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Feasibility Of Corn Stover For Biogas Production In Northwestern Illinois: A Case Study Of Jo Daviess And Carroll Counties, Anthony Amotoe-Bondzie

Masters Theses

The growing demand for renewable energy and sustainable waste management has intensified interest in agricultural residues such as bioenergy feedstocks. This study evaluated the feasibility of converting corn stover into biogas through anaerobic digestion (AD) in Jo Daviess and Carroll Counties, Illinois, with consideration of the Savanna Industrial Park as a potential centralized processing hub. Although corn stover represents one of the largest biomass resources in the United States, this research identifies a critical gap between theoretical availability and practically recoverable feedstock. Using a mixed-methods framework, the study integrates biomass quantification, methane yield modeling, economic analysis, and policy assessment. Results …

Epigenetic Modifications In Dedifferentiated Liver Cells To Restore Lost Liver Function, Shreya Sharma

Masters Theses

The goal of the study is to investigate whether the epigenetic modifications can enhance the restoration of liver gene expression in dedifferentiated hepatoma cells or not. For the study, we used dedifferentiated H11 hepatoma cell lines which overexpress one of a panel of introduced candidate liver-enriched transcription factors H11-HNF1a, H11-CREB3L3, H11-CREG1, H11- HHEX, H11-HNF6, and H11-IGFBP1. The cells were treated with the DNA methyltransferase inhibitor 5-azacytidine and the histone deacetylase inhibitor sodium butyrate, both individually and in combination. Gene expression analysis was determined by RT-qPCR, which revealed that while transcription factor overexpression alone produced limited activation, epigenetic modulation, particularly Histone …

Layers Of Biodiversity: Linking Urban Garden Plants And Arthropods, Chenyang Su

Dartmouth College Ph.D Dissertations

Diverse arthropods play essential roles in urban agriculture, while urban agriculture provides food and habitat that support arthropod biodiversity in fragmented urban landscapes. In urban community gardens, a form of urban agriculture characterized by allotment-style gardens, arthropods interact with plants and green space across multiple spatial scales of management, from individual gardeners' plots to broad urban landscapes. Understanding how plant communities in urban community gardens and urban landscapes shape arthropod biodiversity and interactions across scales can inform both agricultural management and urban biodiversity conservation. In this thesis, I conducted a series of field studies on ecologically and economically important arthropods …

Evaluating Planting Methods For Native Seed Production And Exploring Granivory In The Northern Great Plains, Allison Dollen

Electronic Theses and Dissertations

Temperate grasslands have faced immense losses due to land use change in the last 150 years and less than half of the overall grasslands that once covered North America remain today. A portion of historic and remaining U.S. grasslands are located within the northern Great Plains (NGP) region which is home to over 1,600 species of native plants and provides many ecosystem services and economic benefits. Initiatives to restore grasslands and their ecosystem services are currently underway, but barriers such as limited native seed supply and granivory hinder restoration efforts. My first chapter addresses knowledge gaps in planting methods for …

Impact Of Water Level Fluctuations On Fish Populations In Eastern South Dakota Rivers, Benjamin Schall

Electronic Theses and Dissertations

Riverine systems are highly dynamic, and changes in flow conditions can impact the population dynamics of fishes. Increased flows from historical averages in eastern South Dakota rivers have likely impacted fish populations. The goals of this study were to 1) better understand the changes in resource use by Blue Suckers Cycleptus elongatus through retrospective eye lens stable isotope analysis, 2) determine the effects of record flooding in the James River on complex woody habitat and Flathead Catfish Pylodictis olivaris population structure, and 3) assess the influence of river discharge and temperature on Channel Catfish Ictalurus punctatus and Flathead Catfish condition …

Non-Native Seagrass, Halophila Stipulacea, Reaches Northern Caribbean, Elizabeth R. Whitman, Elizabeth W. Stoner, Stephanie K. Archer

