Digital Commons Network^™

Pan-Cancer Copy Number Analysis Identifies Optimized Size Thresholds And Co-Occurrence Models For Individualized Risk Stratification, Minh P Nguyen, William C Chen, Kanish Mirchia, Abrar Choudhury, Naomi Zakimi, Vijay Nitturi, Tiemo J Klisch, Stephen T Magill, Calixto-Hope G Lucas, Akash J Patel, David R Raleigh

Faculty, Staff and Students Publications

Chromosome instability leading to aneuploidy and accumulation of copy number gains or losses is a hallmark of cancer. Copy number alteration (CNA) signatures are increasingly used for cancer risk stratification, but size thresholds for defining CNAs across cancers are variable and the biological and clinical implications of CNA size heterogeneity and co-occurrence are incompletely understood. Here we analyze CNA and clinical data from 691 meningiomas and 10,383 tumors from The Cancer Genome Atlas to develop cancer- and chromosome-specific size-dependent CNA and CNA co-occurrence models to predict tumor control and overall survival. Our results shed light on technical considerations for biomarker …

Irradiation Of Prostate Cancer Alters Circulating Small Extracellular Vesicle Functions, Aejaz Sayeed, Vaughn Garcia, Cecilia E. Verrillo, Rachel M. Derita, Md Niamat Hossain, Shiv R. Krishn, Samuel Sey, Christopher D. Shields, Adrian D. Altieri, Qin Liu, Khalid Sossey-Alaoui, William K. Kelly, Lucia R. Languino

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

It is known that β1 integrins and a downstream signaling molecule c-Src are upregulated in prostate cancer (PrCa) tissues, are co-expressed in circulating small extracellular vesicles (sEVs) and contribute to cancer progression. Here, we demonstrate that sEVs from PrCa patients show robust expression of both β1 integrins and c-Src. The impact of irradiation, a widely used therapy for the treatment of PrCa, on circulating sEVs is however not fully understood. We show that sEVs isolated from the plasma of transgenic adenocarcinoma of mouse prostate (TRAMP) mice, stimulate migration and anchorage-independent growth of recipient cancer cells, but sEVs are not active …

Detecting Ionospheric Disturbances Using High Frequency Coastal Radar Transmissions From The West Coast Of The United States, Riley N. Troyer, Kenneth Obenberger, Michael Negale, Eugene Dao, Zsolt Balint, Eric Burnside, Kris Robinson, Jeffrey M. Holmes, Pavel Inchin, Jonathan Snively

Space Dynamics Laboratory Publications

Coastal radar system are located around the world and many happen to transmit at frequencies capable of skywave propagation via the ionosphere. Therefore, they can be detected hundreds to thousands of kilometers away. This paper demonstrates the opportunity to detect 39 Coastal Ocean Dynamics Application Radar transmitters located on the western coast of the United States using three HF radio receivers in Utah and New Mexico. It also illustrates the possibility to use the phase and Doppler measurements of these signals to derive displacements of the refracting ionospheric layer up to meter resolution for the 2023 annular solar eclipse, an …

Analyzing The Interfacial Properties Of Natural Fiber Composites, Rahul Kumar Arram

Doctoral Dissertations and Master's Theses

In response to growing environmental concerns and the urgent demand for sustainable development, the composite materials industry is increasingly challenged to balance high performance with environmental responsibility. Conventional composites, typically composed of synthetic fibers and petroleum-based resins, offer outstanding mechanical properties but are associated with significant ecological drawbacks due to their non-biodegradable nature and energy-intensive production. This has led to increased interest in the development of sustainable composites that minimize environmental impact without compromising functionality. This study presents the development of eco-friendly composites reinforced with natural bast fibers—specifically ramie and jute—through a comprehensive program of materials processing and characterization. To …

Effects Of Meeting Exercise Guidelines On Depression And Anxiety In Multiple Sclerosis – A Systematic Review And Meta-Analysis, Sodiq Fakorede, Joseph Peters, Tanner Murphy, Ethan Truong, Libak Abou

Student Publications

Background: Depression and anxiety are common in multiple sclerosis (MS), significantly affecting quality of life. Previous studies on exercise interventions for mental health in persons with MS (PwMS) have shown mixed results, partly due to inconsistent adherence to the Physical Activity Guidelines for Multiple Sclerosis (PAG-MS).

