Digital Commons Network^™

Point-Of-Care Ultrasound For Guiding Pulmonary Artery Catheter Placement, Erik Su, Saul Flores

Faculty, Staff and Students Publications

No abstract provided.

A Phenotypic Screen Identifies Xanthohumol And Other Flavonoids As Killers Of Bladder Cancer, Michael J Bolt, Jessica Oceguera, Alejandra Rivera Tostado, Christopher D Candler, Elina Mosa, Kazem Safari, Maureen G Mancini, Michael A Mancini

Faculty, Staff and Students Publications

Bladder cancer accounts for 4 % of cancer diagnoses in the US. Current treatments primarily involve trans-urethral resection of bladder tumors (TURBT) and immunotherapy with Bacille Calmette-Guerin (BCG). Despite the efficacy of TURBT, issues with residual tumors persist. We chose to utilize Cell Painting to screen a set of 244 flavonoid compounds for bladder cancer cell toxicity. Using multiparametric high content analysis termed SPACe, we discover promising candidates underscoring the potential of flavonoids in targeting bladder cancer cells and elucidating their mechanisms of action. Notably, compounds such as xanthohumol show promise in reducing cancer cell viability by altering lipid metabolism. …

Graphage: Unleashing The Power Of Graph Neural Network To Decode Epigenetic Aging, Saleh Sakib Ahmed, Nahian Shabab, Abul Hassan Samee, M Sohel Rahman

Faculty, Staff and Students Publications

DNA methylation is a crucial epigenetic marker used in various clocks to predict epigenetic age. However, many existing clocks fail to account for crucial information about CpG sites and their interrelationships, such as co-methylation patterns. We present a novel approach to represent methylation data as a graph, using methylation values and relevant information about CpG sites as nodes, and relationships like co-methylation, same gene, and same chromosome as edges. We then use a graph neural network (GNN) to predict age. Thus our model, GraphAge leverages both the structural and positional information for prediction as well as better interpretation. Although, we …

An Electronic, Preclinic, Social Determinants Survey Shows Pediatric Atherosclerotic Risk Factor Referral Identifies At-Risk Families, Justin R Rahman, Bethany S Zachariah, Christina Y Miyake, Deidra Ansah, Justin P Zachariah

Faculty, Staff and Students Publications

Objective: Atherosclerotic risk factors are prevalent in childhood. Risk factors are associated with social determinants of health (SDoH), but have never been demonstrated in a clinical pediatric cardiology cohort. This report details the first use of a remotely deployed, previsit, self-administered electronic survey for the ascertainment of SDoH in youth referred to pediatric cardiology. We hypothesized that patients referred for atherosclerotic risk factors would have higher risk of SDoH factors.

Study design: SDoH were assessed using validated instruments from the PRAPARE toolkit and the Accountable Health Communities Health-Related Social Needs Screening Tool automatically deployed days before a scheduled visit in …

Innovations In Intestinal Organoid Technology Featuring An Open Apical Surface, Ye Chen, Yi Wang

2020-Current year OA Pubs

Since the development of the three-dimensional (3D) "mini-gut" culture system, adult stem cell-derived organoid technology has rapidly advanced, providing in vitro models that replicate key cellular, molecular, and physiological properties of multiple organs. The 3D intestinal organoid system has resolved many long-standing challenges associated with immortalized or cancer cell cultures, offering unparalleled capabilities for modeling gastrointestinal development and diseases. However, significant limitations remain, including restricted accessibility to the epithelial apical surface for studying host-microbe interactions, interruptions in modeling chronic gastrointestinal diseases due to frequent passaging and dissociation, and the absence of mechanical cues such as peristalsis and luminal flow, which …

Rna Interference In Protozoan Parasites And Its Application, Lon-Fye Lye, Deborah E Dobson, Stephen M Beverley, Min-Che Tung

2020-Current year OA Pubs

RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression, via small RNA triggers derived from double-stranded RNA that can target specific genes; it is a natural process that plays a role in both the regulation of protein synthesis and in immunity. Discovery of RNAi by Fire and Mello in 1998 had a profound impact on unraveling novel aspects of eukaryotic biology. RNA interference (RNAi) has proven to be an immensely useful tool for studying gene function and validation of potential drug targets in almost all organisms. A great advance in …

Claustrum Volume Is Reduced In Multiple Sclerosis And Predicts Disability, Nicole Shelley, Bradley Judge, Dmitriy A Yablonskiy, Robert T Naismith, Matthew R Brier, Anne H Cross

2020-Current year OA Pubs

OBJECTIVE: The claustrum is a small, thin structure of predominantly gray matter with broad connectivity and enigmatic function. Little is known regarding the impact of claustrum pathology in multiple sclerosis (MS).

