase in oral infections, difficulty in digestion of food and an overall reduction in the quality of life. Understanding the progression of fibrosis and how it affects human health is a crucial step for designing effective therapeutics. Understanding fibroblast function is integral to advancing the field due to the many roles they play in maintaining the ECM. To perform preliminary analysis, …

Barriers And Corridors: Timber Rattlesnake Habitat Connectivity In New York, Lauren Rose

Electronic Theses & Dissertations (2024 - present)

Habitat fragmentation poses a significant threat to species that rely on landscape connectivity for movement in search of food, water, and mates. The timber rattlesnake (Crotalus horridus), listed as a threatened species in New York State, travels an average of 1.5 miles—and up to five miles—from permanent denning sites to reach habitat suitable for gestation, foraging, basking, and overwintering. Ongoing development in the lower Hudson Valley has increasingly fragmented these critical habitats, restricting movement between den populations. This thesis evaluates landscape barriers that contribute to population isolation and identifies opportunities to restore connectivity among timber rattlesnake metapopulations.

Using …

Inflammation In Early Borrelia Burgdorferi Skin Infection, Ariana Nobles

Electronic Theses & Dissertations (2024 - present)

Borrelia burgdorferi (Bb) is the causative agent of approximately 476,000 cases of Lyme disease in the United States and rising. Bb is spread through infected saliva of the black-legged tick, Ixodes scapularis, to the host. Patients infected with Bb experience short-term symptoms, such as erythema migrans (EMs), fatigue, pain, and cognitive impairment. If left untreated, Bb infection will cause long-term health complications, like Lyme neuroborreliosis and Lyme arthritis. It is postulated that symptoms associated with Lyme disease are driven in part by inflammation.

My thesis focuses on the skin as it holds significant immunological importance in the …

Development And Applications Of Fluorescence Microscopy Protocol To Investigate Borrelia Burgdorferi Immune Interactions In The Skin, Rebecca V. Landry

Electronic Theses & Dissertations (2024 - present)

The skin is an immunological organ that acts as the hosts’ first line of defense against infectious agents. Infectious disease vectors like ticks breach this barrier by feeding on hosts, transmitting pathogens like Borrelia burgdorferi in the process. Uncleared infection with B. burgdorferi causes Lyme disease, the most prevalent vector-borne disease in the United States. Previous research has explained many elements of Lyme disease pathogenesis and immunity including the dissemination of the spirochete, innate immune cells performing phagocytosis, the production of antibodies by the humoral response, and the impact of prophylactic treatment with monoclonal antibodies. A remaining gap in the …

Assessing Fisheries Dependence Of Coastal Communities In Managed Mangrove Forests In Latin America, Ariel Alexander Quintanilla Magana

Open Access Dissertations

Fisheries dependency refers to the action of a person, community, or society linking their social, cultural, and economic actions to different ecosystem services (ES) for covering their food system with essential marine species, developing a governance system to conserve these fishing areas, their local ecological knowledge, and guaranteeing food security in the coastal areas. In Latin America, most fishing activities are practiced within three nautical miles of the shoreline, estuaries, lagoons, and mangrove forest channels, using small vessels and traditional gear such as hooks, trammel nets, and gill nets. Some coastal communities have developed their subsistence and livelihood activities in …

Effects Of Desiccation On Invasive Faucet Snail (Bithynia Tentaculata) And Trematode Survival, Elise Marie Jordahl

Graduate Research Theses & Dissertations

Parasitism is one of the most common and diverse life history strategies, yet relatively little is known about the role of parasites as invasive species. Invasive species, which present one of the greatest threats to biodiversity, often need to overcome adverse environmental conditions as they establish and spread in new habitats. Invasive parasites are subject to these same conditions, though the effects may be mediated through their hosts. Here, I use an invasive snail and its trematode parasites to quantify the effects of desiccation on survival to better understand how processes of invasion play out in host-parasite systems. The faucet …