Objective: This study aimed to evaluate the effects of PAG-MS-compliant exercise on depression and anxiety outcomes in PwMS.

Methods: A systematic search was performed in EMBASE, PsycINFO, Web of Science, SPORTDiscuss, PubMed, Scopus, and CINAHL through October 2024 to identify randomized controlled trials (RCTs). Eligible studies involved adults with MS and focused on exercise …

Vân Lê, Vân Lê '26, Nathalie Romero '25, Posse Legacy Project, Illinois Wesleyan University

All oral histories

Interview of Vân Lê on July 2, 2025 Vân Le is a Posse 6 Scholar who double majored in Political Science and International Global Studies Vân was also a member of the Multilingual Accessibility RSO, Pi Sigma Alpha and Scholars at Risk chapter at IWU. She was also an Eckley Scholar for 2025.

Z-Scores Outperform Similar Methods For Analyzing Crispr Paralog Synthetic Lethality Screens, Juihsuan Chou, Nazanin Esmaeili Anvar, Reem Elghaish, Junjie Chen, Traver Hart

Faculty, Staff and Student Publications

Genetic screens offer a promising strategy for identifying tumor-specific therapeutic targets, but single-gene knockout screens often miss functionally redundant paralogs. Multiplex Cas9 and Cas12a CRISPR systems have been deployed to assay genetic interactions, but analysis pipelines vary considerably. Here we evaluate data from four in4mer CRISPR/Cas12a screens in cancer cell lines, using delta log fold change, Z-transformed dLFC, and rescaled dLFC approaches to identify synthetic lethal interactions. Both ZdLFC and RdLFC provide more consistent identification of synthetic lethal pairs across cell lines compared to the unscaled dLFC method, while ZdLFC benefits from not requiring a training set of known interactors.

Making The New Public Safety Safe, Christopher Slobogin

Vanderbilt Law School Faculty Publications

Shawn Fields' The New Public Safety: Police Reform and the Lurking Threat to Civil Liberties, which will be published by the University of California Press in September, is a brave and wise effort to envision a post-DeFund the Police world. While the defund movement has, at best, been a mixed success, some municipalities have experimented with de-policing routine interactions with people who are unhoused and mentally ill, authorizing civilian "violence interrupters" to roam the streets, and handing over traffic enforcement to unarmed officials. In The New Public Safety, Fields endorses these developments but also cautions that, without regulation, they will …

Vibrio Cholerae Endemic To The Lower Rio Grande Delta Segregate Into Urban And Rural Phylotypes, Daniele Provenzano, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, David Silva, Viviana Trevino, Miguel F. Gonzales, Boris Ermolinsky, Stefan Pukatzki

School of Integrative Biological & Chemical Sciences Faculty Publications

The lifestyle of Vibrio cholerae is primarily environmental, yet a chance encounter with a human host can lead to cholera, a potentially lethal form of diarrhea. Strains belonging to O1 and O139 serogroups have pandemic potential, but the contribution of non-O1/non-O139 serovars towards the genesis of cholera remains unclear. Endemic V. cholerae lineages were investigated given several historical accounts describing cholera epidemics and sporadic, contemporary cholera-like outbreaks along the lower Rio Grande Delta (LRGD). Seven isolates were recovered from an urban segment of the Rio Grande and six from a rural segment where the river empties into the Gulf of …

From Aortic Stenosis To Cardiomyopathy: The Hidden Impact Of Undiagnosed Acommissural Unicuspid Aortic Valve, Muhammad Sabri, Hamza Muhammadzai, Angad Bedi, Eddy Mizrahi, Matthew Collins

Abington Jefferson Health Papers

Unicuspid aortic valve (UAV) is a rare congenital anomaly, diagnosed in individuals aged 30 to 50. It is associated with aortic stenosis or aortic regurgitation, potentially leading to heart failure. We report a case of a 28-year-old male with an acommissural UAV, aortopathy, critical aortic stenosis, and heart failure with reduced ejection fraction, presenting with shortness of breath. This case is notable for late presentation of an acommissural UAV, which typically manifests in childhood.

