Digital Commons Network^™

Characterization Of Inflammatory Pseudotumors In A Large Animal Model Of Liver Cancer, Erik N K Cressman, Samantha Hicks, Natalie W Fowlkes, Danielle L Stolley, Maria Sophia Stenkamp

Faculty, Staff and Student Publications

Background: The development of relevant and robust large animal models of hepatocellular carcinoma is needed to test new therapeutic strategies for this disease. Transgenic approaches hold promise in addressing this complex problem. One such model, the Oncopig, has been reported to develop tumors of up to 4 cm in diameter within 7-14 days at sites of in situ vector inoculation. However, the resulting lesions reportedly contained an extensive inflammatory component that has not been evaluated in detail.

Methods: Herein, we describe our results from multiparametric characterization of the lesions generated using liver biopsy cores incubated in vector solution and replaced …

3d Reconstruction Of Spatial Transcriptomics With Spatial Pattern Enhanced Graph Convolutional Neural Network, Chen Tang, Yuansheng Zhou, Xue Xiao, Lei Dong, Lei Yu, Qiwei Li, Guanghua Xiao, Lin Xu

Faculty, Staff and Student Publications

Spatially resolved transcriptomics (SRT) is a promising new technology that enables simultaneous analysis of gene expression and spatial information for biomedical research. However, the existing statistical and deep learning algorithms used for analyzing SRT data rely solely on two-dimensional (2D) spatial coordinates, which limits their ability to accurately identify spatial domains, spatially variable genes (SVGs), cell-to-cell communications, and developmental trajectories in a three-dimensional (3D) spatial manner. To address these limitations, we introduced Spa3D, which utilized the anti-leakage Fourier transform and graph convolutional neural network model to reconstruct 3D-based spatial structures from multiple 2D SRT slices. We demonstrate that Spa3D is …

Defective Dna Damage Response Is A Targetable Therapeutic Vulnerability In Esr1 Mutant Breast Cancer, Sarah K Herzog, Jessica H Stevens, Guowei Gu, Sandra L Grimm, Kloma Cardoza, Autumn G M Hawkins, Hangqing Lin, Daniela Ramos, Amanda R Beyer, David G Edwards, Derek Dustin, Harry J Yang, Nicole Liang, Ashfia F Khan, Tasneem Bawa-Khalfe, Daniel J Mcgrail, Shiaw-Yih Lin, Cristian Coarfa, Suzanne A W Fuqua

Faculty, Staff and Student Publications

ESR1 mutations are the leading cause of endocrine therapy resistance and progression in ER-positive metastatic breast cancer. ESR1 mutations are detected in ~50% of metastatic breast cancer patients, and identification of effective targeted therapeutics are critically needed. Here, we identified enrichment of dysregulated replication stress and DNA damage responses in multiple ESR1 mutant models. Targeting the replication stress response utilizing checkpoint inhibition in combination with PARP inhibition synergistically suppressed growth, induced cell cycle arrest, and attenuated DNA replication. PARP inhibition blocked metastatic dissemination in vivo and reduced both PARP1 and ER-regulated protein expression. PARP trapping by olaparib treatment with or …

High Spatiotemporal Resolution Monitoring Of Crop Water Stress Across The Contiguous United States Using Harmonized Landsat And Sentinel-2 Data, Na Chen, Yanlei Feng, Na Wang, Jevan Yu, Mohammad Reza Alizadeh, Yifeng Cui, Ning Ye, Wenzhe Jiao, Joshua B. Fisher, César Terrer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Accurate and timely monitoring of crop water stress is essential for efficient agricultural water management, ultimately maintaining and improving crop productivity. While Landsat has been used for this purpose, its temporal resolution hampers timely detection of crop water stress. The recently released Harmonized Landsat and Sentinel-2 Version 2.0 dataset, which enables a higher-frequency time series of satellite observations (2–3 days, 30 m), offers a promising solution to this challenge. However, its potential for crop stress monitoring remained unexplored. In this study, we utilized 923 HLS satellite tiles to assess crop water stress across the contiguous United States (CONUS). Crop water …

Modality-Agnostic, Patient-Specific Digital Twins Modeling Temporally Varying Digestive Motion, Jorge Tapias Gomez, Nishant Nadkarni, Lando S Bosma, Jue Jiang, Ergys D Subashi, William P Segars, James M Balter, Mert R Sabuncu, Neelam Tyagi, Harini Veeraraghavan

Faculty, Staff and Student Publications

No abstract provided.

