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 …

Inhomogeneous Branching Random Walks: Incorporating Genealogy And Density Effects, Lauren Ajax, Beatrice Durham, Pratima Hebbar, Cade Johnston, Jiayi Zhang

Spora: A Journal of Biomathematics

We introduce a novel framework using inhomogeneous branching random walks (BRWs) to model biological processes, specifically by introducing genealogy-dependence in branching rates and displacement distributions to model bacterial colony growth. Current stochastic models often either assume independent and identical behavior of individual agents or incorporate only spatiotemporal inhomogeneity, ignoring the effect of genealogy-based inhomogeneity on the long-time behavior of these processes. Such asymptotics are of independent mathematical interest and are crucial in understanding the emergence of patterns. We propose several inhomogeneous BRW models in 2D space where displacement distributions and branching rates vary with time, space, and genealogy. A combined …

Crispr-Cas9: Transforming Biomedical Technology Through Gene Editing, Zaina Issa

A with Honors Projects

The research paper describe the gene editing technique CRISPR-Cas9 and the implications of its use in different fields, including medicine and agriculture.

Development And Validation Of An Analytical Method For Quantitative Determination Of Small Aldehydes In Plasma, Stephanie T. Clark

Chemistry & Biochemistry Theses - Archive

Small aldehydes such as formaldehyde and acetaldehyde are highly reactive metabolites that play important roles in biological processes related to oxidative stress, metabolism, and DNA damage. Because of their chemical reactivity, volatility, and low endogenous concentrations, accurate measurement of these compounds in biological samples remains analytically challenging. The goal was to develop and evaluate a practical analytical method for detecting small aldehydes in biologically relevant matrices using headspace gas chromatography mass spectrometry (HS-GC-MS). The method combined chemical derivatization with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and headspace sampling to stabilize aldehydes and enable selective detection by mass spectrometry. Method development focused on optimizing derivatization …

Application Of Diatom Indices To Monitor Environmental Shifts In The Downstream Tuntang River, Central Java, Mirza Hanif Al Falah, Tri Retnaningsih Soeprobowati, Hadiyanto -, Muhammad Isnaini Ibnu Sabil, Marta Wojewódka-Przybył, Łukasz Kruszewski, Paweł Rydelek

Applied Environmental Research

Diatoms are widely recognized as sensitive bioindicators for reconstructing past water quality and ecological changes in aquatic ecosystems. In this study, multiple diatom-based indices were applied to sediment cores collected from three downstream stations of the Tuntang River, Central Java, to infer long-term environmental change in a tropical river system. A total of 38 sediment subsamples were analyzed, with dominant taxa including Fragilaria crotonensis (2.4–18.6%), Nitzschia palea (3.1–22.4%), and Aulacoseira granulata (2.0–15.8%), indicating sustained nutrient enrichment. Diatom indices consistently classified conditions as mesotrophic to eutrophic throughout the sediment profiles. The occurrence of the marine diatom Cylindrotheca closterium (up to 6.3%) …

An Ecological-Evolutionary Investigation Of Phenotypic, Genetic, And Environmental Variation And Correlations Among Reproductive Traits Of Tall Goldenrod (Solidago Altissima), Michael J. Wise, Daniel Lavy, David E. Carr, Warren G. Abrahamson Ii

Faculty Journal Articles

Although fitness-related traits are expected to be under strong selection, traits related to reproduction are often quite variable within plant populations. We used data from two large greenhouse experiments to quantify phenotypic, genetic, and environmental variation, as well as genetic tradeoffs that might help explain the maintenance of withinpopulation variation in four traits related to sexual or vegetative reproduction in tall goldenrod (Solidago altissima). The goldenrod population exhibited high levels of both phenotypic and genetic variation for capitulum (flower head) number and size, seed production, and rhizome growth. Significant negative genetic correlations were present between the number of capitula and …

Investigations Into Why Human (But Not Mouse) Ku70/80 Is Essential Reveal A Role For Human Ku70/80 In Ribosome Biogenesis, George Zakusilo

Student Theses and Dissertations

The requirement of Ku70/80 for ribosome biogenesis in higher primates explains otherwise perplexing essential nature of this double-strand break (DSB) repair factor. We have ruled out telomere protection or DSB repair as the essential function ofKu70/80. Instead, unbiased genome-wide analyses pointed to a role in ribosome biogenesis. Human Ku70/80, but not mouse Ku70/80 is enriched in the nucleolus at the Dense Fibrillar Component (DFC) periphery, likely via co-evolved protein-protein interactions with nucleolar factors. Consistent with its localization in the nucleolus, human Ku70/80 null cells exhibit ribosomal RNA (rRNA) processing defect and consequent shutdown of protein synthesis offer a direct explanation …

