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2025

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No Evidence Of Mmr Induced Trained Immunity To Prevent Sars Cov2: Results From A Multi-Centre Rct, Sinead Delany-Moretlwe, George Kyei, Erik Dubberke, Linda Yun, Leon Du Toit, Mary Politi, Ben Swan, Anne Deschryver, Sherry Mckinnon, Ananya Gupta, Shabaana Khader, Michael S Avidan, Et Al. Jan 2025

No Evidence Of Mmr Induced Trained Immunity To Prevent Sars Cov2: Results From A Multi-Centre Rct, Sinead Delany-Moretlwe, George Kyei, Erik Dubberke, Linda Yun, Leon Du Toit, Mary Politi, Ben Swan, Anne Deschryver, Sherry Mckinnon, Ananya Gupta, Shabaana Khader, Michael S Avidan, Et Al.

2020-Current year OA Pubs

BACKGROUND: Measles-containing vaccines (MCV), by training innate immune cells, are hypothesized to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19).

METHODS: In this international, double-blind, placebo-controlled trial, we randomly assigned adults, 18 years and older, to receive MCV or saline. The primary outcome was polymerase chain reaction (PCR) confirmed symptomatic COVID-19, up to 60 days after intervention. Secondary outcomes were PCR-confirmed symptomatic COVID-19 and serologically confirmed SARS-CoV-2 infection, up to 150 days after intervention.

RESULTS: Of 3411 randomised participants, the modified intention-to-treat population included 1607 in the MCV and 1545 in the saline group. …


Characterization Of Tlr9 Responsiveness In Cell Subsets Derived From In Vitro Pdc Differentiation Of Hematopoietic Stem And Progenitor Cells, Sabina Sánchez Hernández, Tobias Wang Bjerg, Ian Helstrup Nielsen, Anders Laustsen, Hai Q Tang, Lars Henning Pedersen, Eynav Klechevsky, Martin R Jakobsen, Rasmus O Bak Jan 2025

Characterization Of Tlr9 Responsiveness In Cell Subsets Derived From In Vitro Pdc Differentiation Of Hematopoietic Stem And Progenitor Cells, Sabina Sánchez Hernández, Tobias Wang Bjerg, Ian Helstrup Nielsen, Anders Laustsen, Hai Q Tang, Lars Henning Pedersen, Eynav Klechevsky, Martin R Jakobsen, Rasmus O Bak

2020-Current year OA Pubs

Plasmacytoid dendritic cells (pDCs) are multifunctional immune cells with roles in both the innate and adaptive immune system. Their hallmark function is production of large amounts of type I interferons in response to viral infections, but they are also capable of producing a range of other cytokines, antigen presentation, and cytotoxicity. Their potential as an immunotherapy for cancer and infectious disease is being explored, but broad application of these cells is challenged by low frequency in the blood and low viability during


Zic1 Is A Context-Dependent Medulloblastoma Driver In The Rhombic Lip, John J Y Lee, Ran Tao, Zhen You, Parthiv Haldipur, Anders W Erickson, Hamza Farooq, Liam D Hendriske, Namal Abeysundara, Cory M Richman, Evan Y Wang, Neha Das Gupta, Jennifer Hadley, Melissa Batts, Christopher W Mount, Xiaochong Wu, Alex Rasnitsyn, Swneke Bailey, Florence M G Cavalli, Sorana Morrissy, Livia Garzia, Kulandaimanuvel Antony Michealraj, Abhi Visvanathan, Vernon Fong, Jonelle Palotta, Raul Suarez, Bryn G Livingston, Miao Liu, Betty Luu, Craig Daniels, James Loukides, Anne Bendel, Pim J French, Johan M Kros, Andrey Korshunov, Marcel Kool, Fernando Chico Ponce De León, Mario Perezpeña-Diazconti, Boleslaw Lach, Sheila K Singh, Sarah E S Leary, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Ji-Yeoun Lee, Teiji Tominaga, William A Weiss, Joanna J Phillips, Shizhong Dai, Gelareh Zadeh, Ali G Saad, László Bognár, Almos Klekner, Ian F Pollack, Ronald L Hamilton, Young-Shin Ra, Wieslawa A Grajkowska, Marta Perek-Polnik, Reid C Thompson, Anna M Kenney, Michael K Cooper, Stephen C Mack, Nada Jabado, Mathieu Lupien, Marco Gallo, Vijay Ramaswamy, Mario L Suva, Hiromichi Suzuki, Kathleen J Millen, L Frank Huang, Paul A Northcott, Michael D Taylor Jan 2025