METHODS: This study assessed whether claustrum volume was reduced in MS and whether reductions were associated with specific disability domains. We compared the impact of claustrum volume reductions on neurological disability versus the well-studied thalamus. Data from the 15,793 participants in the MS PATHS study were used for primary analyses. A second cohort of 71 people with MS and healthy controls from our center was used for validation.

RESULTS: …

Screpertoire 2: Enhanced And Efficient Toolkit For Single-Cell Immune Profiling, Qile Yang, Ksenia R. Safina, Kieu Diem Quynh Nguyen, Zewen Kelvin Tuong, Nicholas Borcherding

2020-Current year OA Pubs

Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a transformative approach to profiling immune responses at unprecedented resolution across diverse pathophysiologic contexts. This work presents scRepertoire 2, a substantial update to our R package for analyzing and visualizing single-cell immune receptor data. This new version introduces an array of features designed to enhance both the depth and breadth of immune receptor analysis, including improved workflows for clonotype tracking, repertoire diversity metrics, and novel visualization modules that facilitate longitudinal and comparative studies. Additionally, scRepertoire 2 offers seamless integration with contemporary single-cell analysis frameworks like Seurat and …

Nf2 Loss-Of-Function And Hypoxia Drive Radiation Resistance In Grade 2 Meningiomas, Bhuvic Patel, Sangami Pugazenthi, Shree S Pari, Tatenda Mahlokozera, William A Leidig, Hsiang-Chih Lu, Alicia Yang, Kaleigh Roberts, Patrick Desouza, Kyle P Mcgeehan, Diane D Mao, Namita Sinha, Joseph E Ippolito, Sonika Dahiya, Hiroko Yano, Albert H Kim, Et Al.

2020-Current year OA Pubs

BACKGROUND: World Health Organization Grade 2 meningiomas (G2Ms) often recur and resist therapies. Grade 2 meningiomas with histopathological necrosis have been associated with worse local control (LC) after radiation therapy, but the drivers and biomarkers of radiation resistance in G2Ms remain unknown.

METHODS: We performed genetic sequencing and histopathological analysis of 113 G2Ms and investigated the role of genetic and microenvironmental factors on clonogenic survival after ionizing radiation. We performed transcriptional profiling of our in vitro model and 18 human G2M tumors by bulk RNA sequencing as well as 8 G2Ms by single nuclei RNA sequencing.

RESULTS: NF2 loss-of-function (LOF) …

Biological Age Acceleration Associated With The Progression Trajectory Of Cardio-Renal–Metabolic Multimorbidity: A Prospective Cohort Study, Yixing Tian, Jinqi Wang, Tianyu Zhu, Xia Li, Haiping Zhang, Xiaoyu Zhao, Xinghua Yang, Yanxia Luo, Lixin Tao, Zhiyuan Wu, Xiuhua Guo

Research outputs 2022 to 2026

Objectives: Previous studies have confirmed that biological age (BA) acceleration is associated with single cardio-renal–metabolic diseases (CRMDs), typically including type 2 diabetes mellitus, cardiovascular disease, and chronic kidney disease. However, its association with progression to cardio-renal–metabolic multimorbidity (CRMM, coexistence of ≥2 CRMDs) and subsequent mortality remains unexplored. Methods: Using the multi-state model, we analyzed 278,927 UK Biobank participants free of CRMDs at baseline to investigate the association between BA acceleration—measured by phenotypic age (PhenoAge) and Klemera–Doubal method age (KDMAge)—and CRMM progression trajectory, from health to the first CRMD and then to CRMM and death. BA acceleration was the residual from …