Lived Experiences Of Sexual Orientation Discrimination Of Gay Male Service Members, Dwayne A. Tyler

Walden Dissertations and Doctoral Studies

The repeal of the Don’t Ask, Don’t Tell policy (DADT) has been an area of study among scholars since 2011. Researchers have demonstrated that discrimination based on sexual orientation is still occurring in the armed forces. However, researchers have not studied the lived experiences of active-duty male service members in the army who self-identified as gay. The purpose of this phenomenological qualitative study was to examine the lived experiences of discrimination based on the sexual orientation of male service members who self-identified as gay in the army since the repeal of the DADT policy. Using semi-structured interviews, four self-identified gay …

Service Provider Practice And Dual Victimization Survivors Seeking Emergency Shelter, Lana Heinen

Walden Dissertations and Doctoral Studies

The Violence Against Women Act supports responses to the crimes of domestic violence, sexual assault, dating violence, and stalking. It does not provide a permanent or guaranteed pathway to safe and stable housing for those experiencing the dual victimization of domestic violence and human trafficking. Service provider practices can alleviate or aggravate barriers faced by this population. These practices are influenced by the education and training service providers receive before entering the field and throughout their career. The purpose of this generic qualitative study was to explore service providers’ perceptions of structures and barriers contributing to the obstacles of accessing …

Staff Education Project An Educational Project To Educating Mental Health Staffs On Stress Management To Improve Knowledge And Staff Retention, Lilian Eneude

Walden Dissertations and Doctoral Studies

This evidence-based educational project addressed the knowledge gap in stress management techniques among mental health nursing staff at an acute psychiatric facility. Mental health professionals experience substantially higher rates of workplace stress and burnout compared to other healthcare workers, affecting staff wellbeing, patient care quality, and organizational outcomes. The practice-focused question was: Does educating mental health nurses on stress management improve knowledge as evidenced by pre- and post-intervention? A comprehensive literature search was done at the Walden University Library using CINAHL, PubMed, and PsycINFO databases that yielded 200 potential articles, with 45 full-text articles reviewed and 20 high-quality studies included …

Lived Experiences Of Ex-Offenders In Securing Stable Employment After Reentry Programs, Tony Lemar Williams

Walden Dissertations and Doctoral Studies

The reintegration of formerly incarcerated individuals into society has garnered increasing attention largely due to structural and social barriers that impede their successful transition. The purpose of this qualitative descriptive phenomenological study was to explore the lived experiences of ex-offenders who successfully obtained gainful employment following their reintegration into society while navigating the enduring consequences of their past convictions. Self-determination, self-efficacy, and implicit theories grounded this study. Ten participants were recruited through social media platforms and flyers on community billboards in a suburban area of Ohio. Data were collected using semistructured in-depth interviews. Narrative coding, according to Saldana, was used …

Personal Social Media Usage And The Effect On Individuals’ Job Satisfaction: A Social Identity Theory Perspective, Daniel Adam Blair

Walden Dissertations and Doctoral Studies

Social networking sites are web-based platforms that serve as tools to enhance connectivity and communication for a broad spectrum of different individuals, but they may be doing a disservice to the users who overuse the platforms as a means to bolster their self-esteem surrounding their different identities. The purpose of this study was to examine the differences in individuals’ job satisfaction levels when using personal social media (PSM) to varying degrees and how individuals’ social identities may influence this interaction. Utilizing the social identity theory framework, this study aimed to determine whether a relationship exists between PSM usage and job …

Experiences Of Post-Secondary Teachers With Using Information And Communication Technologies In Rural Communities, Latonya Shirelle Motley

Walden Dissertations and Doctoral Studies

Teaching and learning in the 21st century requires full access and use of digital technologies but this can be challenging in rural areas. Teachers at post-secondary schools in rural communities often have limited access to information and communication technologies (ICT), which restricts their ability to fully serve their rural students. Guided by the theory of the digital divide, the purpose of this basic qualitative study was to explore the experiences of post-secondary teachers with using ICT in rural areas in the United States. Data for this qualitative study were collected from 44 participant interviews who evaluated their access of digital …

Strategies In Cybersecurity For The Protection Of Patient Health Information (Phi), Denise Holloway