Zic1 Is A Context-Dependent Medulloblastoma Driver In The Rhombic Lip, John J Y Lee, Ran Tao, Zhen You, Parthiv Haldipur, Anders W Erickson, Hamza Farooq, Liam D Hendriske, Namal Abeysundara, Cory M Richman, Evan Y Wang, Neha Das Gupta, Jennifer Hadley, Melissa Batts, Christopher W Mount, Xiaochong Wu, Alex Rasnitsyn, Swneke Bailey, Florence M G Cavalli, Sorana Morrissy, Livia Garzia, Kulandaimanuvel Antony Michealraj, Abhi Visvanathan, Vernon Fong, Jonelle Palotta, Raul Suarez, Bryn G Livingston, Miao Liu, Betty Luu, Craig Daniels, James Loukides, Anne Bendel, Pim J French, Johan M Kros, Andrey Korshunov, Marcel Kool, Fernando Chico Ponce De León, Mario Perezpeña-Diazconti, Boleslaw Lach, Sheila K Singh, Sarah E S Leary, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Ji-Yeoun Lee, Teiji Tominaga, William A Weiss, Joanna J Phillips, Shizhong Dai, Gelareh Zadeh, Ali G Saad, László Bognár, Almos Klekner, Ian F Pollack, Ronald L Hamilton, Young-Shin Ra, Wieslawa A Grajkowska, Marta Perek-Polnik, Reid C Thompson, Anna M Kenney, Michael K Cooper, Stephen C Mack, Nada Jabado, Mathieu Lupien, Marco Gallo, Vijay Ramaswamy, Mario L Suva, Hiromichi Suzuki, Kathleen J Millen, L Frank Huang, Paul A Northcott, Michael D Taylor

Faculty, Staff and Students Publications

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma …


Maternal Rest Improves Growth In Small-For-Gestational-Age Fetuses (<10th Percentile), Greggory R Devore, Bardo Polanco, Wesley Lee, Jeffrey Brian Fowlkes, Emma E Peek, Manesha Putra, John C Hobbins Jan 2025

Maternal Rest Improves Growth In Small-For-Gestational-Age Fetuses (<10th Percentile), Greggory R Devore, Bardo Polanco, Wesley Lee, Jeffrey Brian Fowlkes, Emma E Peek, Manesha Putra, John C Hobbins

Faculty, Staff and Students Publications

BACKGROUND: Optimal management of fetuses diagnosed as small for gestational age based on an estimated fetal weight ofHowever, maternal bed rest has not been recommended based on the results of a randomized clinical trial that showed that maternal rest does not improve fetal growth in small-for-gestational-age fetuses. This study was conducted to revisit this question.

OBJECTIVE: This study aimed to determine whether maternal bed rest was associated with an increase in the fetal biometric parameters that reflect growth after the diagnosis of a small-for-gestational-age fetus.

