Digital Commons Network^™

Characterization Of Long-Noncoding Rnas In Prostate And Pancreatic Cancer Through Single Cell Transcriptomics, Debanjan Saha

Arts & Sciences Graduate Student Theses and Dissertations

Metastatic castration resistant prostate cancer (mCRPC) is a subtype of prostate cancer that develops after metastasis and resistance to hormone therapy, thereby carrying a poor prognosis. Likewise, pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies due to its propensity to present at advanced, unresectable stages in patients. Recent genomic studies have identified molecular features of mCRPC and PDAC, such as the existence of mutations in key driver genes, the extensive transcriptomic intra-tumoral heterogeneity, the role of regulatory elements in dictating driver gene expression, mechanisms of treatment resistance, and the interactions with the immunosuppressive and stromal tumor- microenvironment …

A Cluster Randomized Trial Of Xylitol Chewing Gum For Prevention Of Preterm Birth: The Ppax Trial, Gregory C Valentine, Kathleen M Antony, Haleh Sangi-Haghpeykar, Alexis C Wood, Rose Chirwa, Saukani Petro, Mary Dumba, Deborah Nanthuru, Cynthia Shope, Jesse Mlotha-Namarika, Jeffrey Wilkinson, Joshua Aagaard, Ellen J Aagaard, Maxim D Seferovic, Judy Levison, Peter Kazembe, Kjersti M Aagaard

Children’s Nutrition Research Center Staff Publications

Background: Maternal periodontal disease is associated with preterm and low-birthweight deliveries, but randomized trials of likely efficacious treatments (e.g., dental scaling and root planing) during pregnancy have not reduced these adverse outcomes. As an alternative, we hypothesized that periconception initiation of xylitol chewing gum would reduce the occurrence of preterm or low-birthweight deliveries among a historical high-prevalence population in Malawi.

Methods: We conducted an open-label, parallel-enrollment, matched-pair, cluster-randomized, controlled clinical trial across eight health centers (sites) in and around Lilongwe, Malawi. Sites were paired by anticipated delivery volume and randomized to prenatal and oral health education alone (active control) or …

Modified Interferon-Gamma (Ifn-G) Receptors (Ifngr) To Enhance Cell-Based Immunotherapy, Eric Tran, Myungkyu Jang

Technology Transfer - Patents

No abstract provided.

The Role Of Selfing In The Breeding Of Lolium Italicum, P Rotili, C Scotti, M Romani

IGC Proceedings (1977-2023)

In the irrigated plains of Lombardy (Italy) permanent meadows are continuously eliminated and replaced with maize. This imposes the collection and conservation of Lolium italicum and other species typical of these meadows (dactylis, bromus spp. etc.). Many expeditions were made by the Forage Crops Institute of Lodi, together with English colleagues as well as colleagues from Belgium, Holland, Japan and France. At pre­sent, Lolium italicum is extensively used as catch crop, sown in autumn and harvested in spring, before sowing maize. But we consider this plant useful for artificial meadows, able to give a full production for two years …

Greenhouse Gas Emissions From Flood-Irrigated Rice As Affected By Phosphorus Fertilizer Source, Chandler M. Arel, Kristofor R. Brye, Diego Della Lunga, Trenton L. Roberts, Richard Adams

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Research into alternative phosphorus (P) fertilizer sources that may be able to supplement P resources is necessary. Struvite (MgNH4PO4 · 6H2O) can be made by removing excess nutrients from waste sources and may reduce greenhouse gas (GHG) emissions from cropping systems. This study sought to quantify GHG [i.e., methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2)] fluxes, season-long emissions, and net GHG emissions from chemically precipitated struvite (CPST) and synthetic and real-wastewater-derived electrochemically precipitated struvite (ECST) compared to monoammonium phosphate (MAP) and an unamended control (UC) from flood-irrigated rice (Oryza sativa) grown in P-deficient, silt loam soil in a …

Geographic Divergence Of Methicillin-Resistant Staphylococcus Aureus St5-Scc Mec I In The Aftermath Of A Major Earthquake And Tsunami: Impact Of A Plasmid Harboring Heavy Metal Resistance Genes, Jose R W Martínez, Manuel Alcalde-Rico, Estefanía Jara-Videla, Jinnethe Reyes, Lina P Carvajal, Sandra Rincon, Rafael Ríos, Lorena Diaz, Ana Quesille-Villalobos, Roberto Riquelme-Neira, Lina Rivas, Ahmed M Moustafa, Blake Hanson, Eduardo A Undurraga, Jorge Olivares-Pacheco, Patricia García, Rafael Araos, Paul J Planet, César A Arias, Jose M Munita

