Digital Commons Network^™

A Live Cell Biosensor Protocol For High-Resolution Screening Of Therapy-Resistant Cancer Cells, Viral D. Oza, Colin S. Williams, Jessica S. Blackburn

Molecular and Cellular Biochemistry Faculty Publications

The Genetically Encoded Death Indicator (GEDI) is a ratiometric, dual-fluorescence biosensor that enables real-time detection of cell death through calcium influx. Originally developed for use in neurodegeneration models, GEDI can be applied to cancer cells to quantify therapy-induced death at single-cell resolution. This protocol details how to generate GEDI-expressing cancer cell lines, empirically determine stress-induced GEDI thresholds using radiation or chemotherapeutic agents, and perform time-resolved imaging and image analysis to track cell fate. This workflow is optimized for high-throughput drug and radiation screening in heterogeneous populations and is especially useful for identifying chemo- and radio-resistant subclones. Key limitations include the …

Behavior Of A Komodo Dragon In Relation To Whole-Prey Feeding, Gurkiran Kaur Natt

Williams Honors College, Honors Research Projects

In zoological settings, whole-prey feeding is an enrichment strategy widely used to prompt naturalistic behaviors; yet, the specific behavioral shifts this causes in reptiles are not well-documented. This study focused on the activity budgets and spatial use of a six-year-old male Komodo dragon (Varanus komodoensis) housed at the Akron Zoo, analyzing his movements in direct response to whole-prey feeding sessions. Over an eight-week observation period, instantaneous scan sampling was utilized to quantify behaviors before and after two distinct whole-prey feeding sessions. Although active behaviors and "not visible" instances increased marginally post-feeding, paired t-tests confirmed these shifts were not statistically significant …

Social Influences On Exercise And Physical Activity, Domanick Speelman

Williams Honors College, Honors Research Projects

Background: Regular exercise plays a big role in maintaining an individual’s physical and mental health, preventing diseases, and improving overall well-being. A plethora of things can influence an individual’s exercise habits, for better or worse, including social, environmental, and familial contexts. This study described exercise and social influences among undergraduate college students. More specifically, this study described exercising habits (frequency, duration, type, etc.) as well as the role of social media, environmental conditions, and family support during a typical week of the academic semester.

Design: Cross-sectional, descriptive survey

Methods: A sample of 33 undergraduate students from a public university in …

Biol 225 - Laboratory Manual For Human Physiology, Corey Sullivan, Kristin Thurlby, Gwen Wright

Human Physiology

This laboratory manual for Human Physiology represents the Creative Commons licensed (CC-BY-NC 4.0) material created as an Open Educational Resource.

Deep Learning-Based Quantification Of Tall Fescue Abundance In Pastures, Rose E. Binkley, Samuel R. Revolinski, Echo Elizabeth Gotsick, Ray Smith, Zeya Wang, Katsutoshi Mizuta

Plant and Soil Sciences Faculty Publications

Accurate and rapid measurement of tall fescue abundance is essential for efficient forage management and mitigating livestock exposure to potential endophyte-related toxicity. Traditional visual estimation methods are labor-intensive and are subject to change depending on the observer doing the calculations, which limits their scalability and consistency. This study explores the application of deep learning techniques to automate and improve the classification of tall fescue abundance across pasture systems in Kentucky. Ground-truth abundance classes were evaluated using one of the traditional methods with occupancy grid and compared against estimates derived from red-green-blue images. Two convolutional neural network architectures, YouOnlyLookOnce (YOLO) and …

Consumer Perceptions Of Farmers Market Performance: A Comparative Analysis Across States And Age Groups, Azita Varziri, Timothy A. Woods, Shuoli Zhao

Agricultural Economics Faculty Publications

The USDA Agricultural Marketing Service has invested in direct-to-consumer initiatives to expand local food consumption and enhance farmers market opportunities. To evaluate the effectiveness of these efforts, this study employs a sample-selected ordered probit model to analyze consumer perceptions of farmers market performance across four states in the Southeast United States. Specifically, we examine differences in awareness and performance of product quality, diversity, and market infrastructure. Awareness and perceptions vary significantly by age, other demographics, and state. These insights provide market organizers and policymakers with data-driven strategies to tailor marketing efforts and improve engagement across diverse consumer segments.