STUDY DESIGN: A retrospective study was conducted on fetuses who were diagnosed as small for …


Bcg-Induced Dna Methylation Changes Improve Coronavirus Disease 2019 Vaccine Immunity Without Decreasing The Risk For Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Santiago Carrero Longlax, Kent J Koster, Ashish M Kamat, Marisa Lozano, Seth P Lerner, Rebecca Hannigan, Tomoki Nishiguchi, Abhimanyu, Daanish Sheikh, Malik Ladki, Alexandra Portillo, Amrit Koirala, Tajhal D Patel, Zoe Spieler, Aaron B Benjamin, Maxim Lebedev, Theresa U Ofili, Robert W Hutchison, George Udeani, Lynne A Opperman, Gabriel Neal, Anna M Mandalakas, Mihai G Netea, Moshe Arditi, Pablo Avalos, Sandra L Grimm, Cristian Coarfa, Jeffrey D Cirillo, Andrew R Dinardo Jan 2025

Bcg-Induced Dna Methylation Changes Improve Coronavirus Disease 2019 Vaccine Immunity Without Decreasing The Risk For Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Santiago Carrero Longlax, Kent J Koster, Ashish M Kamat, Marisa Lozano, Seth P Lerner, Rebecca Hannigan, Tomoki Nishiguchi, Abhimanyu, Daanish Sheikh, Malik Ladki, Alexandra Portillo, Amrit Koirala, Tajhal D Patel, Zoe Spieler, Aaron B Benjamin, Maxim Lebedev, Theresa U Ofili, Robert W Hutchison, George Udeani, Lynne A Opperman, Gabriel Neal, Anna M Mandalakas, Mihai G Netea, Moshe Arditi, Pablo Avalos, Sandra L Grimm, Cristian Coarfa, Jeffrey D Cirillo, Andrew R Dinardo

Faculty, Staff and Students Publications

BACKGROUND: The BCG vaccine induces trained immunity, an epigenetic-mediated increase in innate immune responsiveness. Therefore, this clinical trial evaluated if BCG-induced trained immunity could decrease coronavirus disease 2019 (COVID-19)-related frequency or severity.

METHODS: A double-blind, placebo-controlled clinical trial of healthcare workers randomized participants to vaccination with BCG TICE or placebo (saline). Enrollment included 529 healthcare workers randomized to receive BCG or placebo. Primary analysis evaluated COVID-19 disease frequency, while secondary analysis evaluated coronavirus immunity in a subset of participants. Study enrollment ceased early in December 2020 following introduction of COVID-19-specific vaccines.

RESULTS: Study enrollment was halted early, prior to reaching …


Impact Of Methicillin-Resistant Staphylococcus Aureus Surveillance And Decolonization In The Nicu: The Texas Children’S Hospital Experience, Nahid Hiermandi, Catherine Foster, Judith Campbell, Krystal Purnell, Elizabeth Tocco, Tjin Koy, Kenneth Nobleza, Duc Nguyen, Lucila Marquez Jan 2025

Impact Of Methicillin-Resistant Staphylococcus Aureus Surveillance And Decolonization In The Nicu: The Texas Children’S Hospital Experience, Nahid Hiermandi, Catherine Foster, Judith Campbell, Krystal Purnell, Elizabeth Tocco, Tjin Koy, Kenneth Nobleza, Duc Nguyen, Lucila Marquez

Faculty, Staff and Students Publications

OBJECTIVE: To determine the impact of screening and decolonization on methicillin-resistant

STUDY DESIGN: This is a single-center retrospective cohort study comparing patient characteristics among MRSA-colonized and MRSA-infected infants, rates of MRSA infection before and after screening with targeted decolonization, and MRSA infection among those receiving single or combined decolonization agents.

SETTING: Texas Children's Hospital Pavilion for Women is a 42-bed level three neonatal intensive care units (NICU) in Houston, TX.

PATIENTS: Neonates admitted to the NICU from 2012 to 2022 were included in analysis of MRSA colonization and infection. The gestational age ranged from 22 weeks to 42 weeks.

INTERVENTIONS: …


Increasing Premedication For Neonatal Intubation: A Quality Improvement Initiative, Michelle H Lucena, Toshiba Morgan-Joseph, Alecia Thompson-Branch Jan 2025

Increasing Premedication For Neonatal Intubation: A Quality Improvement Initiative, Michelle H Lucena, Toshiba Morgan-Joseph, Alecia Thompson-Branch

Faculty, Staff and Students Publications

INTRODUCTION: Endotracheal intubation is frequent in the neonatal intensive care unit (NICU) but may result in neonatal distress and instability. Premedication reduces adverse effects, such as hypoxia, bradycardia, and pain. The Specific, Measurable, Achievable, Relevant and Time-Bound aim for this project was to increase premedication use for nonemergent neonatal intubation in a specific NICU from 22% to 80% from March 2021 to May 2023.