Faculty, Staff and Student Publications

Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health menace. The global spread of MRSA is characterized by successive waves of epidemic clones dominating specific geographical regions. The acquisition of genes encoding resistance to heavy metals (HMRGs) is thought to be a key feature in the geographic divergence of MRSA. However, the cause-effect relationship between the presence of HMRGs and the divergence of MRSA clones remains to be clarified. In this study, we assessed the role that HMRGs may have played in the evolutionary divergence of the MRSA ST5-SCCmecI lineage in Latin America. We conducted a genomic characterization …

Pilrα Sustains Microglial Capacity To Process Myelin In A Mouse Model Of Demyelination, Kent Lin

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer's disease (AD) is characterized by amyloid-β (Aβ) plaques, neurofibrillary tangles, and neurodegeneration. Microglia, the resident immune cells of the central nervous system (CNS), play a crucial role in AD pathogenesis by containing the spreading of Aβ plaques. Genetic studies have associated a variant of the receptor Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRα) with reduced risk for AD. PILRα is a receptor found on myeloid cells, such as microglia, that binds to endogenous cell surface glycoproteins and sends inhibitory signals within the cell. Additionally, it serves as an entry receptor for Herpes Simplex Virus 1. To elucidate the role …

A Reliable And Efficient Detection Pipeline For Rodent Ultrasonic Vocalizations, Sabah Shahnoor Anis, Devin Mark Kellis, Kris Ford Kaigler, Marlene A. Wilson, Christian O'Reilly

Faculty Publications

Analyzing ultrasonic vocalizations (USVs) is crucial for understanding rodents' affective states and social behaviors, but the manual analysis is time-consuming and prone to errors. Automated USV detection systems have been developed to address these challenges. Yet, these systems often rely on machine learning and fail to generalize effectively to new datasets. To tackle these shortcomings, we introduce ContourUSV, an efficient automated system for detecting USVs from audio recordings. Our pipeline includes spectrogram generation, cleaning, pre-processing, contour detection, post-processing, and evaluation against manual annotations. To ensure robustness and reliability, we compared ContourUSV with three state-of-the-art systems using an existing open-access USV …

Deep Jansen-Rit Parameter Inference For Model-Driven Analysis Of Brain Activity, Deepa Tilwani, Christian O'Reilly

Faculty Publications

Accurately modeling effective connectivity (EC) is critical for understanding how the brain processes and integrates sensory information. Yet, it remains a formidable challenge due to complex neural dynamics and noisy measurements such as those obtained from the electroencephalogram (EEG). Model-driven EC infers local (within a brain region) and global (between brain regions) EC parameters by fitting a generative model of neural activity onto experimental data. This approach offers a promising route for various applications, including investigating neurodevel- opmental disorders. However, current approaches fail to scale to whole-brain analyses and are highly noise-sensitive. In this work, we employ three deep-learning architectures—a …

Examining Physiological Responses To Misophonic Triggers, Christian O'Reilly, Xuan Yang, Sewon Oh, Doug Wedell, Svetlana Shinkareva

Faculty Publications

We collected and analyzed an array of biosignals (face electromyogram, skin electrodermal activity, peripheral temperature, and electrocardiogram) in 60 participants with and without misophonia, a condition characterized by decreased tolerance to innocuous sounds. Our goal was to objectively characterize the physiological response to misophonia triggering sounds. We found that misophonic responses can be objectively identified in some cases through atypical physiological reactions to triggering stimuli, though not all participants exhibited this response. Our analyses suggest a large interindividual variability in response to misophonic triggers and highlights the need for methodological adjustments in future experiments to increase the detectability of misophonic …