Correction: Sadagopan Et Al Reduced Computed Tomography Scan Speed Improves Alignment Errors For Patients Undergoing Thoracic Stereotactic Body Radiation Therapy, Ramaswamy Sadagopan, Rachael M Martin-Paulpeter, Christopher R Peeler, Xiaochun Wang, Paige Nitsch, Julianne M Pollard-Larkin

Faculty, Staff and Student Publications

In the original publication [...].

N-Palmitoyl Glutamine Is A Candidate Mediator Of Cardiorespiratory Fitness, Jeremy M Robbins, Mark Benson, Anthony R P Verkerke, Gaurav Tiwari, Shuliang Deng, Prashant Rao, Usman A Tahir, Julian Avila-Pacheco, Xu Shi, Yuntian Guan, Foje-Geh Tendoh, Jacob L Barber, Patricia E Miller, Andrew S Perry, Michael E Hall, Alexis C Wood, Kent D Taylor, Wendy S Post, Stephen S Rich, Matthew Nayor, James G Wilson, Gregory D Lewis, Ravi V Shah, Jerome I Rotter, Scott A Summers, Laura M Raffield, Shingo Kajimura, Claude Bouchard, Clary B Clish, Mark A Sarzynski, Robert E Gerszten

Children’s Nutrition Research Center Staff Publications

Background: Cardiorespiratory fitness is an integrative measure of cardiometabolic health and predictor of survival, yet little is known about its molecular underpinnings. Small molecule metabolites and lipids are increasingly recognized as exercise-stimulated signaling molecules and candidate molecular transducers of cardiorespiratory fitness.

Methods: We performed nontargeted liquid chromatography mass spectrometry-based plasma metabolomics in 654 participants (mean age, 35 years; 55% women) from the HERITAGE Family Study (Health, Risk Factors, Exercise Training, and Genetics) who had cardiorespiratory fitness (maximal oxygen uptake [VO2max]) measured by cardiopulmonary exercise testing and underwent 20 weeks of supervised endurance training. Metabolite-VO2max relationships were assessed using linear regression …

Prevalence And Characteristics Of Prescription Errors In Community Pharmacies In Mbarara City, South Western Uganda, Tadele Mekuriya Yadesa, Ashaba Comfort, Komukyeya Esther Marvel, Namakula Angela, Tikolu Hope Nancy, Narayana Goruntla, Sarad Pawar Naik Bukke, Bontu Aschale Abebe, Efrata Ashuro Shegena

AUIQ Complementary Biological System

A prescription error is a failure in the prescription writing process that results in a wrong instruction about one or more of the standard features of a prescription. Most adverse drug events are preventable through promoting rational drug use; primarily by mitigating the outstanding high burden of prescribing errors. The main aim of this study is to assess the prevalence and characteristics of prescription errors in the community pharmacies in Mbarara, Uganda. A cross-sectional study was conducted in selected community pharmacies in Mbarara City, South Western Uganda. Consecutive sampling of all prescriptions availed at the selected pharmacies was conducted until …

Conclusions Are Not Supported By The Published Statistical Analysis Comment On López-Toledo Et Al Flaxseed Improves Glucose And Lipid Metabolism In Mexican Subjects With Type 2 Diabetes: A Parallel Randomized Clinical Trial, Robert W Spitz, Deependra K Thapa, Thirupathi Reddy Mokalla, Wasiuddin Najam, Andrew W Brown, David B Allison

Children’s Nutrition Research Center Staff Publications

López-Toledo et al [...].

Celltra: Aligning Cell Names With Gene Expression Via A Pathway-Informed Transformer, Zhao Li, Zaiyi Zheng, Rongbin Li, Wenbo Chen, Yuntao Yang, Meer A Ali, Jundong Li, W Jim Zheng

Faculty, Staff and Student Publications

Motivation: Single-cell RNA sequencing (scRNA-Seq) technology enables detailed exploration of gene expression at the individual cell level, crucial for annotating cell types and understanding cellular diversity. Traditional methods for cell type annotation often rely on marker genes and manual labeling, posing challenges due to low data quality and incomplete reference datasets.