METHODS: We use quality improvement methodology to explain our theory for improvement. Our key driver diagram depicts this initiative's aims, key drivers, and interventions to increase premedication use for neonatal intubation. We defined exclusion criteria and …


Comparative Analysis Of Aav Serotypes For Transduction Of Olfactory Sensory Neurons, Benjamin D W Belfort, Johnathan D Jia, Alexandra R Garza, Anthony M Insalaco, J P Mcginnis, Brandon T Pekarek, Joshua Ortiz-Guzman, Burak Tepe, Hu Chen, Ascent-Pd Investigators, Zhandong Liu, Benjamin R Arenkiel Jan 2025

Comparative Analysis Of Aav Serotypes For Transduction Of Olfactory Sensory Neurons, Benjamin D W Belfort, Johnathan D Jia, Alexandra R Garza, Anthony M Insalaco, J P Mcginnis, Brandon T Pekarek, Joshua Ortiz-Guzman, Burak Tepe, Hu Chen, Ascent-Pd Investigators, Zhandong Liu, Benjamin R Arenkiel

Faculty, Staff and Students Publications

Olfactory sensory neurons within the nasal epithelium detect volatile odorants and relay odor information to the central nervous system. Unlike other sensory inputs, olfactory sensory neurons interface with the external environment and project their axons directly into the central nervous system. The use of adeno-associated viruses to target these neurons has garnered interest for applications in gene therapy, probing olfactory sensory neuron biology, and modeling disease. To date, there is no consensus on the optimal AAV serotype for efficient and selective transduction of olfactory sensory neurons


The Pointer Imaging Baseline Cohort: Associations Between Multimodal Neuroimaging Biomarkers, Cardiovascular Health, And Cognition, Theresa M Harrison, Tyler Ward, Jacinda Taggett, Pauline Maillard, Samuel N Lockhart, Youngkyoo Jung, Laura C Lovato, Robert Koeppe, William J Jagust, Danielle Harvey, Joseph C Masdeu, Hwamee Oh, Darren R Gitelman, Neelum T Aggarwal, Mark A Espeland, Maryjo L Cleveland, Rachel Whitmer, Sarah Tomaszewski Farias, Stephen Salloway, Valory Pavlik, Melissa Yu, Christine Tangney, Heather Snyder, Maria Carrillo, Laura D Baker, Prashanthi Vemuri, Charles Decarli, Susan M Landau Jan 2025

The Pointer Imaging Baseline Cohort: Associations Between Multimodal Neuroimaging Biomarkers, Cardiovascular Health, And Cognition, Theresa M Harrison, Tyler Ward, Jacinda Taggett, Pauline Maillard, Samuel N Lockhart, Youngkyoo Jung, Laura C Lovato, Robert Koeppe, William J Jagust, Danielle Harvey, Joseph C Masdeu, Hwamee Oh, Darren R Gitelman, Neelum T Aggarwal, Mark A Espeland, Maryjo L Cleveland, Rachel Whitmer, Sarah Tomaszewski Farias, Stephen Salloway, Valory Pavlik, Melissa Yu, Christine Tangney, Heather Snyder, Maria Carrillo, Laura D Baker, Prashanthi Vemuri, Charles Decarli, Susan M Landau

Staff and Researcher Publications

Introduction: The U.S. Study to Protect Brain Health Through Lifestyle Intervention to Reduce Risk (U.S. POINTER) is evaluating lifestyle interventions in older adults at risk for cognitive decline and dementia. Here we characterize the baseline data set of the POINTER Imaging ancillary study.