Do Food Safety Certifications Improve The Safety Of Our Food System? Evidence From The U.S. Meat, Poultry, And Egg Industry, Lijiao Hu, Yuqing Zheng

Agricultural Economics Faculty Publications

Private food safety certifications have become increasingly popular in the global agri-food supply chain over the last three decades. We examine a fundamental yet unaddressed question of whether food safety certifications make our food system safer. Focusing on the U.S. processing industry for meat, poultry, and eggs, the most likely contaminated foods, we matched unique establishment-level food safety certification data collected over the period of 2015–2018 with the microbial testing data from the government for processing establishments. By applying a penalized maximum likelihood method to address the rare event problem in the data, we found that the certification to the …

Where Mussels Hang Out: A Multiscale Analysis Of Zebra Mussel (Dreissena Polymorpha) Spread In South Dakota, Justin Verner Sorensen

Dissertations and Theses

The spread of the invasive zebra mussel (Dreissena polymrpha) poses significant ecological and economic threats to freshwater systems across North America. Understanding population dynamics and how this aquatic invasive species spreads is essential for making natural resource management decisions. South Dakota represents an active frontline of the zebra mussel invasion, highlighting the importance of understanding the spread in this region. Statewide habitat suitability modeling of available aquatic habitat was performed using MaxEnt, a robust machine learning algorithm. Individual waterbody suitability means were also extracted to rank waterbodies within highly suitable regions. This work revealed that South Dakota possesses widespread suitable …

Investigation Of Factors Influencing Electric Vehicle Adoption In Indonesia: Ev Owners’ Perspectives, Desrina Yusi Irawatia, Nur Aini Masruroh, Nur Mayke Eka Normasari

ASEAN Journal on Science and Technology for Development

Electric vehicle (EV) uptake in Indonesia remains markedly below policy benchmarks. This study applies the Unified Theory of Acceptance and Use of Technology version 3 (UTAUT3), an extension of UTAUT2 that incorporates personal innovativeness as an additional construct to examine its impact on both behavioral intention and actual EV adoption within the Indonesian context. Unlike studies that typically survey the general public, this study focuses on actual EV users and owners, providing more representative and responsive insights into real-world EV usage. A total of 208 respondents participated, with 135 from the Jabodetabek area and 73 from Surabaya. The UTAUT3 framework …

A Deep Neural Approach To Network-Based Obfuscated Malware, Meera Parmar, Sunil Gautam

ASEAN Journal on Science and Technology for Development

The rising prevalence of obfuscated malware poses a critical threat to network security, undermining traditional detection methods and jeopardizing data integrity and system reliability in an increasingly connected world. This growing danger highlights the urgent need for advanced solutions to protect against evolving cyber risks. This research intro-duces a novel framework to enhance malware detection, employing a hybrid architecture that integrates spatial and temporal analysis with attention mechanisms. The approach leverages a large dataset subsample, focusing on key feature selection and augmentation to improve robustness against evasion techniques. This innovative framework offers a significant advancement in identifying malicious network traffic, …

Evaluation Of Peptides And Peptide–Doxorubicin Conjugates Designed And Synthesized For Targeting Triple-Negative Breast Cancer Via Cell-Surface Receptors, Shih-Jing (Jane) Yao

Pharmaceutical Sciences (PhD) Dissertations

A significant problem faced in oncology is the lack of chemotherapeutic agents that are tumor site-specific, resulting in reduced therapeutic efficacy and unintended infliction of harm to surrounding healthy tissues and cells that often lead to serious side effects. Current strategies being explored to circumvent this issue aim to refine delivery of  chemotherapeutic agents specifically to tumor sites, which may be achieved via conjugation of these agents to biomarker-specific ligands. This forms the foundation of ligand-targeted drug delivery. Among different breast cancers, treatment of the triple-negative breast cancer (TNBC) subtype has been particularly challenging, largely due to the absence of …

Anticancer Efficacy Of Methyl-Cantharidimide (Mca) In Liver Cancer, Yidong Li

Theses and Dissertations

Cancer is still one of the major public health challenges worldwide to the present day. Multi-drug resistance (MDR) that occurs in cancer chemotherapies is a non-negligible cause of cancer treatment failure and tumor recurrence. Overexpression of ATP-binding cassette (ABC) transporters is one of the most frequent mechanisms of MDR occurrence. Therefore, the establishment of a chemotherapy agent whose anticancer efficacy would not be affected by the overexpression of ABC transporters is in demand. Methyl-cantharidimide (MCA), a cantharidin (CTD) analog, has been approved in China for clinical liver cancer treatment. This study revealed that MCA was efficacious in the ABCB1-, ABCG2-mediated …