Results: We developed CeLLTra, a novel contrastive learning framework that leverages a Transformer-based model integrating biological pathway information to group genes into super tokens, effectively capturing comprehensive gene expression from scRNA-Seq data. By combining this pathway-informed Transformer with a pretrained domain-specific language model, CeLLTra accurately aligns cell-type annotations with …

Predicting The Peak Bloom Of Yoshino Cherry Blossoms In Washington, Dc With Random Forest Regression, James Watkins, Ian Forde, Rene Salinas

Spora: A Journal of Biomathematics

Springtime ushers in a bouquet of flowering arrangements that create ripe economic and social opportunities. Since the Japanese ambassador's gift of 3020 Yoshino cherry trees to the National Mall in Washington, DC, the National Cherry Blossom Festival has occurred annually beginning in 1935. This festival is unique in that over one million visitors parade the Capitol area each year, drawing inspiration from the peak blooming date of the characteristic cherry trees. The NPS provided data on the several stages of Yoshino cherry trees leading to peak bloom from 2004–2024, while local climate data exists for temperature, rainfall, and other factors …

Decoding Early Covid-19 Responses Using Mathematical Modeling Of Social Distancing Strategies Across Multiple Countries, Sri Gunturu, Suki Lewis, Katelyn Nguyen, Asma Azizi

Spora: A Journal of Biomathematics

During the early phase of the COVID-19 pandemic, before vaccines were available, countries implemented diverse combinations of social-distancing (SD) measures shaped by cultural norms and public acceptance. These differences produced varied outcomes in controlling viral spread, offering lessons for future health-crisis preparedness. We performed a reverse-engineering analysis of early COVID-19 case data from five socioculturally distinct countries—India, Vietnam, Italy, Finland, and the United States—selected to capture a range of initial prevalence levels. Using mathematical modeling and data fitting, we inferred the relative contributions of three SD interventions: face masking, quarantine, and isolation of infected individuals. We then employed an efficiency …

Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye

Faculty Publications

A series of potassium rare earth double vanadates is presented. Single crystals of double vanadates with stoichiometry K₃Ln(VO₄)₂ (Ln = La, Pr, Nd, and Sm) and crystallizing in the glaserite structure type were synthesized via a molten alkali chloride/fluoride flux reaction. Different structures were observed depending on the constituent rare earth: K₃La(VO₄)₂ crystallizes in an as-of-yet unreported modification of the typical glaserite structure in the space group P2₁/c, likely due to its larger ionic size that results in an increase in the lanthanide coordination number …

Circadian-Shaped Immune Variability Predicts Infection Outcome, Jonathan Lalsiamthara, Mariko Locke, Alejandro Aballay

Faculty, Staff and Student Publications

Disease risk and severity are influenced by genetics, epigenetics, and environmental factors. However, immune responses vary even among genetically similar or related individuals, shaped by inherited and noninherited factors. Using Caenorhabditis elegans, we found that pathogen susceptibility can be predicted by preinfection biomarkers. Individuals with high-basal expression of irg-5, an infection response gene regulated by the p38 mitogen-activated protein kinase-1 (PMK-1) pathway, were more susceptible to Pseudomonas aeruginosa infection. A genome-wide screen identified the myeloid ecotropic viral integration site-1 (MEIS) homeobox protein UNC-62 as a regulator of irg-5 expression, acting through PMK-1 and GATA binding erythroid-like transcription factor …

Peptide Sequencing Via Protein Language Models, Thuong Le Hoai Pham

Computer Science and Engineering Theses - Archive

Protein sequencing is fundamental to understanding biological processes, disease mechanisms, and therapeutic developments. Current protein sequencing techniques, primarily relying on mass spectrometry and Edman degradation, face significant limitations in accurately identifying all amino acids within a protein, hindering comprehensive proteome analysis. Recent advances in click chemistry and bioorthogonal chemistry have enabled the identification of specific amino acids and their positions within a peptide; however, these techniques are still limited by the number of amino acids that can be identified with high accuracy and specificity, resulting in partially known sequences. This thesis presents a novel computational approach that leverages protein language …

Elli’S Liquid Flow In A Wavy Channel With Slip Effect, Wall Properties, And Heat Transfer, P. Devaki, Yatin Sood

Mansoura Engineering Journal

The dual behavior of Elli’s fluid motivated us to work on it. The fluid behaves as both Newtonian/ non-Newtonian based on the low and high shear rates, respectively. The paper focused on the flow of Ellis fluid in a peristaltic channel with wall properties and heat transfer. The channel is symmetric in nature, and slip conditions are considered near the elastic walls. The governing equations of the flow are solved analytically using suitable boundary conditions, which yield velocity and temperature functions. The novelty of the paper is to analyze the nature of Newtonian/non-Newtonian fluids under the same conditions so that …