Methods: Participants underwent health and cognitive assessments and neuroimaging with multimodal positron emission tomography (PET) (beta-amyloid [Aβ] and tau) and magnetic resonance imaging (MRI). Framingham risk score (FRS) was used to quantify cardiovascular disease (CVD) risk.

Results: A total of 1052 participants (31% from underrepresented ethnoracial groups) were enrolled. Compared to Aβ-, Aβ+ (29%) participants were older, …


Flyphonedb2: A Computational Framework For Analyzing Cell-Cell Communication In Drosophila Scrna-Seq Data Integrating Alphafold-Multimer Predictions, Mujeeb Qadiri, Ying Liu, Ah-Ram Kim, Myeonghoon Han, Eric Zhou, Austin Veal, Tzu-Chiao Lu, Hongjie Li, Yanhui Hu, Norbert Perrimon Jan 2025

Flyphonedb2: A Computational Framework For Analyzing Cell-Cell Communication In Drosophila Scrna-Seq Data Integrating Alphafold-Multimer Predictions, Mujeeb Qadiri, Ying Liu, Ah-Ram Kim, Myeonghoon Han, Eric Zhou, Austin Veal, Tzu-Chiao Lu, Hongjie Li, Yanhui Hu, Norbert Perrimon

Center on Aging Staff Publications

Cell-cell communication (CCC) plays a critical role in the physiological regulation of organisms and has been implicated in numerous diseases. Previously, we introduced FlyPhoneDB, a tool designed to explore CCC in Drosophila single-cell RNA-sequencing datasets. The core algorithm of FlyPhoneDB infers tissue-specific signaling events between cell types by calculating cell-cell interaction scores based on curated ligand-receptor (L-R) expression across major signaling pathways. However, the utility of FlyPhoneDB was limited by the relatively small number of available L-R pairs.

Here, we present FlyPhoneDB2, a major upgrade featuring a significantly expanded knowledgebase that includes a greater number of L-R pairs, incorporating annotations …


The Impact Of Insurance On Adolescent Transition To Adult Care, Diane V Murrell, Cassandra J Enzler, Lauren Bretz, Beth H Garland, Albert C Hergenroeder, Christine Markham, Constance M Wiemann Jan 2025

The Impact Of Insurance On Adolescent Transition To Adult Care, Diane V Murrell, Cassandra J Enzler, Lauren Bretz, Beth H Garland, Albert C Hergenroeder, Christine Markham, Constance M Wiemann

Faculty, Staff and Student Publications

Background: This study sought to examine how adolescents and young adults with special health care needs (AYA) prepare for managing medical insurance (private and public) as an adult and the role of insurance in locating an adult provider and engaging in care.

Methods: Twenty-eight AYA aged 18-24 years with renal, inflammatory bowel, or rheumatologic diseases completed individual semi-structured interviews designed to evaluate the impact of insurance (private vs. public) on their health care transition experiences. An interdisciplinary team of coders analyzed transcripts using The Framework Method.

Results: Three themes emerged: continuum of accepting health insurance responsibility; the impact of insurance …


Digital Otoscopy With Computer-Aided Composite Image Generation: Impact On The Correct Diagnosis, Confidence, And Time, Seda Camalan, Carl D Langefeld, Amy Zinnia, Brigham Mckee, Matthew L Carlson, Nicholas L Deep, Michael S Harris, Taha A Jan, Vivian F Kaul, Nathan R Lindquist, Jameson K Mattingly, Jay Shah, Kevin Y Zhan, Metin N Gurcan, Aaron C Moberly Jan 2025

Digital Otoscopy With Computer-Aided Composite Image Generation: Impact On The Correct Diagnosis, Confidence, And Time, Seda Camalan, Carl D Langefeld, Amy Zinnia, Brigham Mckee, Matthew L Carlson, Nicholas L Deep, Michael S Harris, Taha A Jan, Vivian F Kaul, Nathan R Lindquist, Jameson K Mattingly, Jay Shah, Kevin Y Zhan, Metin N Gurcan, Aaron C Moberly

Faculty, Staff and Student Publications

Objective: This study investigated the comparative performance of ear, nose, and throat (ENT) physicians in correctly detecting ear abnormalities when reviewing digital otoscopy imaging using 3 different visualization methods, including computer-assisted composite images called "SelectStitch," single video frame "Still" images, and video clips. The study also explored clinicians' diagnostic confidence levels and the time to make a diagnosis.

