Digital Commons Network^™

Spectral Divergence Prioritizes Key Classes, Genes, And Pathways Shared Between Substance Use Disorders And Cardiovascular Disease., Everest Castaneda, Elissa J Chesler, Erich Baker

Faculty Research 2025

Introduction: Substance use disorders (SUDs) are heterogeneous diseases with overlapping biological mechanisms and often present with co-occurring disease, such as cardiovascular disease (CVD). Gene networks associated with SUDs also implicate additional biological pathways and may be used to stratify disease subtypes. Node and edge arrangements within gene networks impact comparisons between classes of disease, and connectivity metrics, such as those focused on degrees, betweenness, and centrality, do not yield sufficient discernment of disease network classification. Comparatively, the graph spectrum's use of comprehensive information facilitates hypothesis testing and inter-disease clustering by using a larger range of graph characteristics. By adding a …

Response Of Cultured Primary Gingival And Periodontal Ligament Cells To Angiotensin Ii And Il1Β Challenges., Thais Francini Garbieri, Thiago José Dionísio, Bella Luna Colombini-Ishikiriama, Rafaela Alves Da Silva, Vanessa Soares Lara, Sandra Helena Penha Oliveira, Maria Helena Fernandes, Andrew S Greene, Carlos Ferreira Santos

Faculty Research 2025

Angiotensin II (Ang II) releases inflammatory mediators from several cell types. The objective of this study was to investigate the potential of Ang II to induce mRNA expression of inflammatory mediators in primary cultured fibroblast-like cells isolated from gingival and periodontal ligament tissues. A synergistic effect of co-treatment with Ang II and Interleukin-1β (IL1β) on the mRNA expression of inflammatory mediators was explored. Immunophenotyping of STRO-1, Ang II type 1 receptor (AT1R), and Ang II type 2 receptor (AT2R) was performed using flow cytometry. Cell cultures were challenged with Ang II (1 µM) for 3, 6, and 24 h with …

Opportunities And Considerations For Using Artificial Intelligence In Bioinformatics Education., Stephen R Piccolo, Aparna Nathan, Michelle D Brazas, Manoj Kandpal, Aida T Miró-Herrans, Adam J Kleinschmit, Susan Mcclatchy, Pertunia Mutheiwana, Dusanka Nikolic, Luciana I Gallo, Rolanda Sunaye Julius, Marta Lloret-Llinares, Nicola Mulder, Danielle Presgraves, Sonal Shewaramani, Jorge Xool-Tamayo, Frédéric J J Chain, Silvia Arantza Sanchez Guerrero

Faculty Research 2025

Artificial intelligence (AI) tools and techniques are undoubtedly being used in bioinformatics education, reflecting broader trends in education. However, many instructors and learners may be unaware of the full scope of potential uses for these tools within bioinformatics education, as well as effective practices for using them. Building on discussions held at the 6th Global Bioinformatics Education Summit, this perspective article provides insights about ways that AI might be used to generate or adapt instructional content, provide personalized help for learners, and automate assessment and grading. Additionally, we highlight AI skills that are important for bioinformatics learners to develop in …

From Gene Modules To Gene Markers: An Integrated Ai-Human Approach Selects Cd38 To Represent Plasma Cell-Associated Transcriptional Signatures., Basirudeen Syed Ahamed Kabeer, Bishesh Subba, Darawan Rinchai, Mohammed Toufiq, Taushif Khan, Marina Yurieva, Damien Chaussabel

Faculty Research 2025

BACKGROUND: Knowledge-driven prioritization of candidate genes derived from large-scale molecular profiling data for targeted transcriptional profiling assays is challenging due to the vast amount of biomedical literature that needs to be harnessed. We present a workflow leveraging Large Language Models (LLMs) to prioritize candidate genes within module M12.15, a plasma cell-associated module from the BloodGen3 repertoire, by integrating knowledge-driven prioritization with data-driven analysis of transcriptome profiles.