Evaluation Of Pulmonary Toxicity To Inhaled Erbium Oxide Nanoparticles In Golden Syrian Hamsters, Randy Liang

Theses and Dissertations

Erbium oxide nanoparticles (Er2O3 NPs) are used in various products from simple pottery to semiconductors and such usage leads to an elevated risk of accidental occupational exposure. In the present study, the pulmonary toxicity of Er2O3 NPs was assessed by examining tissues and bronchoalveolar lavage fluid (BALF) from the lungs of Golden Syrian Hamsters following inhalation exposure. The study’s goal was to determine the severity and mechanism of toxicity upon exposure to inhaled Er2O3 NPs. Animals were divided into 4 groups all being exposed for 4 hours a day for 8 days: Group-1: room air, Group-2: vehicle control (water), Group-3: …

Evaluation Of The Mechanism Of Cell Death After Exposure To Amorphous Silicon Dioxide Nanoparticles In Rat Pleural Mesothelial Cells And Golden Syrian Hamsters, Rachel P. Renda

Theses and Dissertations

Amorphous Silicon Dioxide Nanoparticles (SiO2 NPs) are widely used in the industrial processes, chemical, and cosmetics industries. Amorphous SiO2 NPs are abundant in the earth’s crust and can be released into the air through industrial and manufacturing activities. Such particles are overlooked and not as commonly studied when compared to their crystalline counterpart. Amorphous SiO2 NPs are pulmonary toxicants; however, the mechanism of toxicity is uncertain. In the current study, toxicity was assessed using both in vitro and in vivo systems to understand a possible mechanism of cell death. Rat Pleural Mesothelial Cells (RPMCs) were exposed to 50-800 μg/ml SiO2 …

Utilizing A Genetically Diverse Species To Investigate Gene-Drug Interactions And Drug Efficacy, Jerry Nawongbay Gbarlea

Theses and Dissertations

Gene-drug interactions are fundamental to understanding variability in drug response and therapeutic efficacy. In this project, we leverage the natural genetic divergence between ecotype morphs of the blind Mexican cavefish (Astyanax mexicanus) to investigate differential responses to neuroactive compounds—specifically, the convulsant pentylenetetrazol (PTZ) and the anxiolytic Buspirone Hydrochloride. Astyanax Mexicanus is a tetra species consisting of both surface-dwelling (ancestral) and cave-dwelling (mutant) populations that have highly variable genetic backgrounds. Independently evolved populations of cavefish exhibit a suite of convergent traits that can be functionally interrogated to discover new genetic functions and interactions. These attributes make A. mexicanus an ideal model …

The Yeast Checkpoint Kinase Mec1p Functions In Transcription Termination By Facilitating Recruitment Of Pcf11p And Regulating The Torpedo Exonuclease Rat1p, Riddhi Patel

Theses and Dissertations

My dissertation includes two projects, centered on transcription regulation by checkpoint kinases of the DNA damage response (DDR). The first project focused on the role of checkpoint kinase Mec1p in transcription termination and regulation of the torpedo exonuclease Rat1p. Termination, closely linked with pre-mRNA 3’ processing, dissociates RNA polymerase II (RNAPII) from DNA and releases the nascent RNA transcript. Efficient termination is required for maintaining a pool of RNAPII that is available for re-entry into new transcription cycle. Previous results showed that inactivation of Mec1p in the absence of exogenous genotoxic stress downregulates the efficiency of transcription termination. This study …

Evaluating Cow/Calf And Stocker Performance When Grazing Sudangrass With And Without Sunnhemp, Shelby L. Davis-Jenkins, Daren D. Redfearn, Mary E. Drewnoski

Nebraska Beef Cattle Reports

Summary with Implications

Sudangrass can provide high-quality summer forage, supporting cow/calf pairs and growing cattle. In this study, sudangrass or a sudangrass–sunnhemp mix was grazed over two years by cow/calf pairs and heavy stockers (~880 lb). There was no difference in carrying capacity between forage types. Sunnhemp inclusion had no effect on cow body condition or nursing calf gain. Cows maintained condition through peak lactation, and nursing calves gained 2.27 lb/day. Stockers gained 1.56 lb/day on sudangrass alone and 1.73 lb/day on the mix. However, the added seed cost of sunnhemp increased the cost of gain in year 1 and …