Study design: Clinician diagnostic reader study.

Setting: Online diagnostic survey of ENT physicians.

Methods: Nine ENT physicians reviewed digital otoscopy examinations from 86 ears with various diagnoses (normal, perforation, retraction, middle ear effusion, tympanosclerosis). Otoscopy examinations used artificial-intelligence (AI)-based computer-aided composite image …


Ethical Considerations For Teaching With Artificial Intelligence: A Scoping Review In Medical Education Settings, Amani Itani, Susie L Gronseth, Salma Musaad, Thuy Nguyen, Yiming Mirabile, Bettina M Beech Jan 2025

Ethical Considerations For Teaching With Artificial Intelligence: A Scoping Review In Medical Education Settings, Amani Itani, Susie L Gronseth, Salma Musaad, Thuy Nguyen, Yiming Mirabile, Bettina M Beech

Children’s Nutrition Research Center Staff Publications

In the evolving realm of medical education, where artificial intelligence (AI) technologies play an increasingly pivotal role, embedding AI ethics within educational frameworks has become crucial. This scoping review explores the breadth of literature concerning ethical considerations for teaching with AI in medical education settings. Following the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for Scoping Reviews (PRISMA-ScR) guidelines, the team analyzed 82 peer-reviewed English-language articles published between 2018 and October 2023, sourced from PubMed, Embase, and Web of Science. The review presents insights into the geographic distribution of studies, publication trends, article types, common keywords, areas of …


Consumption Pressure In Estuaries Peaks At Intermediate Salinities, Catherine E. De Rivera, Amy A. Larson, Benjamin G. Rubinoff, Luna R. Soto, Seth L. Wright, Edwin D. Grosholz, Gregory M. Ruiz, Andrew L. Chang Jan 2025

Consumption Pressure In Estuaries Peaks At Intermediate Salinities, Catherine E. De Rivera, Amy A. Larson, Benjamin G. Rubinoff, Luna R. Soto, Seth L. Wright, Edwin D. Grosholz, Gregory M. Ruiz, Andrew L. Chang

Environmental Science and Management Faculty Publications and Presentations

The nature and strength of biotic interactions change along stress gradients, but the importance of these interactions across estuarine gradients is under studied. Here, we examined how consumption varies across estuarine salinity gradients by deploying standardized baits (‘squidpops’) to measure consumption pressure along the gradients of five estuaries in Oregon, USA. The relationship between consumption and stress was nonlinear: consumption pressure peaked slightly at mid salinity and decreased at low salinity, especially as temperature increased, in the five estuaries studied. This finding does not support either of two existing models for consumption across gradients, including the Consumer Stress Model and …


Fueling Adaptation: Collaborative Wildfire Governance In The Colorado Front Range Landscape, Mahmood Muttaqee, Cody Evers, Lindsay K. Campbell, Max Nielsen-Pincus, Olivia Awbrey, Kathryn Hixson, Michelle Johnson, Erika Svendsen Jan 2025

Fueling Adaptation: Collaborative Wildfire Governance In The Colorado Front Range Landscape, Mahmood Muttaqee, Cody Evers, Lindsay K. Campbell, Max Nielsen-Pincus, Olivia Awbrey, Kathryn Hixson, Michelle Johnson, Erika Svendsen

Environmental Science and Management Faculty Publications and Presentations

Collaborative governance plays a critical role in wildfire risk mitigation efforts. This study examines collaborative wildfire governance networks within the Colorado Front Range, a landscape that was designated under the USDA Forest Service's Wildfire Crisis Strategy (WCS). Collaborative governance networks in the Colorado Front Range leverage partnerships across multiple organizational actors including federal, state, and local agencies, non-profits, fire districts, and research institutions. Through survey data collected from 281 respondents revealing a collaborative network of 401 organizations, the study aimed to identify the structure, capacity, and gaps in governance networks addressing wildfire risk in the Colorado Front Range. Survey results …