Pre-Amplification Of Cell-Free Dna: Balancing Amplification Errors With Enhanced Sensitivity, Wei Yen Chan, Ashleigh Stewart, Russell J. Diefenbach, Elin S. Gray, Jenny H. Lee, Richard A. Scolyer, Georgina V. Long, Helen Rizos

Research outputs 2022 to 2026

Circulating tumour DNA (ctDNA) is a promising biomarker for personalised oncology. However, its clinical utility is limited by detection sensitivity, particularly in early-stage disease. T-Oligo Primed Polymerase Chain Reaction (TOP-PCR) is a commercial amplification approach utilising an efficient “half-adapter” ligation design and a single-primer-based PCR strategy. This study evaluated the clinical value and application of cell-free DNA (cfDNA) pre-amplification. cfDNA amplification with TOP-PCR preserved DNA size profiles and resulted in a 22 bp size increase due to the half-adaptor ligation. Gene target amplification rates varied, showing lower efficiency for the GC-rich TERT promoter amplicon and higher efficiency for the BRAF …

The Evolution Of Sprinting Performance: Technological And Regulatory Influences From 1976 To 2024, Dariusz Tadeusz Skalski, Magdalena Prończuk, Kinga Łosińska, Ewelina Lulińska, Joanna Motowidło, Petr Stastny, Adam Maszczyk, Grzegorz Trybek

Baltic Journal of Health and Physical Activity

Background: This study examines the progression of sprinting performance across the 100m, 200m, and 400m events from 1976 to 2024, highlighting the influence of technological advancements and regulatory changes. Over the past decades, sprinting has been significantly shaped by developments in track surfaces, footwear technology, training methodologies, and regulatory frameworks. Understanding these factors is essential for assessing how sprint times have evolved and what future trends might emerge. Materials and methods: Utilizing a comprehensive dataset from international athletics federations, this research applies time series analysis, regression modeling, and variance testing to assess trends, gender disparities, and performance variability. Data sources …

Gamified Gait Rehabilitation Via Real-Time Biofeedback And Adaptive Hip-Exoskeleton Control, Mariya Huzaifa Tohfafarosh

Theses

Gait impairments arise from systemic diseases, age-related degeneration, musculoskeletal dysfunctions, or neurological conditions. While traditional rehabilitation can be effective, they often face challenges such as high costs, inaccessibility, and low patient engagement. To address these challenges, my work introduces a virtual reality-based rehabilitation (VRBR) system, integrating real-time motion and electromyographic (EMG) muscle activation feedback with a gamified virtual environment for enhanced adaptability and engagement. The system includes a custom-designed hip-exoskeleton that provides adaptive spring-like assistance or resistance, supporting both mobility-impaired users and strength training. Assistance levels can be tuned to match the user's progress. Additionally, a custom pressure insole was …

High Prevalence Of Diabetes Mellitus Among Patients With Fabry Disease In Taiwan: A Cross-Sectional Study, Shih Han Hung, Sudha Xirasagar Mbbs., Ph.D, Yen Fu Cheng, Herng Ching Lin, Chin Shyan Chen

Publications

Objectives This study aimed to investigate the prevalence of diabetes mellitus in patients with Fabry disease using a nationwide population-based dataset. We hypothesised that patients with Fabry disease would have a higher prevalence of diabetes mellitus compared with the general population. Design A cross-sectional study. Setting Taiwan. Participants We identified a study sample from Taiwan's LHID2010 Database. There were 9408 sampled patients in this study, 2352 study patients with Fabry disease and 7056 propensity-score-matched comparison patients. Primary outcome measures Multiple logistic regression analyses were conducted to explore the association between diabetes mellitus and Fabry disease after taking the variables of …

Gust, Stroll, Veil, Jungeun Park

Masters Theses

I witness the unsettling and chaotic moments of everyday life:

blood clots in fried eggs, a dead rat on my porch, mites crawling on our skin . . .

These quiet tragedies exist with almost brutal indifference!

We eat, digest, excrete. We menstruate. We parasitize. We coexist.