Walden Dissertations and Doctoral Studies

Health information technology (IT) professionals are consistently seeking better ways to balance the availability of patient health information (PHI) with data breach prevention, as these breaches negatively impact health organizations legally and ethically due to the exposure of PHI. However, some health IT professionals lack strategies to protect PHI against cybersecurity attacks. Grounded in Dr. Edward Hutchins’ distributed cognition framework, the purpose of this qualitative pragmatic inquiry was to understand what strategies health IT professionals use to protect PHI against cybersecurity attacks. The participants were six IT professionals from Washington D.C., Maryland, and Virginia with at least five to seven …

Genetic Gain And Loss In The Evolution Of Amniote T Cell Receptor And Immunoglobulin Genes, Jordan M. Sampson

Biology ETDs

The immune system of most jawed vertebrates consists of three major cell types: αβ T cells, γδ T cells, and B cells. Every species evaluated contains the loci that encode the highly conserved αβ T cells, however, γδ T cells are less conserved and have been lost in squamate reptiles. The loci that encode the B cell receptor have also varied across evolution. Seven immunoglobulin (Ig) heavy chain isotypes have been identified in amniotes: IgM, IgD, IgY, IgG, IgE, IgO, and IgA. Some are found in most species (IgM and IgD) and others only in specific lineages (IgY or IgG). …

Environmental Exposures Increase Health Risks In Childhood Cancer Survivors., Omar Shakeel, Nicole Wood, Hannah M. Thompson, Michael E. Scheurer, Mark D. Miller

Manuscripts, Articles, Book Chapters and Other Papers

Childhood cancer survivors (CCSs) are at increased risk for chronic health issues due to late effects of cancer and its treatment. We address the impact of environmental exposures, such as air pollution, tobacco smoke, extreme weather events, and pesticides, on the health and survival of CCSs. These environmental hazards have been associated with worsening health outcomes and decreased survival among CCSs on a global scale. We also highlight that providers at a major pediatric cancer center in the United States have limited knowledge and practical skills about environmental risk factors and how to reduce exposures. Our survey results show that …

Current Landscape Of Preclinical Models For Pediatric Gliomas: Clinical Implications And Future Directions., Syed M. Faisal, Monika Yadav, Garrett R. Gibson, Adora T. Klinestiver, Ryan M. Sorenson, Evan Cantor, Maria Ghishan, John R. Prensner, Andrea T. Franson, Kevin Ginn, Carl Koschmann, Viveka Nand Yadav

Manuscripts, Articles, Book Chapters and Other Papers

Pediatric high-grade gliomas (pHGGs), particularly diffuse midline gliomas (DMGs), are among the most lethal brain tumors due to poor survival and resistance to therapies. DMGs possess a distinct genetic profile, primarily driven by hallmark mutations such as H3K27M, ACVR1, and PDGFRA mutations/amplifications and TP53 inactivation, all of which contribute to tumor biology and therapeutic resistance. Developing physiologically relevant preclinical models that replicate both tumor biology and the tumor microenvironment (TME) is critical for advancing effective treatments. This review highlights recent progress in in vitro, ex vivo, and in vivo models, including patient-derived brain organoids, genetically engineered mouse models (GEMMs), and …

Medical Biotechnology Symposium Sultan Qaboos University, Muscat, Oman 5th And 6th February 2024 Gene Hunting In Breast Tumours And Cells To Reveal Chemotherapy Resistance As Predictive Markers Of Response, Sultan Qaboos University

Sultan Qaboos University Medical Journal

No abstract provided.

Oxytocin Reduces Asymmetries In Dominance Relationships Between Pairs Of Captive Female Lions, Jessica C Burkhart, Abby Guthmann, Evianne M Dubois, Sarah R Heilbronner, Craig Packer

Faculty, Staff and Students Publications

Free-ranging female African lions maintain symmetrical social relationships by respecting each other's "ownership" of valuable food items rather than by supplanting subordinates according to well-defined dominance hierarchies. However, captivity often skews relationships in captive carnivores, hence we investigated whether captive female lions demonstrate obvious dominance relationships. Oxytocin has been shown to elicit context-specific impacts that equalize dominant subordinate relationships, thus we hypothesized that oxytocin would reduce any asymmetries found between dominants and subordinates in captive lions. We designed two experimental protocols for investigating pairwise relationships. We first identified dominant individuals by performing neutral trials that allowed each female equal opportunity …