METHODS: The workflow involves a two-step process: (1) high-throughput screening using LLMs to score and rank the 17 genes of module M12.15 based on six predefined criteria, and (2) prioritization employing high-resolution scoring and …

Ct-Derived Fat Density As A Predictor Of Cause-Specific Mortality In Patients Undergoing Tavi: Findings From A Large Registry Subanalysis., Matej Pekař, Piotr Branny, Radim Špaček, Otakar Jiravský, Jan Novák, Jakub Balušík, Daniel Daniš, Jan Hečko, Marek Kantor, Bogna Jiravská Godula, Lubomír Blaha, Radek Neuwirth, Martin Šimek

Faculty Research 2025

Transcatheter aortic valve implantation (TAVI) is increasingly performed in older and frailer patients with severe aortic stenosis. Pre-procedural computed tomography (CT) scans at the third lumbar vertebra (CTL3) can estimate overall patient survival after TAVI [1, 2]. This subanalysis investigated whether CTL3 parameters can predict specific causes of death, potentially allowing for more tailored post-operative therapy.

Marmosets As Model Systems For The Study Of Alzheimer's Disease And Related Dementias: Substantiation Of Physiological Tau 3r And 4r Isoform Expression And Phosphorylation., Hasi Huhe, Sarah M Shapley, Duc M Duong, Fang Wu, Seung-Kwon Ha, Sang-Ho Choi, Julia Kofler, Yongshan Mou, Thais Rafael Guimaraes, Amantha Thathiah, Caroline M Watson, Lauren K H Schaeffer, Gregory W. Carter, Nicholas T Seyfried, Afonso C Silva, Stacey J Sukoff Rizzo

Faculty Research 2025

INTRODUCTION: Marmosets spontaneously develop pathological hallmarks of Alzheimer's disease (AD) including amyloid beta plaques. However, tau expression in the marmoset brain has been understudied.

METHODS: Isoforms of tau were examined by western blot, mass spectrometry, immunofluorescence, and immunohistochemical staining.

RESULTS: 3R and 4R tau isoforms are expressed in marmoset brains at both the transcript and protein levels across ages. Mass spectrometry analysis revealed that tau peptides in marmoset corresponded to the 3R and 4R peptides in human brain, with 3R predominating at birth and an ≈40%:60% 3R:4R ratios in adolescents and adults; tau was distributed widely in neurons, with localization …

Biological Databases In The Age Of Generative Artificial Intelligence., Mihai Pop, Teresa K Attwood, Judith A. Blake, Philip E Bourne, Ana Conesa, Terry Gaasterland, Lawrence Hunter, Carl Kingsford, Oliver Kohlbacher, Thomas Lengauer, Scott Markel, Yves Moreau, William S Noble, Christine Orengo, B F Francis Ouellette, Laxmi Parida, Natasa Przulj, Teresa M Przytycka, Shoba Ranganathan, Russell Schwartz, Alfonso Valencia, Tandy Warnow

Faculty Research 2025

SUMMARY: Modern biological research critically depends on public databases. The introduction and propagation of errors within and across databases can lead to wasted resources as scientists are led astray by bad data or have to conduct expensive validation experiments. The emergence of generative artificial intelligence systems threatens to compound this problem owing to the ease with which massive volumes of synthetic data can be generated. We provide an overview of several key issues that occur within the biological data ecosystem and make several recommendations aimed at reducing data errors and their propagation. We specifically highlight the critical importance of improved …

Replacing Non-Biomedical Concepts Improves Embedding Of Biomedical Concepts., Enock Niyonkuru, Mauricio Soto Gomez, Elena Casarighi, Stephan Antogiovanni, Hannah Blau, Justin T Reese, Giorgio Valentini, Peter N Robinson

Faculty Research 2025

Embeddings are semantically meaningful representations of words in a vector space, commonly used to enhance downstream machine learning applications. Traditional biomedical embedding techniques often replace all synonymous words representing biological or medical concepts with a unique token, ensuring consistent representation and improving embedding quality. However, the potential impact of replacing non-biomedical concept synonyms has received less attention. Embedding approaches often employ concept replacement to replace concepts that span multiple words, such as non-small-cell lung carcinoma, with a single concept identifier (e.g., D002289). Also, all synonyms of each concept are merged into the same identifier. Here, we additionally leveraged WordNet to …