Investigating The Presence Of Amyloid In The C. Elegans Germline And Embryos, Sereen M. El Jamal

Biochemistry and Molecular Biology

Amyloids, insoluble protein aggregates of cross ß-sheet structure, are commonly associated with amyloidosis diseases. However, more recent studies support that some amyloids serve essential functions evolutionarily conserved across several taxa, particularly in reproduction. The nematode Caenorhabditis elegans serves as an excellent model organism in reproductive research. Prior to this study, no research has investigated the presence of functional amyloid in the C. elegans reproductive system. We hypothesize that similar to the presence of functional amyloid in the eggshells and epididymides of other organisms, functional amyloid will also be present in the germline and embryos of C. elegans. Using immunostaining, …

When Words Flow Like Water: How The Enbridge Line 3 Pipeline Environmental Impact Statement Failed To Prevent Hydrogeologic Harm In Minnesota, Carly Gutzmann

Journal of Earth and Life Science

For the aquifers of Minnesota, the environmental impact statement (EIS) was a promise of protection that never left the page. An environmental impact statement is meant to be an aid in the decision making process in order to ensure that projects consider potential environmental harms that may occur. However, they are often used instead as another regulatory box to check, rather than as active considerations when planning. As such, a project plan can be flawed from the start—if project developers only consider environmental impacts after they have already put considerable time, effort, and funding into their project as-is, they may …

Largemouth Bass Diet Changes Through The Summer In Central Minnesota, Ethan Kunz

Journal of Earth and Life Science

Largemouth Bass Micropterus nigricans is one of the most widespread fish species in the world, due in part to human introduction for angling. Largemouth Bass are opportunistic predators that will consume the largest prey they can often find; however, it has been shown that their diet mainly consists of invertebrates such as crayfish, with less focus on other fish species. This research aimed to determine what the Largemouth Bass diets in Central Minnesota consist of, and how they may change from the beginning of summer through the beginning of fall. A total of 174 Largemouth Bass were sampled from late …

Relationship Between Ratio Of Hybrid Sunfish To Their Parent Species And Latitude, Maxwell Kattner

Journal of Earth and Life Science

Hybrid sunfish of the Lepomis genus make up a generally small but notable portion of the population of sunfish in Minnesota lakes. Hybrid sunfish play a significant role in freshwater ecosystems across the United States. They are both morphologically and behaviorally distinct in some ways and similar in other ways to their parent species, causing them to both fill and compete with their parent species for niches occupied by multiple Lepomis species. Despite this, the ratio of hybrid sunfish to their parent species has never been properly explored. This study observed if the ratio of hybrid sunfish to their parent …

Captive Model Test For Hydrodynamic Derivatives Of Ship Maneuvering In Regular Head Waves, Pin-Yuan Huang, Zih-Yao Lin, Tsung-Yueh Lin, Fu-En Lee, Yan-Wei Lai

Journal of Marine Science and Technology–Taiwan

The motion of ship in wave can be discussed in seakeeping and maneuvering. In model tests, the former is found by the motion response of waves while the latter requires captive model test to acquire hydrodynamic derivatives. The hydrodynamic derivatives in waves are discovered to be different from those in calm water. To understand better the behavior of maneuverability in waves, maneuvering tests in a wide range of waves are performed in this study. This study presents an experimental investigation into the maneuvering behavior of a container ship in regular waves, covering a wide range of wavelengths from half to …

Cell Surface Expansion And Tension Regulation: How Cellular Forces Shape Embryonic Development, Samantha A. Pressman, Sophia M. Micale, Bing He

Wetterhahn Science Symposium Posters

Congenital birth deformities often arise during epithelial morphogenesis, displaying the need to understand the mechanisms underlying this process. Cell shape changes that mediate morphogenesis often require cell surface expansion to accommodate shifts in 3D tissue geometry. Our lab has identified Four Wheel Drive (Fwd), a Golgi-localized phosphatidylinositol 4-kinase (PI4K) IIIβ ortholog, as a regulator for cell surface expansion during Drosophila ventral furrow formation, a well-characterized model for epithelial folding. We hypothesize that Fwd and Rab11, a regulator of exocytosis and endocytic recycling, coordinate the trans-Golgi network and recycling endosomes to promote vesicle trafficking. Using live imaging of fluorescently tagged Fwd …