Does Fishery Management For Groupers (Teleostei: Epinephelidae) Protect Them Effectively? Context From The Iucn's Red List Of Threatened Species, Sean T. Fennessy, Christi Linardich, Kevin Rhodes, Joao P. Barreiros, David Pollard, Eloy Sosa-Cordero, Felicia Coleman, Alfonso Aguilar-Perera, Christopher R. Malinowski, Thierry Brulé, Pedro Afonso, Kayan Ma, Min Liu, Muktha Menon, Colin Wen, Stanley K. H. Shea, Sean N. Porter, Matthew Craig, Yvonne Sadovy De Mitcheson

Biological Sciences Faculty Publications

Worldwide, groupers (Epinephelidae) are commercially valued fishes, which also play key ecological roles on tropical and subtropical reefs. In 2007 and 2016, the IUCN's Groupers and Wrasses Specialist Group assessed all 160+ grouper species, with 17 of these being identified as threatened in 2016 and the major threat factor being overexploitation. Our present study aimed to identify whether management measures (MMs) for previously assessed groupers were established, whether these measures aligned with IUCN's Red List categories, and whether they effectively protect grouper populations. Experts in grouper biology and management assigned scores per grouper species based on the extent to which …

Loan-Heavy Aid: Consequences On Academic And Early-Career Outcomes, April Zhang

CMC Senior Theses

This study examines how the composition of financial aid, specifically the balance between loans and grants, shapes students’ academic performance, major selection, and early career outcomes. Using administrative data from the University of California system (2007-2019) and post-graduation records from UC Irvine, I analyze how loan reliance influences both educational trajectories and labor-market results. The key measure, loanshare, captures the fraction of total aid financed through loans rather than grants. This allows for comparisons among students with similar financial need, expected family contribution, and total aid levels. Results show that students with more loan-heavy aid packages earn significantly lower …

Commissioning & Daily Qa Of Converted Linac For Electron Flash, Tomaj Javidtash

Theses and Dissertations

Ultra-high dose rate (FLASH) radiotherapy has demonstrated promising normal tissue sparing in preclinical studies; however, the lack of standardized dosimetry, commissioning, and quality assurance (QA) methodologies remains a major barrier to its reproducible and safe implementation. In particular, conventional clinical commissioning and QA protocols are not directly applicable at FLASH dose rates due to challenges associated with detector response, dose-per-pulse effects, and beam control limitations.

This thesis presents the commissioning of a converted Varian 21EX linear accelerator for electron FLASH operation within the Division of Medical Physics at the Virginia Commonwealth University (VCU) Department of Radiation Oncology. Comprehensive beam characterization …

Golden Symbiosis, Marta Susperregui Muñoz

Grado en Diseño de Interiores

The concept of Golden Symbiosis emerges from the desire to redefine the relationship between aesthetics, wellbeing, and nature. The term Golden refers to the therapeutic and symbolic value of bee-derived products such as honey, propolis, royal jelly, beeswax, and pollen. For centuries, these natural substances have been associated with healing, nourishment, and regeneration. Within the project, they form the basis of the clinic’s treatment philosophy while representing a return to more restorative and preventative approaches to skin health. The term Symbiosis refers to a mutually beneficial relationship between different living systems. Applied to this project, it becomes the guiding architectural …

Application Of Paper Spray Mass Spectrometry For Screening Acetylcholinesterase Inhibitors, Diksha Gautam

Graduate Research Theses & Dissertations

Paper spray mass spectrometry (PS-MS) is a novel ambient ionization method that allows chemical and biological samples to be rapidly analyzed with little preparation being required. In this paper, PS-MS was set up and streamlined as an acetylcholinesterase (AChE)-monitoring platform in addition to screening an existing and newly produced AChE-inhibitors. The detection of the substrate, acetylcholine (m/z 146), and the AChE catalysis product, choline (m/z 104) was performed without applying chromatographic separation or derivatization to the dried paper substrates. Assay conditions were optimized in a systematic way, to develop a robust MS-compatible enzymatic workflow.

Calibration curves for both, acetylcholine and …

Integrating Environmental Awareness In Underwater Acoustic Networks: A Comprehensive Review, Sadaf Vahabli, Iftekhar Ahmad, Quoc Viet Phung, Daryoush Habibi, Walid K. Hasan, Ruba Zaheer

Research outputs 2022 to 2026

Underwater Acoustic Networks (UANs) are critical for enabling long-range underwater communication, supporting a wide range of applications, such as environmental monitoring, resource exploration, disaster prevention and marine security. Unfortunately, UANs operate within a limited acoustic spectrum, where these spectrums often overlap with those used by marine animals for communication, navigation and foraging. Additionally, anthropogenic noise from industrial activities contributes to acoustic pollution, intensifying this problem. This frequency overlap poses significant risks to marine life. Therefore, this review highlights the urgent need to develop environmentally aware UANs that minimize harmful acoustic interference with marine mammals, fish and invertebrates. Further, it focuses …

Luckett Davis Lecture Notes Collection - Accession 1846, Luckett Vanderford Davis

Manuscript Collection

The Dr. Luckett Davis Lecture Notes Collection documents the teaching and academic work of Luckett Vanderford Davis, Professor of Biology at Winthrop University, where he served from 1964 until his retirement and later held the title of Emeritus Professor of Biology. The collection consists primarily of lecture notes, seminar materials, laboratory manuals, and instructional aids used by Dr. Davis in teaching a wide range of undergraduate biology courses.