Merritt-Putnam Symposium | Developmental And Epileptic Encephalopathies-Current Concepts And Novel Approaches., Rodney C Scott, Jenny Hsieh, Amy Mctague, J Matthew Mahoney, Catherine A Christian-Hinman

Faculty Research 2025

Developmental and epileptic encephalopathies (DEEs) are among the most severe and difficult to treat epilepsies. Two broad strategies for understanding the etiology and impacts of DEEs include genetic and complex adaptive systems approaches. This review, inspired by the 2024 Merritt-Putnam Symposium, describes current perspectives of DEE, identifies limitations of current views, and discusses potential novel ways forward. First, we discuss the rationale for a reevaluation of the role of seizures in the pathogenesis of cognitive and behavioral impairments in DEE. Second, we discuss newly emerging methods employing neural organoids to study brain development and DEE in vitro. Third, we present …

Comprehensive Single-Cell Aging Atlas Of Healthy Mammary Tissues Reveals Shared Epigenomic And Transcriptomic Signatures Of Aging And Cancer., Brittany Lynn Angarola, Siddhartha Sharma, Neerja Katiyar, Hyeon Gu Kang, Djamel Nehar-Belaid, Sunghee Park, Rachel Gott, Giray N Eryilmaz, Mark A Labarge, Karolina Palucka, Jeffrey Chuang, Ron Korstanje, Duygu Ucar, Olga Anczuków

Faculty Research 2025

Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. In this study, we investigated how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single-cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory and cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk⁺, memory CD4⁺, γδ) and M2-like macrophages expand with age. …

Reproductive Experience Drives Changes In Behaviour And Physiology In Male California Mice, Peromyscus Californicus, Maria E. Colt, Priyanka Agarwal, David Kolb, Erica Glasper, Heidi Fisher

Faculty Research 2025

Paternal experience improves memory and reduces anxiety-like behaviour in males, but it is unclear whether these changes are due to mating, siring offspring or caregiving behaviour. Likewise, paternal males have larger testes, a measure of sperm production, but again, the effects of siring and caregiving experience are difficult to disentangle. We examined behavioural and physiological outcomes in three groups of male mice: (1) virgins, (2) males paired with sterile females (‘nonfathers’) and (3) experienced fathers (experiment 1). Compared to virgins and nonfathers, experienced fathers exhibited increased recognition memory (novel object recognition) and decreased anxiety-like behaviour (elevated plus maze). Virgin males, …

Cell-Based High-Content Approach For Sars-Cov-2 Neutralization Identifies Unique Monoclonal Antibodies And Pi3k Pathway Inhibitors., Carly R Cabel, Briana A Guzman, Elaheh Alizadeh, Shuaizhi Li, Cameron Holberg, Chonlarat Wichaidit, Darren A Cusanovich, Andrew L Paek, Gregory R J Thatcher, Koenraad Van Doorslaer, Rachel S Nargi, Rachel E Sutton, Naveenchandra Suryadevara, James E Crowe, Robert H Carnahan, Samuel K Campos, Curtis A Thorne

Faculty Research 2025

The sudden rise of the SARS-CoV-2 virus and the delay in development of effective therapeutics for mitigation made evident a need for ways to screen compounds that can block infection and prevent further pathogenesis and spread. However, identifying effective drugs that are efficacious against viral infection and replication with minimal toxicity for the patient can be difficult. Monoclonal antibodies were shown to be effective, but as the SARS-CoV-2 mutated, these antibodies became ineffective. Small-molecule antivirals were identified using pseudovirus constructs to recapitulate infection in nonhuman cells, such as Vero E6 cells. However, the impact was limited due to poor translation …

Intracranial Germ Cell Tumors: Advancement In Genomic Diagnostics And The Need For Novel Therapeutics., Kee Kiat Yeo, Joanna J Gell, Girish Dhall, Ching C Lau

Faculty Research 2025

INTRODUCTION: The outcomes for patients with intracranial germ cell tumors (GCT) has improved over the past few decades. However, there remains a lack of a consensus on a standard diagnostic and treatment approach of these tumors. The diagnostic work-up of intracranial GCT remains variable, and the treatment for patients with recurrent disease remains challenging.