Innovating For Improvement — Improving Pressure Damage Prevention And Treatment In The Community Using Continuous Pressure Monitoring, Bridie Kent, Nicci Aylward-Wotton, Peter R. Worsley

School of Nursing and Midwifery

Each year, approximately half a million people in the UK develop pressure ulcers (PUs), with most occurring in the community among individuals with underlying comorbidities, frailty, mobility issues and a dependence on carers. Pressure relief is essential for healing, however, some patients find pressure-relieving equipment uncomfortable, hot and noisy, thus refusing to use it and are, therefore, often labelled as non-concordant. This service improvement project evaluated the ForeSite PT® pressure monitor to identify PU risk, support healing and influence patient and carer decision making, assessing its useability, alongside patient and carer education. The technology consisted of a mattress- and chair-sized …

A Scoping Review Of Personalised Uk Maternity Care: Where Are We Now?, Louisa Tompkins, Gary Hodge, Jill Shawe, Lisa Burrows, Annick Bogaerts, Susie Pearce

School of Nursing and Midwifery

Background/AimsPersonalised care has been recommended continuously to improve UK maternity services. The aim of this review was to explore the current provision of personalised care and consider why it may not yet be fully embedded in practice.MethodsThis review of Embase, Medline, the Healthcare Management Information Consortium, the British Nursing Index, CINAHL, Google Scholar and reference lists found 15 articles published between 2014 and 2024, which were included for thematic analysis and synthesis.ResultsThe themes included the complexities of personalised care, different perspectives when implementing personalised care and the effect of cultural factors embedded in maternity services.ConclusionsBarriers to implementing personalised care include …

Differential Efficacy Of Bevacizumab And Erlotinib In Preclinical Models Of Renal Medullary Carcinoma And Fumarate Hydratase-Deficient Renal Cell Carcinoma, Niki M Zacharias, Manuel Ozambela, Menuka Karki, Rong He, Pankaj K Chauhan, Pedro I Pesquera, Andres E Hernandez Gonzalez, Oscar Ochoa, Alberto Pieretti, Huiqin Chen, Carolyn De La Cerda, Zhiyuan Yu, Abha Grover, Samantha Hicks-Peña, Natalie W Fowlkes, Lei Wang, Tapati Maity, Priya Rao, Giannicola Genovese, Nizar M Tannir, Jose A Karam, Pavlos Msaouel

Faculty, Staff and Student Publications

Renal medullary carcinoma (RMC) and fumarate hydratase (FH)-deficient renal cell carcinoma (RCC) are rare and highly aggressive cancers. Although the combination of vascular endothelial growth factor (VEGF) inhibition by bevacizumab and epidermal growth factor receptor (EGFR) inhibition by erlotinib is clinically used for both diseases, the differential effect of each component has not been investigated. Transcriptomic profiling revealed that RMC and FH-deficient tumor tissues demonstrate increased EGFR but not VEGF expression compared with adjacent normal kidney. Subsequent in vitro studies revealed that RMC and FH-deficient cell lines are sensitive to erlotinib treatment, whereas clear cell RCC cell lines are resistant. …

Structural And Functional Characterization Of Creb-Binding Protein (Crebbp) As A Histone Propionyltransferase, Guiling Cui, Marie Ley, Ariel E Mechaly, Linh-Chi Bui, Christina Michail, Jérémy Berthelet, Julien Dairou, Haopeng Yang, Guillaume Chevreux, Gautier Moroy, Michael R Green, Ahmed Haouz, Fernando Rodrigues Lima

Faculty, Staff and Student Publications

In addition to histone acetylation, histone lysine propionylation (such as the H3K18Pr mark) has recently attracted significant attention as a common and abundant modification linking the cellular metabolic state and gene expression. CREB-binding protein (CREBBP) and EP300 are key histone acetyltransferases that play a critical role in gene expression through their catalytic activity. Although CREBBP and EP300 are homologous enzymes with high structural similarities, they exhibit both redundant and specific functions. Dissecting the shared and divergent properties of CREBBP and EP300 is thus important to understand their roles. However, despite the importance of CREBBP, most mechanistic and structural studies have …

Cat: A Conditional Association Test For Microbiome Data Using A Permutation Approach, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert R Jenq, Christine B Peterson