The bulk of the collection contains handwritten and typed lecture notes prepared for courses in zoology, genetics, evolution, ecology, and marine biology. These materials document Dr. Davis’s approach to teaching biological sciences …

Poly(A) Probe Hcr Rna-Fish Specifically Marks Pyriform Nurse Cells In The Brown Anole Lizard Ovary, Zoe B Griffin, Bonnie K Kircher, Richard R Behringer

Faculty, Staff and Student Publications

Hybridization chain reaction RNA-fluorescent in situ hybridization (HCR RNA-FISH) is a powerful and increasingly used method for visualizing gene expression in cells and tissues. A probe set against polyadenylated RNA (poly(A)) is often used as a positive control for RNA integrity and staining quality. While optimizing this technique in the ovary of the brown anole lizard (Anolis sagrei), we found that the poly(A) probe produced a strikingly specific and intense signal in pyriform cells, a specialized lizard-specific nurse cell type. This staining pattern was found in both whole-mount samples and paraffin sections, suggesting that poly(A) signal intensity can serve as …

Investigation Of A Global Mouse Methylome Atlas Reveals Subtype-Specific Copy Number Alterations In Pediatric Cancer Models., Melanie Schoof, Tuyu Zheng, Martin Sill, Roland Imle, Alessia Cais, Lea Altendorf, Alicia Fürst, Nina Hofmann, Kati Ernst, Dominik Vonficht, Kenneth Chun-Ho Chan, Tim Holland-Letz, Andreas Postlmayr, Ryo Shiraishi, Wanchen Wang, Alaide Morcavallo, Michael Spohn, Carolin Göbel, Judith Niesen, Levke-Sophie Peter, Franck Bourdeaut, Zhi-Yan Han, Yanxin Pei, Najiba Murad, Fredrik J. Swartling, Jessica Taylor, Monika Yadav, Garrett R. Gibson, Richard J. Gilbertson, Matthias Dottermusch, Rajanya Roy, Kornelius Kerl, Rainer Glass, Jiying Cheng, Martin A. Horstmann, Gerrit Wolters-Eisfeld, Haotian Zhao, Dominik Sturm, Viveka Nand Yadav, Louis Chesler, Simon Haas, William A. Weiss, Paul A. Northcott, Lena M. Kutscher, Ana Guerreiro Stucklin, Olivier Ayrault, Julia E. Neumann, Daisuke Kawauchi, David T W Jones, Kristian Pajtler, Ana Banito, Stefan M. Pfister, Ulrich Schüller, Marc Zuckermann

Manuscripts, Articles, Book Chapters and Other Papers

Copy number alterations (CNAs) are hallmarks of cancer, yet investigation of their oncogenic role has been hindered by technical limitations and missing model systems. Here we generated a genome-wide DNA methylation and CNA atlas of 106 genetic mouse models across 31 pediatric tumor types, including 18 new models for pediatric glioma. We demonstrated their epigenetic resemblance to human disease counterparts and identified entity-specific patterns of immune infiltration. We discovered that mouse tumors harbor highly recurrent CNA signatures that occur distinctly based on the tumor subgroup and driving oncogene and showed that these CNAs share syntenic regions with the matching human …

Semantic Discovery Of Genomic Datasets With Ai, Lawrence Allibah

Electronic Theses and Dissertations

Traditional keyword-based search in genomic databases often fails to capture the latent semantic context of biological studies, leading to a ``Lexical Gap" in research discovery. This thesis presents a high-performance dual-engine discovery system built upon 10,000 studies. By utilizing 1,536-dimensional vector embeddings, with large language models (LLMs) we implement a search engine coupled with a novel Hybrid Boosting layer that integrates semantic intent with factual metadata. Furthermore, we apply a high-dimensional K-Means clustering algorithm for unsupervised topic discovery. Empirical benchmarking demonstrates that the Hybrid Boosting engine achieves a 38.1% gain in precision and a 41.2% increase in Mean Reciprocal Rank …

Ecological And Evolutionary Divergence Of A Shared Sympatric Color Polymorphism In Paracirrhites Hawkfish, Samuel Greaves