Genetic Determinants Associated With Persistence Of Listeria Species And Background Microflora From A Dairy Processing Environment, Vaishali Poswal, Sanjeev Anand, Jose L. Gonzalez-Hernandez, Brian Kraus

Dairy Science and Food Science Faculty Publications: 2022 to Present

Listeria monocytogenes is a persistent foodborne pathogen capable of surviving in food processing environments, often in association with diverse environmental microflora. This study examines genomic determinants of persistence, specifically stress adaptation and biofilm-associated traits, in environmental Listeria species and other environmental microflora from a dairy processing facility by analyzing whole-genome sequences of 6 environmental Listeria isolates, 4 ATCC reference strains, and 22 air and floor swab cultures, annotated using the RAST platform. Subsystem analysis revealed that Listeria isolates carried a defined set of genes linked to biofilm formation, antimicrobial resistance, and stress response, though in lower abundance than environmental cultures. …

Are There Ecological Consequences Of Urban Adaptation? A Test Of Eco-Evolutionary Dynamics In A Terrestrial Isopod (Oniscus Asellus), Aaron Yilmaz, Grace Bellino, Ryan A. Martin

Faculty Scholarship

Urbanization affects many aspects of the environment with the potential to alter both ecological and evolutionary processes. However, while examples of urban evolution are accumulating, tests of urban eco-evolutionary dynamics are rare. We carried out a reciprocal transplantation experiment using the terrestrial isopod Oniscus asellus to test how adaptation to the urban heat island influenced ecological processes. As isopods are important decomposers, we asked if leaf-litter decomposition differed among reciprocal transplant treatments and used a separate laboratory experiment to isolate the effects of temperature on rates of isopod leaf consumption. We found that leaf-litter decomposition was greater in urban habitats, …

Optimizing Poultry Production And Enhancing Egg Nutrient Composition Through Kelp Supplementation In Laying Hens, Meghan Clifford

Open Access Dissertations

The development of sustainable feed supplements is a crucial component in addressing the current global need for resilient and environmentally responsible food systems. This dissertation has explored the potential of brown algae (Saccharina latissima) as a sustainable feed supplement for poultry with the potential to benefit production efficiency, product quality, and the global food supply. With both controlled feeding trials and a producer-based survey, the work in this dissertation investigates the nutritional, biological and practical implications of adopting kelp into poultry diets.

Chapter one provides a comprehensive overview of the current literature surrounding the use of marine sources …

Investigating The Effects Of Nucleopore Defects On The Cellular Response To Stress In Als/Ftd Ipsc-Derived Neurons, Alicia Christine Collins

Open Access Dissertations

Amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) is a progressive neurodegenerative disease spectrum characterized by motor dysfunction, cognitive decline, and death within a few years of clinical onset. Hallmark features of ALS/FTD include defects in nucleocytoplasmic transport (NCT) and abnormal cytoplasmic mislocalization and aggregation of the RNA-binding protein TDP-43, both of which have been shown to be exasperated by oxidative stress (OS). It remains unclear how these processes are connected and how they collectively contribute to neurodegeneration. To fill this gap of knowledge, we used human embryonic kidney cells, neuroblastoma cells, and induced pluripotent stem cell-derived cortical neurons harboring the ALS/FTD C9ORF72 …

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 …

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 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 …

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 …

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 …

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, …

Uncovering The Mechanism Of Reep2-Mediated Emt-Driven Membrane Trafficking In Lung Adenocarcinoma, Kevin Fulp

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking is frequently disrupted during cancer progression, and the underlying mechanisms remain largely unknown. Currently, no effective drugs target dysregulated membrane trafficking for cancer treatment. Recent evidence has demonstrated that epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma (LUAD) employs a membrane trafficking program to coordinate cancer cell invasion and immunosuppression. To further dissect the pro-tumorigenic membrane trafficking program, we initiated an in vivo CRISPRi screen to assess more than 2,000 membrane trafficking-related genes in a syngeneic mouse LUAD model. We identified REEP2, an endoplasmic reticulum (ER) shaping protein, as a novel regulator of EMT-driven membrane trafficking. High REEP2 expression is …