I seek the intersection of repulsion and wonder in my daily experience and body sensations, visualizing unseen stimuli. I employ veil as a strategy. It conceals yet reveals. Sometimes, it acts as a transparent layer, sharpening what lies beneath. Other times, it blurs colors and forms, rendering them ambiguous. Veil transforms, entices, and …

Navigating Crisis: A Qualitative Exploration Of Parents' Journeys With Suicidal Adolescents In Australian Emergency Departments, Demee Rheinberger, Lauren Mcgillivray, Fiona Shand, Sally Ann Pollard, Susanne Oliver Armstrong, Julia Lessing, Katherine Boydell

The Qualitative Report

Rates of emergency department (ED) presentations for suicide crisis (thoughts, feelings, plans and behaviours) in adolescents are increasing. Parents play a key role in supporting adolescents during and after the ED presentation, however little is known about parental experiences in the ED. Interviews with 20 parents from across Australia were undertaken to help understand this experience. A reflexive thematic analysis was conducted, resulting in three themes which explore the impact of the suicide crisis and ED presentation on the parents’ sense of identity. First, parents’ identity was threatened as they were faced with the juxtaposition between the role of protector …

Gradiance: A Mindfulness Intervention, Kip Geddes

Masters Theses

People in cities live life at a fast paced forward march that results in a mental state called ‘hurry sickness’. This prevents them from living in the moment, which often leads to a disconnection to those around them. Mindfulness techniques have been proven to increase people’s levels of happiness and openness to the people around them. However, many people are too busy to practice these methods. My thesis looks at ways for mindfulness to intervene into their established routines. Illumination has been shown to promote mental well-being, either in therapy lamps, or circadian rhythm based lighting; the liminal spaces that …

Field Journal: The Excluded Middle, Carrie E. Kouts

Masters Theses

What does it look like to engage with organisms and landscapes at the periphery of anthropocentric value structures? How does one break the internalized myth that the “built” environment is excluded from the natural world? When does a hyper-mobile and hyper-commodified society confront the exponential crisis of animal death? Within this series of journal entries, field notes, collection observations, weird prose, and sensory musings, one will find questions on the nature of being human and the complex narratives of care we encounter in a world shared with more-than-humans. Each handwritten vignette and photograph from daily life weaves a non-linear and …

Investigating The Associations Of Cognitive Health, Health Behaviors, And Personality In Older Community-Dwelling Adults, Yan-Jhu Su

Graduate Doctoral Dissertations

Cognitive decline poses a significant public health challenge, with profound implications for aging populations. This dissertation investigates the associations between health behaviors, leisure activities, personality traits, and cognitive function in older U.S. adults, using data from the Health and Retirement Study (HRS) and the Consumption and Activities Mail Survey (CAMS). This work comprises three studies that explore both cross-sectional and longitudinal perspectives on cognitive aging.

Study 1 examines the complex interactions between personality traits, education, health behaviors, and cognitive function. The study is divided into two parts: Study 1a explores the role of health behaviors—smoking, alcohol use, and physical activity—as …

Development Of A Novel Biomarker Platform For Profiling Key Protein-Protein Interactions To Predict The Efficacy Of Bh3-Mimetic Drugs, Andrew J Kinloch, Faiyaz Rahman, Bahriye Karakas, Muhammad Shahid, Bora Lim, Stephanie J Bouley, James A Walker, Erinna F Lee, Walter D Fairlie, Kevin R Kelly, Michael H Cardone

Faculty, Staff and Student Publications

One of the hallmarks of cancer cells is their failure to respond to the cellular mechanism of apoptosis. The B-cell lymphoma 2 (BCL-2) family of proteins regulate apoptosis. Their ability to do so can be measured using several methods that in turn anticipate the fate of the cancer cell in response to apoptosis-inducing treatment. These assays ultimately identify the readiness of the cancer cell to undergo apoptosis, which is referred to as the mitochondrial priming state. These metrics, however, have been challenging to implement in the clinic.