METHODS: We review the current approach in the diagnosis and treatment of intracranial GCT. Given the heterogeneity of these tumors, we highlight the challenges and controversy with these conventional approaches.

RESULTS: We discuss the advancements in the understanding of the underlying genetic changes in intracranial GCT …

The Cd123 Antibody-Drug Conjugate Pivekimab Sunirine Exerts Profound Activity In Preclinical Models Of Pediatric Acute Lymphoblastic Leukemia., Ben Watts, Christopher M Smith, Kathryn Evans, Andrew J Gifford, Sara M A Mohamed, Stephen W Erickson, Eric J Earley, Steven Neuhauser, Timothy M Stearns, Vivek M. Philip, Jeffrey Chuang, Patrick A Zweidler-Mckay, Sribalaji Lakshmikanthan, Emily L Jocoy, Carol J Bult, Beverly A Teicher, Malcolm A Smith, Richard B Lock

Faculty Research 2025

Antibody–drug conjugates (ADCs) combining monoclonal antibodies with cytotoxic payloads are a rapidly emerging class of immune‐based therapeutics with the potential to improve the treatment of cancer, including children with relapse/refractory acute lymphoblastic leukemia (ALL). CD123, the α subunit of the interleukin‐3 receptor, is overexpressed in ALL and is a potential therapeutic target. Here, we show that pivekimab sunirine (PVEK), a recently developed ADC comprising the CD123‐targeting antibody, G4723A, and the cytotoxic payload, DGN549, was highly effective in vivo against a large panel of pediatric ALL patient‐derived xenograft (PDX) models (n = 39). PVEK administered once weekly for 3 weeks resulted …

Rapid Changes In Plasma Corticosterone And Medial Amygdala Transcriptome Profiles During Social Status Change Reveal Molecular Pathways Associated With A Major Life History Transition In Mouse Dominance Hierarchies., Tyler M Milewski, Won Lee, Rebecca L Young, Hans A Hofmann, James P Curley

Faculty Research 2025

Social hierarchies are a common form of social organization across species. Although hierarchies are largely stable across time, animals may socially ascend or descend within hierarchies depending on environmental and social challenges. Here, we develop a novel paradigm to study social ascent and descent within male CD-1 mouse social hierarchies. We show that mice of all social ranks rapidly establish new stable social hierarchies when placed in novel social groups with animals of equivalent social status. Seventy minutes following social hierarchy formation, males that were socially dominant prior to being placed into new social hierarchies exhibit higher increases in plasma …

Single-Cell And Bulk Transcriptional Profiling Of Mouse Ovaries Reveals Novel Genes And Pathways Associated With Dna Damage Response In Oocytes., Monique Mills, Chihiro Emori, Parveen Kumar, Zachary Boucher, Joshy George, Ewelina Bolcun-Filas

Faculty Research 2025

Immature oocytes enclosed in primordial follicles stored in female ovaries are under constant threat of DNA damage induced by endogenous and exogenous factors. Checkpoint kinase 2 (CHEK2) is a key mediator of the DNA damage response (DDR) in all cells. Genetic studies have shown that CHEK2 and its downstream targets, p53, and TAp63, regulate primordial follicle elimination in response to DNA damage. However, the mechanism leading to their demise is still poorly characterized. Single-cell and bulk RNA sequencing were used to determine the DDR in wild-type and Chek2-deficient ovaries. A low but oocyte-lethal dose of ionizing radiation induces ovarian DDR …

Wild Horse Overpopulation- Consequences And Environmental Effects, Tessa M. Eslick Ms.