Gulf and Caribbean Research

Halophila stipulacea, a seagrass native to the western Indian Ocean, has become an established invader throughout the western Atlantic, where it often outcompetes native seagrass species across diverse environmental conditions. Here, we report its presence in the northern Bahamas, ca. 2300 km northwest of the first Caribbean record in Grenada and 304 km northeast of the recent observation in Florida, USA. This range expansion represents the northernmost Caribbean record to date and highlights the species’ capacity for long-distance dispersal and continued spread within the region. Our observation underscores the need for coordinated monitoring efforts to track the trajectory of …

Notes On The Ichthyofauna Associated With Artisanal Fishing In A Severely Impacted Estuary In The Southwestern Gulf Of Mexico During The Rainy Season, Rodrigo Vivanco-Cadena, César Meiners-Mandujano, Roberto Martín Cruz-Castán

Gulf and Caribbean Research

No abstract provided.

Manatee Dock Sign Distribution And Its Influence On Publicly-Sourced Sighting Reports In Alabama, Daniela Payán Arias, Sophia C. Corde, Ruth H. Carmichael

Gulf and Caribbean Research

No abstract provided.

A Marine Science Career In The Eastern Caribbean: Witnessing Four Decades Of Change, Hazel A. Oxenford

Gulf and Caribbean Research

Reflecting back on a long and rewarding career from 1980—2023 at the University of the West Indies, based on the small island of Barbados, this paper tracks the many and often remarkable changes in the marine environment, in attitudes and policies, and available opportunities that have influenced my journey as a marine scientist in an ever—changing but resilient Caribbean. From free—access fisheries to degraded stocks, from coral to algal dominated reefs, from flyingfish to Almaco Jacks, from sandy beaches and clear water to a Sargassum crisis — these are just some of the fundamental changes in the marine environment that …

A Comparative Analysis Of The Ecophysiology Between The Invasive Macroalgae Starry Stonewort And The Native Macroalgae Chara To Predict Invasion Potential, Thomas J. Zellmer

All Graduate Theses, Dissertations, and Other Capstone Projects

Starry stonewort (Nitellopsis obtusa) is an invasive macroalga from Eurasia. Currently, starry stonewort’s invasive range consists of the upper Midwest and Great Lakes region, including the Mississippi River. Starry stonewort poses recreational and ecological problems by forming dense canopies that extend through the water column. Starry stonewort occupies a late-season niche space with dense biomass occurring in late July and persisting well into autumn. There is a lack of information on the ecophysiology of starry stonewort. In this study, two populations of starry stonewort, Minnesota and New York, were analyzed to compare regional differences in ecophysiology, along with chara (native …

An Exploratory Analysis Of The Role Of Sex In Load Carriage, Rachel E. Perez, Dustin R. Slivka, Brent C. Ruby

Graduate Student Theses, Dissertations, & Professional Papers

Axially loaded weight may impose a metabolic demand equivalent to that of fat mass (FM) during load carriage. Males (M) typically have a lower body fat percentage than females (F), resulting in metabolic demand differences during load carriage that may be mitigated by accounting for FM in pack loads. PURPOSE: To determine whether normalizing pack load to FM equalizes metabolic cost across sexes during load carriage. METHODS: Twenty-eight participants (14M, 23 ± 5 y, 1.81 ± 0.07 m, 78.7 ± 10.0 kg, 12.7 ± 5.4% body fat, VO₂peak 4.18 ± 0.54 L·min^-1; 14F, 22 ± 4 …

A Complete Diploid Human Genome Benchmark For Personalized Genomics, Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, Arang Rhie, Hailey Loucks, Glennis A. Logsdon, Mitchell R. Vallger, Jessica M. Storer, Juhyun Kim, Eleni Adam, Nicolas Alternose, Dmitry Antipov, Mobin Asri, Sofia Barreira, Stephanie C. Bohaczuk, Andrey V. Bzikadze, Sara A. Carioscia, Andrew Carroll, Kuan-Hao Chao, Yanan Chu, Arun Das, Peter Ebert, Adam English, Mark Fleharty, Laura E. Fleming, Giulio Formenti, Andrea Guarracino, Gabrielle A. Hartley, Katharine Jenike, Jenna Kalleberg, Yu Kang, Robert King, Josipa Lipovac, Mira Mastoras, Matthew W. Mitchell, Shloka Negi, Nathan D. Olson, Keisuke K. Oshima, Luis F. Paulin, Brandon D. Pickett, David Porubsky, Jane Ranchalis, Desh Ranjan, Mikko Rautiainen, Harold Riethman, Robert D. Schnabel, Fritz J. Sedlazeck, Kishwar Shafin, Mile Sikic, Steven J. Solar, Alexander P. Sweeten, Winston Timp, Justin Wagner, Dongahn Yoo, Ying Zhou, Erik Garrison, Evan E. Eichler, Michaeel C. Schatz, Andrew B. Stergachis, Rachel J. O'Neill, Karen H. Miga, Steven L. Salzberg, Sergey Koren, Justin M. Zook, Adam M. Phillippy