Anti-Viral Cd8 Central Memory Veto Cells As A New Platform For Car T Cell Therapy, Wei-Hsin Liu, Anat Globerson Levin, Assaf Lask, Galit Horn, Tova Waks, Bar Nathansohn Levi, Irit Milman Krentsis, Einav Shoshan, Xiaohua Su, Maksim Mamonkin, Richard E Champlin, Yair Reisner, Esther Bachar Lustig

Faculty, Staff and Student Publications

Central memory CD8 T cells exhibit marked veto activity enhancing engraftment in several mouse models of T cell-depleted bone marrow (TDBM) allografting. Graft-versus-host disease (GVHD) can be prevented by stimulation of mouse or human memory CD8 T cells against their cognate antigens under cytokine deprivation, in the early phase of culture followed by further expansion with IL21, IL15, and IL7. Thus, human anti-viral CD8 central memory veto T cells generated from CMV and EBV-positive donors are currently evaluated in a clinical trial at MD Anderson Cancer Centre (MDACC). Results in 15 patients indicate a low risk of GVHD. Considering that …

A Century Of Innovation: The Ada And The Forsyth Institute Partnership, Manish Chopra Dmd

Metro Denver Dental Society Articulator Magazine

This article details the new partnership between the Forsyth Institute, a century-old leader in dental and craniofacial research, and the American Dental Association to create the ADA Forsyth Institute (AFI). This global research powerhouse is pioneering breakthroughs in oral microbiology, fluoride research, saliva diagnostics and AI-driven smart fillings. The partnership represents a strategic alliance aimed at elevating dental science, education and professional standards.

From 3d-Printed Dentures To Craniofacial Discoveries: The Next Chapter In Dental Research, Laura Ramsey

Metro Denver Dental Society Articulator Magazine

This article highlights the details and importance of the University of Colorado School of Dental Medicine 40th annual Research Day by spotlighting research initiatives shaping the future of oral health. Faculty, students, and guest experts explored topics ranging from 3D-printed antimicrobial dentures and craniofacial development to global cleft care in Nepal and the integration of sex and gender in research methodologies. Dual keynotes also highlighted the importance of evidence-based education and inclusive research practices.

Risk Factors Associated With Long Covid Among Hospitalized Adults In Several Hospitals In Palembang City, Indonesia, Hotma Martogi Lorensi Hutapea, Mondastri Korib Sudaryo, Arli Aditya Parikesit, Tri Yunis Miko Wahyono, Nelda Aprilia Salim

Kesmas

Long COVID is characterized by one or more symptoms experienced by individuals prior to a COVID-19 infection that last for ≥2 months, and its risk factors remain unclear. This study aimed to identify risk factors associated with long COVID among patients admitted between June 1, 2020, and October 31, 2023, at three referral COVID-19 hospitals in Palembang City, Indonesia. This cohort study included adults who were admitted for ≥5 days. The participant’s medical records were reviewed for admission and discharge dates, sociodemographic and clinical characteristics, and vaccination and therapy status. A standardized and validated instrument was used to assess fatigue …

Colorectal Cancer And The Risk Of Mortality Among Individuals With Suicidal Ideation, Srikanta Banerjee, Jagdish Khubchandani, Stanley Nkemjika

Department of Psychiatry and Human Behavior Faculty Papers

Suicide is a major public health problem that has grown at alarming rates in the last two decades. Colorectal cancer (CRC) is one of the most common causes of cancer deaths in the United States in both males and females. However, the influence of suicidal ideation (SI) on the association between CRC and risk of mortality has not been well examined.

METHODS: For this study, the 2005-2018 National Health and Nutrition Examination Survey (NHANES), a nationally representative survey of United States adults aged 20 years or older, was utilized. CRC survivorship was determined from self-reported data on CRC, and mortality …

Characterizing Genetic, Epigenetic, Nutritional, And Clinico-Biochemical Profile Of Women With Polycystic Ovary Syndrome: A Case-Control Study, Woroud M. Majd Chaker, Raghda Mohammed Adi, Mohamed Madkour, Nada Farhat, Dana N. Abdelrahim, Maha Saber-Ayad, Jibran Sualeh Muhammad, Ghada Mohammed, Noha Ahmed Mousa, Ameenah Saadi, Arathy Lakshmi, Mai Kazim, Nagla Elhadi Abdalla, Nariman Awad, Fatme Al Anouti, Moezalislam E. Faris