Faculty, Staff and Student Publications

In microbiome analysis, researchers often seek to identify taxonomic features associated with an outcome of interest. However, microbiome features are intercorrelated and linked by phylogenetic relationships, making it challenging to assess the association between an individual feature and an outcome. This paper proposes a novel conditional association test, CAT, that can account for other features and phylogenetic relatedness when testing the association between a feature and an outcome. CAT adopts a permutation approach, measuring the importance of a feature in predicting the outcome by permuting operational taxonomic unit/amplicon sequence variant counts belonging to that feature from the data and quantifying …

Pol Θ-Mediated End-Joining Uses Microhomologies Containing Mismatches, Yuzhen Li, Ngoc K Dang, Wei He, Mark Returan, Denisse Carvajal-Maldonado, Adele T Guerin, Han Xu, Bin Liu, Richard D Wood

Faculty, Staff and Student Publications

DNA polymerase theta (Pol θ) initiates repair of DNA double-strand breaks by pairing single strands at short "microhomologies". It is important to understand microhomology selection, as some cancer cells rely on Pol θ for survival. Here, we investigate end-joining by purified human Pol θ, employing DNA sequencing of products generated from oligonucleotide libraries having diverse 3' ends. Pol θ overwhelmingly selects short internal microhomologies found within 15 nucleotides of the terminus of single-stranded DNAs, restricting deletion size during end-joining. Significantly, we find that the selected microhomologies are usually interrupted by mismatches and that base pairing within 6 nucleotides of the …

Immature Acta2r179c/+ Smooth Muscle Cells Cause Moyamoya-Like Cerebrovascular Lesions In Mice Prevented By Boosting Oxphos, Anita Kaw, Suravi Majumder, Jose E Esparza Pinelo, Ting Wu, Zbigniew Starosolski, Zhen Zhou, Albert J Pedroza, Xueyan Duan, Kaveeta Kaw, Angie D Gonzalez, Ripon Sarkar, Michael P Fischbein, Philip L Lorenzi, Lin Tan, Sara A Martinez, Iqbal Mahmud, Laxman Devkota, L Maximilian Buja, Heinrich Taegtmeyer, Ketan B Ghaghada, Sean P Marrelli, Callie S Kwartler, Dianna M Milewicz

Faculty, Staff and Student Publications

ACTA2 pathogenic variants altering arginine 179 cause childhood-onset strokes due to moyamoya disease (MMD)-like occlusions of the distal internal carotid arteries, but the mechanisms of pathogenesis are unknown and no preventive treatments exist. Here we show that Acta2R179C/+ smooth muscle cells (SMCs) fail to fully differentiate and maintain stem cell-like features, including increased migration and glycolytic flux compared to wildtype (WT) SMCs. Increasing mitochondrial respiration with nicotinamide riboside (NR) drives differentiation and decreases migration of Acta2R179C/+ SMCs. Carotid artery injury of Acta2SMC-R179C/+ mice leads to premature death, intraluminal SMC accumulation leading to MMD-like occlusive lesions, neurologic symptoms, …

A Hedgehog-Foxf Axis Coordinates Dental Follicle-Derived Alveolar Bone Formation, Mizuki Nagata, Gaurav T Gadhvi, Taishi Komori, Yuki Arai, Chiaki Tsutsumi-Arai, Angel Ka Yan Chu, Seth N Nye, Yuntao Yang, Shion Orikasa, Akira Takahashi, Peter Carlsson, W Jim Zheng, Joshua D Welch, Noriaki Ono, Wanida Ono

Faculty, Staff and Student Publications

The alveolar bone is a specialized mineralized structure supporting the lifelong functionality of the tooth in mastication. The alveolar bone develops from the dental follicle (DF) during tooth root formation due to deliberate epithelial-mesenchymal interactions. However, how DF progenitor cell fates are regulated toward alveolar bone osteoblasts remains unknown. We find that Hedgehog signaling activities are transiently activated during the onset of tooth root formation and alveolar bone formation. Parathyroid hormone-related protein (PTHrP)-expressing DF cells are highly responsive to Hedgehog signaling, yet constitutive Hedgehog activation using Pthrp-creER and Ptch1-floxed alleles potently suppresses alveolar osteoblast and ligament differentiation of PTHrP+ DF …