School of Medical Diagnostics & Translational Sciences Publications

Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of …

Evaluating Multi-Year Transferability Of Single- And Multi-Class Machine Learning For Remote Monitoring Of Beaver-Engineered Landscapes, Harris J. Sloan

Graduate Student Theses, Dissertations, & Professional Papers

Long-term satellite image archives enable ecological monitoring at large scales, but manual extraction of fine-grained features (e.g., beaver dams) remains time-consuming. Machine learning models may automate these tasks, but their temporal transferability for multiannual monitoring is still poorly resolved.

We evaluated the performance of two complementary neural-network frameworks across a 100,000-hectare watershed in Montana USA, using a decade of satellite imagery (2014-2024): (i) a single-class ResNet-50 beaver dam detector, and (ii) a multi-class ResU-Net landcover classifier.

In 2024, the dam detector identified 352 of 404 mapped dams, achieving balanced accuracy = 93.6%, precision = 79.8%, recall = 87.1%, F1 = …

Predicting Tilt In Esports: A Psychophysiological Approach To Understanding Player Emotional Regulation, Nathan Rhea

University of the Pacific Theses and Dissertations

Emotional regulation and stress management are important to both casual and competitive esports players. When players become dysregulated, they experience a phenomenon known as “tilt” within the gaming community, where they often lose control of their emotions and their performance declines. This study aimed to investigate whether a psychophysiological variable in heart rate variability could predict tilt in college-age esports players. Additionally, the relationship between heart rate variability and emotions predicted by the Tiltometer system with gameplay performance and winning or losing was tested.

This study used a quantitative correlational research design. Participants for this study were college-age players (N=23) …

Chromnet: A Multi-Task Learning Framework For Cross-Cell Type Prediction Of 3d Chromatin Interactions Using Epigenetic Signals, Bin Wang, Shaokai Wang, Liqing Ding, Hongdong Li, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi-C, remain costly and labor-intensive, limiting their application in large-scale and disease-related studies. To address this challenge, ChromNet is presented, a multi-task learning framework that integrates epigenetic signals across diverse cell types to enable high-precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell-type-specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by …

A Comprehensive Overview Of Neurophysiological Correlates Of Cognitive Impairment In Amyotrophic Lateral Sclerosis, Seyyed Bahram Borgheai, Brie E. Achorn, Alyssa H. Zisk, Sarah M. Hosni, Karl E. G. Richter, Frank S. Menniti, Yalda Shahriari

Computer Science Faculty Publications

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that leads to the gradual loss of motor control, typically resulting in paralysis and death within 3 to 5 years of diagnosis. ALS shares neuropathological and genetic associations with fronto-temporal dementia (FTD), a neurodegenerative condition primarily impacting cognitive functions. These two conditions are increasingly viewed as manifestations of a single molecular disease process that affects distinct brain systems, impacting motor neuronal pathways in ALS and fronto-cortical functions in FTD. However, this simple dichotomy belies the complexity of these conditions. In particular, patients with primary motor ALS can also experience significant cognitive …

Larval Crowding In Culex Pipiens Generates Cumulative Cascading Effects Under Changing Environmental Conditions, Sengul Talay, Zafer Sakaci, Michele C. Weigle, Bugrahan Regaip Kilinc, Jenah Parman, Holly Gaff, Deniz Sirin, Bulent Alten, Dennis Bente, Sirri Kar