Undergraduate Theses, Professional Papers, and Capstone Artifacts

When considering wild horse overpopulation, there are many different facets of the issue that need to be addressed. Wild horse overpopulation is a significant issue across the American West, particularly on lands managed by the Bureau of Land Management( BLM). The largest populations are often found in Nevada, other states include California, Oregon, Utah, Wyoming, Washington, and Arizona. Whether there are thousands of horses on many acres of land, or hundreds spread across smaller reservations or public lands, the effects of their overpopulation remain as imminent as ever. Overpopulation is causing ecological damage and strain on resources leading to concerns …

Moving Beyond Traditional Multiculturalism: Dis/Ability Awareness In Counselor Education, Alicia B. Becton, Eunae Han, Leeza Ong, Amber Johnson, Roy K. Chen, Gabriela Rangel, Stephanie Lusk

School of Rehabilitation Services & Counseling Faculty Publications

This chapter explores the experiences of individuals with disabilities, emphasizing how they navigate educational and societal norms while balancing various identities. It emphasizes the impact of societal issues, such as racism and sexism, on individuals with disabilities. The authors delve into current multiculturalism trends, advocating for culturally responsive approaches in counselor education and rehabilitation services. The goal is to advance discussions on the future directions of multiculturalism by exploring the following key areas (a) the sociopolitical aspects of disability, (b) the inclusion of disability in counselor education, (c) accessibility and the universal design for learning (UDL), (d) culturally competent counselor …

The Path To Zero Clabsis: The Benefits Of Central Line Care Teams, Supplemental Checklist, Increased Education And Utilizing Clabsi Bundles, Lauren A. Bondurant

Doctor of Nursing Practice Projects

Central line-associated bloodstream infections (CLABSIs) result in a plethora of deaths each year and cost the U.S. healthcare system billions of dollars (Centers for Disease Control and Prevention, 2024). CLABSIs have been a type of bloodstream infection that has affected a plethora of individuals for years and one that does not discriminate patient type. Many articles were reviewed, but they all inferred that CLABSIs bundles,supplemental checklists, and central line care teams all showed the most significant data and resulted in the most decreased CLABSI rates. Upon assessment of the project unit, it was noted that the issue that most impacted …

Exploring Law Enforcement Officers' Experiences With Athletic Trainers And Work-Related Injury, Stephanie H. Clines, Rubie Gaudette, Amanda Wheeler, Jennifer Ostrowsk

Athletic Training Faculty Publications

Law enforcement is an emerging clinical setting for athletic trainers (ATs), yet little is known regarding law enforcement officers (LEOs) perceptions of the profession. This qualitative study following a general inductive approach explored LEOs' experiences with musculoskeletal injury and their interactions with ATs. Seven officers (N = 7) participated in one-on-one semi-structured interviews. Three themes emerged: (1) roles and responsibilities of ATs, (2) education and training, and (3) impact of injury on LEOs. While participants viewed ATs positively, they demonstrated limited understanding of the profession's scope and expertise. Participants commonly described managing musculoskeletal injuries on their own due to …

Weeping In The Household: Equipping Pastoral Caregivers Among Grieving Families At Grace Presbyterian Church In Baltimore, Maryland, Charles Brandon Brewer

Doctor of Ministry Projects

This project sought to equip pastoral care ministry members of Grace Presbyterian Church to explore communal grief and deepen their own understanding of family systems in intergenerational grief. Participants engaged in a four-week training series aimed at reducing fear surrounding discussions of death, dying, and grief, empowering pastoral caregivers in the church to offer compassionate care to grieving individuals and families. Participants were trained to facilitate Bible studies, group discussions and were equipped with the skills necessary to guide and expand the church’s existing bereavement ministry beyond crisis intervention, strengthening pastoral care efforts, and the pastoral care ministry of the …

Contracting For Children: Frozen Embryo Disposition Through The Lens Of Assent, Gabrielle Gomozias

California Western Law Review

No abstract provided.

University Of New Mexico Health Sciences Center Discovery Research Annual Report 2025, Michael Haderle, Kandace Donaldson, Brianna Mortensen, Christina V. Rodriguez, Jill Rothenberg, Bryan Schroeder

Research Annual Reports

Annual research report from the University of New Mexico Health Sciences Center.

Contents 43(1)

Aliso: A Journal of Systematic and Floristic Botany

No abstract provided.