Molecular Subtyping Of Hypertensive Disorders Of Pregnancy, Michal Elovitz, Elaine Gee, Nathaniel Delaney-Busch, Alison Moe, Mitsu Reddy, Arkady Khodursky, Johnny La, Ilma Abbas, Kay Mekaru, Hunter Collins, Farooq Siddiqui, Rory Nolan, Rupsa Boelig, Daniel Kiefer, Pamela Simmons, George Saade, Antonio Saad, Ebony Carter, Thomas Mcelrath, Stephen Quake, Mark Depristo, Carrie Haverty, Manfred Lee, Eugeni Namsaraev, Vincenzo Berghella, Ai-Ris Collier, Antonia Frolova, Esther Park-Hwang, Luis Pacheco, Elizabeth Sutton, Maneesh Jain, Kara Rood, William A Grobman, Joseph Biggio, Cynthia Gyamfi-Bannerman, Arun Jeyabalan, Morten Rasmussen

Department of Obstetrics and Gynecology Faculty Papers

Hypertensive disorders of pregnancy (HDP), including preeclampsia, affect 1 in 6 pregnancies, are major contributors to maternal morbidity and mortality, yet lack precision medicine strategies. Analyzing transcriptomic data from a prospectively-collected diverse cohort (n = 9102), this study reveals distinct RNA subtypes in maternal blood, reclassifying clinical HDP phenotypes like early/late-onset preeclampsia. The placental gene PAPPA2 strongly predicts the most severe forms of preeclampsia in individuals without pre-existing high risk factors, months before symptoms, and its overexpression correlates with earlier delivery in a dose-dependent manner. Further, molecular subtypes characterized by immune genes are upregulated in less severe forms of HDP. …

Ai Beliefs And Practices In Community College Classrooms, Julie Eng, Heather Umphlett, Jocelyn Gilchrist, Alicia Howell, Mary Ann Howell, Wendy Miller-Edwards, Laurel Pope

Inquiry: The Journal of the Virginia Community Colleges

The country, the Commonwealth of Virginia, and Virginia Community College System initiatives all promote generative AI within education. It is a topic of great concern and interest for higher education instructors, yet at the same time many faculty members feel uncertain about effectively integrating it into class material. To further add pressure to the AI explosion, community colleges particularly face a responsibility to prepare their students for success in this new AI-focused environment. In this article, seven faculty members from Camp Community College discuss the implications of generative AI programs, including subscriptions and chatbots, within their particular courses and how …

A Scoping Review Of Omop Cdm Adoption For Cancer Research Using Real World Data, Liwei Wang, Andrew Wen, Sunyang Fu, Xiaoyang Ruan, Ming Huang, Rui Li, Qiuhao Lu, Heather Lyu, Andrew E Williams, Hongfang Liu

Faculty, Staff and Student Publications

The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) supports large-scale research by enabling distributed network analyses. However, the breadth of its adoption in cancer research is not well understood. We conducted a scoping review to describe the adoption of the OMOP CDM in cancer research. A total of 49 unique articles were included in the review, with 30 on the data analysis theme, and 20 on the infrastructure theme. This review highlighted that while the OMOP CDM ecosystem has enabled successful data support for cancer research, particularly for collaborative studies, ongoing model development and iterative improvement remain needed …

A Folding-Docking-Affinity Framework For Protein-Ligand Binding Affinity Prediction, Ming-Hsiu Wu, Ziqian Xie, Degui Zhi

Faculty, Staff and Student Publications

Accurate protein-ligand binding affinity prediction is crucial in drug discovery. Existing methods are predominately docking-free, without explicitly considering atom-level interaction between proteins and ligands in scenarios where crystallized protein-ligand binding conformations are unavailable. Now, with breakthroughs in deep learning AI-based protein folding and binding conformation prediction, can we improve binding affinity prediction? This study introduces a framework, Folding-Docking-Affinity (FDA), which folds proteins, determines protein-ligand binding conformations, and predicts binding affinities from three-dimensional protein-ligand binding structures. Our experimental results indicate that FDA performs comparably to state-of-the-art docking-free methods. We anticipate that our proposed framework serves as a starting point for integrating …

Daily Acute Intermittent Hypoxia Elicits Age & Sex-Dependent Changes In Molecules Regulating Phrenic Motor Plasticity, Jayakrishnan Nair, Alexandria Marciante, Carter Lurk, Mia Kelly, Maclain Capron, Gordon Mitchell