Computer Science Faculty Publications

Density-dependent population regulation is a fundamental driver in the population dynamics of living systems, ensuring a balanced and sustainable maintenance in nature. It has been suggested that the adverse developmental and morphological effect of high larval density in container mosquitoes represents a significant limiting factor for population density, and the need to investigate this possible importance within the framework of field-based principles has been emphasized. This semi-field study, conducted under the natural thermal regime and using a natural population in Turkish Thrace, aimed to examine the effects of non-food-limiting larval density (crowding effect) in the mosquito species, Culex pipiens ( …

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

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, …

Identifying Rna Splicing Changes During Alcohol Withdrawal Using An Optimized Rna-Seq Analysis Pipeline, Yasaswi Veera, Luana Martins De Carvalho, Amy Lasek

UROP Posters

Alcohol use disorder (AUD) causes long-lasting changes in brain gene expression and RNA splicing, particularly in the ventral hippocampus. This study analyzes RNA-Seq data from rats exposed to chronic alcohol and withdrawal to identify transcript-level and splicing alterations. An optimized RNA-Seq pipeline using STAR, FeatureCounts, edgeR, and WGCNA improved efficiency by 25-40% while maintaining consistency across 25 datasets. Results reveal changes in neural signaling and stress-response pathways associated with withdrawal. This work provides both biological insight into AUD and a reproducible computational framework for transcriptomic analysis.

A Novel 3d Imaging Approach To Study Evolutionary Innovations In Solanaceae Inflorescences, Devin L. Jackson, Joonseog Kim, Wenheng Zhang Dr.

UROP Posters

Understanding the relatedness of angiosperms and the evolution of their inflorescence remains challenging, as these structures are highly modified and prone to convergent evolution. The current research describing inflorescence architecture, whether genetically or morphologically focused, typically relies on text based explanations, 2D images, or 3D based models created with CAD modeling software. This creates a disparity in the reader's understanding of these models since descriptions rely heavily on the author's interpretation of the inflorescence. The goal of our study is to bridge this disconnection by producing anatomically and color-correct 3D inflorescence models using Solanaceae flowers that readers can explore directly, …

The Myopia Epidemic: Integrating Genetic, Environmental, And Epigenetic Pathways To Define A Critical Window For Intervention, Pranavika Balaji

UROP Posters

Myopia, or nearsightedness, has increased rapidly worldwide and is now a major public health concern caused by both genetic and environmental factors. Current understanding shows that too much near work, limited time spent outdoors, and prolonged screen use contribute to abnormal eye growth in individuals who may already have a genetic predisposition. At the molecular level, epigenetic changes and shifts in DNA activity, often influenced by environmental conditions, affect the signaling pathways that regulate eye development and may help explain why myopia is increasingly common among children. This paper synthesizes recent environmental, genetic, and epigenetic research to explain how these …

Patterns Of Ovarian And Gonadotropin Hormones In Emerging Adult Oral Contraceptive Users, Summer Mcormond

UROP Posters

Oral contraceptives (OCs) are often initiated during adolescence and emerging adulthood, a period of continued maturation of the hypothalamic–pituitary–gonadal (HPG) axis. Because hormonal exposure during this window may shape emotional, biological, and reproductive outcomes, it is important to understand the specific formulations young women take and the hormonal profiles these formulations produce. This study characterizes OC formulation features and measured hormone levels in young adult OC users (n = 30).

Ethinyl estradiol (EE) doses ranged from 0.01–0.035 mg (mean = 0.022 mg), with 70% using ≤0.02 mg. Pill regimens included 21/7 packs (83%), 24/4 packs (10%), and 84/7 regimens (3%). …

Determining Genes Involved In Recovery From Chemotherapy In 4t1, Emt6, And Eo771 Breast Cancer Cells, Akash Jagdeesh, Joseph Landry Ph.D.