Meta-Analysis Of Probiotic Yeast Factors And Methodologies, Mones J. Hajizadeh

Biology Theses

In recent years, there has been an expanding interest in ameliorating the gut microbiome through the use of yeast probiotics, in contrast to the general focus on bacterial probiotics. The goal of this paper is to determine trends and variations in the probiotic evaluation of the yeast species Kluyveromyces marxianus, Pichia kudriavzevii, and Saccharomyces cerevisiae var. boulardii across 48 studies, and determine probiotic gene homology amongst the three yeasts. Much of the literature on novel yeast strains employs various approaches to assess probiotic efficacy. In this study, the evolutionary divergence of these three species of interest was also evaluated. Furthermore, …

Mitochondria In Local Control Of Programmed Cell Killing & Resilience, Rashna Sharmin

Biology Dissertations - Archive

Specialized cells are commonplace and defined by different compartments. Organelle transport across cell compartments is critical for cell function, as in morphologically complex neurons. Specialized cells can undergo programmed elimination, an essential facet of normal development. My central thesis question asks how intracellular transport of mitochondria, the cell’s energy producers, regulate fated elimination of complex cells. I explored this using the specialized tail-spike cell (TSC) of the roundworm C. elegans. The TSC dies embryonically through the novel ‘tripartite’ developmental killing program, Compartmentalized Cell Elimination (CCE).  In my study, I defined and characterized events at the CCE initiation compartment of the …

Protecting Wetlands In The State Of Texas: Assessing Gaps In Regulations, Knowledge, And Professional Roles And Responsibilities, Grace A. Moy

Landscape Architecture Masters & Design Theses

Wetlands rank among earth's most productive ecosystems, providing crucial ecological services such as hydrological regulation, water purification, and habitat support (US EPA, 2015). In Texas, however, rapid urbanization, inconsistent policy enforcement, and the absence of statewide protection frameworks of hastened wetland degradation (Brody & Kang, 2011). Without a robust state regulatory framework (Environmental Law Institute [ELI], 2020), these ecosystems face increasing threats from development and hydrological disturbances.

This thesis aims to identify regulatory and knowledge deficiencies that influence Texas’ current wetland protection status and to offer targeted professional recommendations for landscape architecture professionals to address these shortcomings in future public …

Timber Use And Forest Management In The Ancient Mediterranean, Tobey Russell

Undergraduate Papers

No abstract provided.

The Ecological Consequences Of Horizontal Transmission Of Symbionts, Bibek Singh Parajuli

Biology Dissertations

Most multicellular organisms depend on their microbial symbionts for various functions, such as digestion, nutrient supplementation, pesticide degradation, and defense. While many insects acquire their symbionts vertically from their parents, thousands of species of true bugs (Hemiptera) across different families acquire their microbial symbiont, Caballeronia, from the environment each generation. Acquiring symbionts from the environment (horizontal transmission) has various ecological consequences for the host. In this study, I used the bug-Caballeronia model 1) to understand whether the free-living symbionts benefit from association with multicellular hosts, 2) to evaluate whether host specialization on symbiont strains varies across taxonomic levels, …

Effects Of Fermented Soybean Products On The Human Gut Microbiome, Microbial Metabolism, And Host Physiology, Shannon Moncier

Biology Dissertations

Fermented soybean products (FSPs) contain soybean-derived substrates, fermentation-associated microorganisms, and bioactive compounds that may interact with the human gut microbiome and host physiology. However, despite the growing interest in FSPs, longitudinal human studies specifically evaluating traditional Korean-FSPs (K-FSPs), particularly among United States-based populations, remain limited. The objective of this work was to evaluate the effects of three K-FSPs, including Cheonggukjang, Gochujang, and Doenjang, on host physiological responses, gut microbial community structure, predicted microbial functional potential, and fecal butyrate responses in healthy adults. Three independent dietary intervention cohorts were conducted using FSP formulations produced either by traditional artisan methods (Product A) …

Identifying Relevant Covariates In Rna-Seq Analysis By Pseudo-Variable Augmentation, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

RNA-sequencing (RNA-seq) technology allows for the identification of differentially expressed genes, which are genes whose mean transcript abundance levels vary across conditions. In practice, RNA-seq datasets often include covariates that are of primary interest in addition to a set of covariates that are subject to selection. Some of these covariates may be relevant to gene expression levels, while others may be irrelevant. Ignoring relevant covariates or attempting to adjust for the effect of irrelevant covariates can compromise the identification of differentially expressed genes. To address this issue, we propose a variable selection method that uses pseudo-variables to control the expected …