Department of Physical Therapy Faculty Papers

Acute intermittent hypoxia (AIH) elicits a form of respiratory motor plasticity known as phrenic long-term facilitation (pLTF). Exposure to repetitive daily AIH (dAIH) enhances pLTF, a form of metaplasticity. Little is known concerning cellular mechanisms giving rise to dAIH-induced metaplasticity and the age-dependent sexual dimorphism of AIH associated pro-plasticity mRNA expression. To test if age, sex, and dAIH effects are associated with differential expression of molecules that regulate the Q- and S-pathways and their cross-talk interactions to phrenic motor facilitation, we analyzed key regulatory molecules in ventral spinal (C3-C5) homogenates from young (3-month) and middle-aged (12-month) male and female Sprague-Dawley …

Vestibular Neurons Link Motion Sickness, Behavioural Thermoregulation And Metabolic Balance In Mice, Longlong Tu, Xing Fang, Yongjie Yang, Meng Yu, Hailan Liu, Hesong Liu, Na Yin, Jonathan C Bean, Kristine M Conde, Mengjie Wang, Yongxiang Li, Olivia Z Ginnard, Qingzhuo Liu, Yuhan Shi, Junying Han, Yi Zhu, Makoto Fukuda, Qingchun Tong, Benjamin Arenkiel, Mingshan Xue, Yang He, Chunmei Wang, Yong Xu

Children’s Nutrition Research Center Staff Publications

Motion sickness is associated with thermoregulation and metabolic control, but the underlying neural circuitry remains largely unknown. Here we show that neurons in the medial vestibular nuclei parvocellular part (MVePC) mediate the hypothermic responses induced by motion. Reactivation of motion-sensitive MVePC neurons recapitulates motion sickness in mice. We show that motion-activated neurons in the MVePC are glutamatergic (MVePCGlu), and that optogenetic stimulation of MVePCGlu neurons mimics motion-induced hypothermia by signalling to the lateral parabrachial nucleus (LPBN). Acute inhibition of MVePC-LPBN circuitry abrogates motion-induced hypothermia. Finally, we show that chronic inhibition of MVePCGlu neurons prevents diet-induced obesity and improves glucose homeostasis …

Effect Of Heat Stress On Ileal Epithelial Barrier Integrity In Broilers Divergently Selected For High- And Low-Water Efficiency, Elizabeth S. Greene, Brooklee Roach, Maria Fernandez Cuadrado, Sara Orlowski, Sami Dridi

Poultry Science Faculty Publications and Presentations

Water scarcity and rising global temperatures are two of the greatest current and future threats to poultry sustainability. Therefore, selection for water efficiency (WE) and heat resilience are of vital importance. Additionally, intestinal integrity is of critical importance under challenging conditions to maintain nutrient absorption and therefore, growth and performance of broilers. Here, we examined the effect of chronic cyclic heat stress (HS) on the ileal expression profile of tight-junction, gap-junction, adherens, and desmosome genes in the fourth generation of divergently selected low (LWE)- and high water efficient (HWE)-chicken lines. LWE birds exhibited higher levels of gut permeability, regardless of …

Benchmarking Large Language Models For Biomedical Natural Language Processing Applications And Recommendations, Qingyu Chen, Yan Hu, Xueqing Peng, Qianqian Xie, Qiao Jin, Aidan Gilson, Maxwell B Singer, Xuguang Ai, Po-Ting Lai, Zhizheng Wang, Vipina K Keloth, Kalpana Raja, Jimin Huang, Huan He, Fongci Lin, Jingcheng Du, Rui Zhang, W Jim Zheng, Ron A Adelman, Zhiyong Lu, Hua Xu

Faculty, Staff and Student Publications

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs-GPT and LLaMA representatives-on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with the traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here, we show that traditional fine-tuning outperforms zero- or …

Registration Of R19-42848 As A Drought-Tolerant, High-Yielding Soybean Germplasm Line, Chengjun Wu, Derrick Harrison, Liliana Florez-Palacios, Andrea Acuna, Daniel Rogers, Rafael Marmo, John Carlin, Ben Fallen, Leandro Mozzoni, Caio Cenella Vieira

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

R19-42848 (Reg. no. GP-532, PI 706865) is a high-yielding soybean [Glycine max (L.) Merr.] germplasm with drought tolerance released by the University of Arkansas System - Division of Agriculture Research & Extension Center in 2024. It is an F4-derived selection from the cross R12-2237 (drought-tolerant) x R12-519 (high-yielding). R19-42848 is a conventional (non-genetically modified) soybean with a relative maturity of 5.2. Plants have determinate growth habit with purple flower color, gray pubescence, and tan pod wall at maturity. Seed of R19-42848 has buff hilum color, 100-seed weight of 13.8 g, and contains on average 404.5 and 211.5 g kg-1 of …