Graduate Studies Theses and Dissertations 2026

Color polymorphism provides a tractable window into how selection, gene flow, and ecology interact to maintain phenotypic diversity and initiate divergence. I investigate the ecological and genomic basis of sympatric light and melanistic morphs in two reef hawkfishes, Paracirrhites arcatus and P. hemistictus, across Guam and Hawai‘i. This study aims to determine whether the color morphs of these hawkfishes are a stable polymorphism or have begun the process of ecological speciation. For P. arcatus revealed substantially lower density on Guam (0.086 ind/m²) than reported for Hawai‘i (0.292 ind/m²) and a strong skew away from the melanistic morph on Guam …

Volumetric Fluorescence Microscopy For High-Throughput And High-Sensitivity Imaging: From Single Molecules To Tissues, Le-Mei Wang

Graduate Studies Theses and Dissertations 2026

Fluorescence microscopy is an indispensable tool in the biological sciences, enabling researchers to investigate intricate subcellular structures, particularly for volumetric studies. However, conventional optical microscopy for volumetric imaging remains fundamentally constrained by imaging speed and throughput. To bypass traditional serial z-scanning, we introduce an axially scan-free method using a phase layer cake to modulate the system's point spread function. This approach projects volumetric information onto a 2D plane in a single shot, offering high flexibility in tuning axial depth alongside simultaneous multicolor imaging with high spatial resolution and sensitivity. This dissertation divides these technical advancements into cellular and tissue imaging …

Essays On Accelerated Failure Time Models For Recurrent Event Data, Emmanuel Masavo Djegou

Doctoral Dissertations

Recurrent event data arise in many fields such as medicine, reliability, insurance, and economics, where the same event may occur repeatedly for a subject. Accelerated Failure Time (AFT) models provide an intuitive framework for relating covariates to event times and offer a useful alternative to proportional hazards models, allowing direct prediction of event timing under right censoring. However, existing AFT extensions for recurrent events, such as accelerated gap time (AGT) models, often fail to account for interventions between events and may not capture complex temporal patterns.

In this work, we first propose a class of semiparametric AGT models incorporating an …

Corrigendum To "Human Umbilical Cord Mesenchymal Stem Cells Secretome And Nanoemulsion Propolis Combination Ameliorate Osteoclastogenesis In Lipopolysaccharide-Induced Osteolysis In Hyperglycemia Rats"

Journal of Dental Sciences

No abstract provided.

Mesenchymal Stem Cells Derived From Gingiva Normoxic Or Hypoxic-Preconditioning Allogenous Transplantation Affect Orthodontic Tooth Movement In Vivo, Alexander Patera Nugraha, Guang Hong

Journal of Dental Sciences

No abstract provided.

Biological Performance Enhancement Of Ni-Free Zr-Based Bulk Metallic Glass For Dental Implants Via Nitrogen Plasma Immersion Ion Implantation, Hsun-Miao Huang, Ying-Sui Sun, Ya-Lin Huang, Kai-Yi Lin, Thantrira Porntaveetus, Thanaphum Osathanon, Wei-Cheng Chen, Her-Hsiung Huang

Journal of Dental Sciences

Background/purpose: Improving the biocompatibility of bulk metallic glass (BMG) alloys is critical for expanding their applications in biomedical fields, particularly in dental implants. This study systematically investigated the suitability of nitrogen plasma immersion ion implantation (NPIII)-treated Zr-based BMG alloy for next-generation dental implant applications, focusing on protein adsorption, platelet responses, and cell behavior.

Materials and methods: NPIII was employed as a surface modification approach to enhance the biological performance of a Ni-free Zr₆₂.₅Cu₂₂.₅Fe₅Al₁₀ BMG alloy. The effects of NPIII treatment on surface characteristics, including crystallinity, chemical composition, layer thickness, roughness, and hydrophilicity, were comprehensively analyzed. Protein adsorption …

Changes Of Rna Expression In Aging Periodontal Ligament Cells, Su Kang Kim, Ju Ri Ye, Gyutae Kim, Ju Yeon Ban, Sang Wook Kang

Journal of Dental Sciences

Background/purpose: Aging is a major risk factor for periodontal disease and is associated with impaired tissue homeostasis and regenerative capacity. The periodontal ligament (PDL) plays a central role in periodontal integrity; however, the molecular mechanisms underlying PDL cell aging remain incompletely understood.

Materials and methods: In this study, we established an in vitro passage-dependent cellular aging model using human periodontal ligament fibroblasts serially passaged from early to late stages. Transcriptomic changes associated with aging were analyzed using RNA sequencing, followed by principal component analysis, hierarchical clustering, pathway enrichment, and protein–protein interaction network analyses.

Results: Global transcriptomic profiling revealed that PDL …