UROP Posters

Breast cancer is one of the most common types of cancer, and often has poor prognosis. Traditional treatments for breast cancer include chemotherapy, which involves a chemical attack on all growing cells within the body. However, these treatments are not 100% effective, and patients might experience recurrence in their cancer months or years after achieving remission. Cancer cells can evade chemotherapy through five mechanisms: senescence, quiescence, cytoprotective autophagy, and apoptosis/necroptosis suppression. Prior studies have conducted CRISPR screens and experiments involving inhibition of epigenetic regulators, to alter the regulation of genes that can contribute to breast cancer chemotherapy resistance. This study …

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 …

Shedding Light On Cellular Glycolysis Pathway Kinetics: Combining Kinetic, Mechanistic Modelling Approaches With Label Free Microspectroscopic Imaging. (Spectralomics), Nitin Patil

Doctoral

Cellular metabolism and its intricate biochemical mechanisms which allow the conversion of nutrients into energy to sustain life are well understood, leading to numerous breakthroughs in science and technology, human health and wellbeing. From an industrial perspective the pathway kinetics are significant for monitoring cellular bioprocesses, screening desired metabolite phenotypes in drug discovery processes, etc.

An initial review of glycolysis pathway kinetics highlighted the lack of sophisticated approaches to monitor the metabolic pathway kinetics as a function of time in a non-destructive, non-invasive, label-free manner. Fluxomics, a metabolomics based approach providing high-throughput insights, can be considered a gold standard approach, …

Channel-Opening Kinetics Of Complex Kainate Receptors, Noah S. Saunders

Electronic Theses & Dissertations (2024 - present)

Ionotropic glutamate receptors (iGluRs) are found both pre- and postsynaptically in neuronal membranes, and mediate the majority of fast excitatory synaptic transmission in response to the binding of glutamate, a major excitatory neurotransmitter in the central nervous system (CNS). Ionotropic glutamate receptors are divided into three distinct subtypes: kainate, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and N-methyl-D-aspartic acid (NMDA) receptors. Auxiliary proteins specific to each receptor subtype also play a role in tuning both receptor expression and gating properties, such as neuropilin and tolloid-like (NETO) proteins that modulate kainate receptors, and transmembrane AMPA receptor regulatory proteins (TARPs) that regulate AMPA receptors. Like …

Combating Antibiotic Resistance With Plasmid-Dependent Phages, Rhiannon T. Mariano

Electronic Theses & Dissertations (2024 - present)

The alarming rise of carbapenem-resistant bacteria poses an urgent global health threat, driven in large part by the horizontal spread of carbapenemase-encoding plasmids (Ma et al., 2023). These plasmids are often highly mobile and transmissible, enabling rapid dissemination of resistance genes across diverse bacterial populations. Their mobility is largely mediated by conjugation, a process dependent on the formation of pili, which serve as physical bridges for plasmid transfer between cells (Murray et al. 2022; San Millan and MacLean 2017; Virolle et al. 2020). Beyond their role in gene exchange, these pili also act as entry points for a unique class …

Fluorescent Protein Imaging Approaches Uncover Dynamic Subcellular Distribution Of Core Clock Proteins In Neurospora Crassa, Ziyan Wang

Dartmouth College Ph.D Dissertations

Circadian clocks are endogenous self-sustained timekeeping systems that allow organisms to anticipate and adapt to daily environmental cycles. Found in diverse forms of life, these molecular clocks regulate the expression of ~ 40% of the genome in animals, fungi, and plants. In animals and fungi, circadian oscillators are built on transcription-translation feedback loops (TTFLs), in which positive regulators drive the expression of negative regulators which, once synthesized and imported into the nucleus, inhibit their own activators. This precisely regulated negative feedback incorporates multiple steps of delays that are essential for generating ~24-hour rhythms. Through these mechanisms, circadian clocks temporally coordinate …

Climate And Environmental Controls On Forest Soil Organic Matter Cycling, Genevieve Goebel

Dartmouth College Ph.D Dissertations

Climate change factors act on the soil environment in complex ways, known to disturb soil organic carbon (C). Rising global temperatures and alterations to regional precipitation and nitrogen deposition regimes may contribute to the intensification of global change by accelerating the rate of biological decomposition and CO2 efflux to the atmosphere. The magnitude and endurance of the disturbance to soil organic C across landscapes and throughout time that climate change factors may pose to soil C cycling are not comprehensively understood. These knowledge gaps in our field make it challenging to anticipate how soil environments and the vast ecosystems that …