A Vascular Flora Of Ladd Canyon, Santa Ana Mountains, Orange And Riverside Counties, California, Daniel P. Donovan, Amanda E. Fisher

Aliso: A Journal of Systematic and Floristic Botany

The Santa Ana Mountains are a coastal range on the border of Orange and Riverside counties in southern California. Ladd Canyon, covering 18.2 km² in the Cleveland National Forest, is a botanical black hole relative to the rest of the Santa Ana Mountains because of limited access. It is dominated by chaparral and coastal sage scrub and includes significant knobcone pine (Pinus attenuata) stands and riparian woodland. Features that make it an intriguing area to study include the only serpentine soil in the Santa Ana Mountains, large tracts of habitat that have no recorded fire history, steep …

Contents 43(2)

Aliso: A Journal of Systematic and Floristic Botany

No abstract provided.

The Rare, Endangered And Endemic Plants Of The California Floristic Province Portion Of Baja California, Mexico, Bart C. O'Brien, Jon P. Rebman, José Delgadillo-Rodríguez, Kanchi Natarajan Gandhi, Steven A. Junak, Thomas A. Oberbauer, Hugo Riemann, Sula E. Vanderplank

Aliso: A Journal of Systematic and Floristic Botany

The California Floristic Province (CFP) is one of the world’s biodiversity hotspots, known for high levels of plant endemism. The CFP extends from southwestern Oregon, through cismontane California, south to northwestern Baja California, Mexico. The flora of the California Floristic Province portion of Baja California (CFP Baja) has historically been poorly documented and understood. This study provides data to address this deficiency by inventorying and assessing the native flora of CFP Baja from a conservation perspective: evaluating the rarity, endangerment and endemism of its native taxa. A total of 2392 taxa were assessed to determine this listing of rare, endangered …

Swosu Research And Scholarly Activity Fair 2025, Swosu Office Of Sponsored Programs

SWOSU Research and Scholarly Activity Fair Programs

On behalf of the members of the University Research and Scholarly Activity Committee (USRAC) and the Office of Sponsored Programs (OSP) at Southwestern Oklahoma State University (SWOSU) — welcome to the Thirty-Third SWOSU Research and Scholarly Activity Fair!

This year’s event features 99 poster presentations and 9 oral presentations, showcasing the work of over 170 student and faculty researchers, writers, presenters, artists, collaborators, and faculty sponsors. These presentations represent a wide array of scholarly and academic activity from across SWOSU’s academic community, including the Departments of Art, Communication, and Theatre; Allied Health Sciences; Biological Sciences; Business; Chemistry & …

Overcoming Judicial Innumeracy: A Proposal To Bring The Venerable Process Of Peer Review To The Enduring Problem Of Courts’ Scientific Illiteracy, David L. Faigman

Faculty Scholarship

Lawyers are not known for their proficiency in math and science. Most of us who went to law school reached a point in our math and science studies when we realized that neither medicine nor engineering were likely to be successful career paths. It is these lawyers who become judges. Yet, the United States Supreme Court has increasingly put the burden for deciding complex scientific and technical questions in the hands of judges. This Article explores this trend of putting greater responsibility for deciding scientific and technical issues on judges, particularly in the areas of evidence law, administrative law, and …

Folliculin (Flcn) In Thyroid Tumors: Incidence, Significance, And Role As A Driver Gene And Secondary Alteration, Faisal Hassan, Camryn Slone, Robert J. Mcdonald, Julie C. Dueber, Adeel M. Ashraf, Melina Windon, Oliver J. Fackelmayer, Cortney Y. Lee, Therese J. Bocklage, Derek B. Allison

Pathology and Laboratory Medicine Faculty Publications

Thyroid carcinomas are driven by diverse molecular alterations, but the tumor suppressor gene folliculin (FLCN), best known for its role in Birt–Hogg–Dubé (BHD) syndrome, has received limited attention in thyroid tumors. Here, we describe two thyroid tumors with pathogenic FLCN alterations—one germline and one somatic—and analyze the broader prevalence and significance of FLCN in thyroid carcinomas using multiple large sequencing datasets, including ORIEN-AVATAR. Patient 1, with a germline FLCN mutation and a history of BHD syndrome, presented with a well-circumscribed oncocytic adenoma. Molecular testing confirmed biallelic FLCN inactivation, but no additional mutations or aggressive features were observed, and the patient …