All Works

Objectives: Polycystic ovary syndrome (PCOS) is among the most frequently encountered endocrinopathies in women. This study aimed to characterize the genetic (INSR, FTO, DENND1A, and Nrf2) expressions and epigenetic (DNA methylation) modifications, nutritional, metabolic, inflammatory, and hormonal markers for patients with PCOS in comparison with their age-matched healthy controls. Design & Methods: The study also aimed to assess the genetic expressions concerning vitamin D status. Sixty-six patients with PCOS and 69 age-matched healthy controls were recruited. Fasting blood samples were used to measure genetic and biochemical variables. Real-time PCR was used to assess gene expressions, the bisulfite conversion method was …

The Evidence Behind The Risk Of Fluoride Use, Margherita Fontana Dds, Phd, Carlos González-Cabezas D.D.S., M.S.D., Ph.D., Livia Tenuta D.D.S., M.Sc., Ph.D.

Metro Denver Dental Society Articulator Magazine

This article explores the evidence behind the safety of community water fluoridation. The authors establish that no clear link to lower IQ has been proven at U.S. levels (0.7 ppm). Major health organizations, including the ADA and WHO, continue to support fluoridation as safe and effective for preventing tooth decay.

Articulator Q2 2025

Metro Denver Dental Society Articulator Magazine

The 2^nd Quarter 2025 issue focuses on new frontiers in dental research. Articles include:

• A feature from Dr. Manish Chopra on the ADA Forsyth Institute.
• Highlights from the University of Colorado’s School of Dental Medicine’s Research Day.
• The research behind the safety of community water fluoridation from Margherita Fontana, DDS, PhD; Carlow Gonzalez-Cabezas, DDS, MSD, PhD; and Livia Tenuta, DDS, MSc, PhD.

Plus, updates on local nonprofits, a reflection on leading with integrity and tips on maintain resilience in today’s volatile financial landscape.

The Tweak/Fn14 Signaling Mediates Skeletal Muscle Wasting During Cancer Cachexia, Meiricris Tomaz Da Silva, Anirban Roy, Anh Tuan Vuong, Aniket S Joshi, Cristeena Josphien, Meghana V Trivedi, Sajedah M Hindi, Vihang A Narkar, Ashok Kumar

Faculty, Staff and Student Publications

Cancer cachexia is a multifactorial syndrome characterized by progressive skeletal muscle wasting. The TWEAK-Fn14 system regulates muscle mass in diverse conditions. However, its role in the regulation of muscle mass during cancer cachexia remains less understood. Here, we demonstrate that the levels of Fn14 are induced in skeletal muscle of multiple mouse models of cancer cachexia. Muscle-specific deletion of Fn14 reduces myofiber atrophy in mouse models of pancreatic and lung cancer cachexia. Silencing of Fn14 in KPC pancreatic cancer cells prior to their implantation in mice attenuates tumor growth without affecting myofiber size. Muscle-specific deletion of Fn14 reduces the gene …

Neovascular Pruning By Ido1 Inhibitors Can Potentiate Immunogenic Cytotoxicity Of Ischemia-Targeted Agents To Synergistically Enhance Anti-Pd-1 Responsiveness, Shih-Chun Shen, Souvik Dey, James B. Duhadaway, Erika Sutanto-Ward, Maurice T. Hampton, Serguei V. Kozlov, George C. Prendergast, Alexander J. Muller

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Strategies for deploying indoleamine 2,3-dioxygenase 1 (IDO1)-targeted therapies for use against cancer have focused on IDO1's role in promoting peripheral immune tolerance that shields tumors from effector T cells. However, preclinical investigation of both primary and metastatic tumor development in the lungs has uncovered a previously unappreciated role for IDO1 in directing a counterregulatory response to interferon (IFN)-γ that realigns the local inflammatory environment to promote tumor neovascularization. Understanding how to therapeutically leverage the ability of IDO1 inhibitors to subvert inflammatory neovascularization within the tumor microenvironment has potential ramifications for future clinical development of these compounds.

METHODS: Pulmonary metastases …