Understanding Strain-Level Dynamics In Gut Commensal-Pathogen-Host Interactions, Anna Louise Deveaux

Arts & Sciences Graduate Student Theses and Dissertations

The human gut microbiome is a consortium of trillions of bacteria, archaea, fungi, and viruses that colonizes the gastrointestinal tract and promotes health under homeostatic conditions. This microbial community trains the immune system, modulates inflammation and anticancer immunity, promotes cardiometabolic health, enables nutrient extraction, and prevents pathogen overgrowth. The latter function manifests through colonization resistance, in which microbes occupy spatial and nutritional niches thereby excluding pathogens from the community entirely, and through limiting pathogen population growth if colonization occurs. These roles are facilitated by complex host-microbe and microbe-microbe interactions that underlie differences in susceptibility to microbiome-mediated infectious diseases. The strain-level …

Video Tracking As An Effective High Throughput Method For Mtbi Detection, Julie Mcintyre, Julie A. Semon

Miners Solving for Tomorrow Research Conference

No abstract provided.

Phylogenetic Relationships And Species Delimitation Of Bunchgrass Lizards Of The Genus Sceloporus From Mexico With The Description Of A New Species, Tristan Charran, Jesús A. Loc-Barragan, Rafael Alejandro Calzada-Arciniega, Liz A. Alfaro-Juantorena, Raúl Cueva Del Castillo, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

Molecular data continue to serve as an invaluable tool to assess species limits and patterns of cryptic diversity, particularly in areas harboring high levels of biodiversity. The Sceloporus scalaris group, known as bunchgrass lizards, contains 13 described and one undescribed species distributed throughout high elevation biotas of Mexico. However, recent studies suggest that diversity in the group may be substantially underestimated. We collect new sequence data from four independent loci to determine the evolutionary distinctiveness and phylogenetic relationships of an isolated population of bunchgrass lizard in the Sierra San Juan (SSJ) in the Mexican state of Nayarit. Concatenation and coalescent-based …

Dissecting The Contribution Of Stmn2 To Als Pathogenesis, Kelsey Krus

Arts & Sciences Graduate Student Theses and Dissertations

TDP-43 is required for splicing of Stathmin-2 (STMN2) transcript, so STMN2 is reduced in most ALS patients. TDP-43 does not regulate STMN2 in mice as it does in humans. Thus, mouse models of ALS do not reflect patient loss of STMN2. To test the hypothesis that a reduction in STMN2 contributes to ALS pathogenesis, we generated STMN2 knockout mice. Constitutive STMN2 loss induces an early sensory and motor neuropathy with disrupted motor behavior and dramatic distal neuromuscular junction (NMJ) denervation. This NMJ pathology occurs in fast-fatigable motor units, which are the most vulnerable in ALS. In contrast, motoneurons and axons …

Cytokinesis & Dbf2, Katharine Gray, Katie Shannon

Miners Solving for Tomorrow Research Conference

No abstract provided.

Discovering Localization Of Fun19 Orf In Yeast, Megan Percy, Galayna Baur, Katie Shannon

Miners Solving for Tomorrow Research Conference

No abstract provided.

Carrier Analysis Of Alc Lipid Nanoparticles With Lung Cancer Drug, Noah Sparks, Lei Xu, Hu Yang

Miners Solving for Tomorrow Research Conference

No abstract provided.

Characterization Of An Iqg1 Phosphorylation Mutant, Lindsay Scheider, Alexis Ham, Katie Shannon

Miners Solving for Tomorrow Research Conference

No abstract provided.

Effects Of Ally Confrontation On Target Outcomes, Sophie Firle, Gemma Flores-Olivas

Miners Solving for Tomorrow Research Conference

No abstract provided.

What's That Sound?: Characterizing Chemical Signals In Bradyrhizobium Japonicum Strains, Sophia Nicolette Militante

Miners Solving for Tomorrow Research Conference

No abstract provided.

The Effects Of Preventing Dephosphorylation Of Iqg1 On Cytokinesis, Jenna L. Mueller, Katie Shannon

Miners Solving for Tomorrow Research Conference

No abstract provided.