Urban Heterogeneity Drives Dissolved Organic Matter Sources, Transport, And Transformation From Local To Macro Scales, Rebecca L. Hale, Kristina G. Hopkins, Krista A. Capps, John S. Kominoski, Jennifer L. Morse, Allison H. Roy, Shuo Chen, Annika Quick, Andrew J. Blinn, Liz Ortiz Muñoz, Gwendolynn Folk Jan 2025

Urban Heterogeneity Drives Dissolved Organic Matter Sources, Transport, And Transformation From Local To Macro Scales, Rebecca L. Hale, Kristina G. Hopkins, Krista A. Capps, John S. Kominoski, Jennifer L. Morse, Allison H. Roy, Shuo Chen, Annika Quick, Andrew J. Blinn, Liz Ortiz Muñoz, Gwendolynn Folk

Environmental Science and Management Faculty Publications and Presentations

Urbanization reshapes dissolved organic matter (DOM) sources, transport, and transformations through changes in vegetation, hydrology, and management of waste and water. Yet the impacts of urbanization on DOM are variable within and among cities. Predicting heterogeneous responses to urbanization is challenged by diverse human activities and underlying biophysical variation along stream networks. Using data from the 486 largest urban areas in the continental United States and seven focal cities, we identified macro and local scale urban gradients in social, built, and biophysical factors that are expected to shape DOM. We used these gradients and the literature to develop hypotheses about …


Gout Flare Burden In The United States: A Multiyear Cross-Sectional Survey Study, Jasvinder A Singh, Amy Morlock, Robert Morlock Jan 2025

Gout Flare Burden In The United States: A Multiyear Cross-Sectional Survey Study, Jasvinder A Singh, Amy Morlock, Robert Morlock

Faculty, Staff and Students Publications

OBJECTIVE: The objective of this study was to assess the burden of gout flares and examine associated patient characteristics and outcomes in a sample of US adults.

METHODS: Data were collected via an online survey of US adults ≥18 years using a random stratified sampling framework. Participants with gout completed questions about treatments, serum urate (SU) levels, severity, satisfaction with control, and gout flares. All participants completed the Veterans RAND 12-Item Health Survey, the Generalized Anxiety Disorder 7-Item Scale, and the Patient Health Questionnaire 9-Item Scale. Data were summarized using descriptive statistics. Multivariable-adjusted logistic regression analyses examined factors predictive of …


Resort Enhances Reference-Based Cell Type Deconvolution For Spatial Transcriptomics Through Regional Information Integration, Linhua Wang, Ling Wu, Guantong Qi, Chaozhong Liu, Wanli Wang, Xiang H-F Zhang, Zhandong Liu Jan 2025

Resort Enhances Reference-Based Cell Type Deconvolution For Spatial Transcriptomics Through Regional Information Integration, Linhua Wang, Ling Wu, Guantong Qi, Chaozhong Liu, Wanli Wang, Xiang H-F Zhang, Zhandong Liu

Duncan NRI Faculty and Staff Publications

Motivation: Spatial transcriptomics (ST) captures positional gene expression within tissues but lacks single-cell resolution. Reference-based cell type deconvolution methods were developed to understand cell type distributions for ST. However, batch/platform discrepancies between references and ST impact their accuracy.

Results: We present Region-based Cell Sorting (ReSort), which utilizes ST's region-level data to lessen reliance on reference data and alleviate these technical issues. In simulation studies, ReSort enhances reference-based deconvolution methods. Applying ReSort to a mouse breast cancer model highlights macrophages M0 and M2 enrichment in the epithelial clone, revealing insights into epithelial-mesenchymal transition and immune infiltration.

Availability and implementation: Source codes …


Survey And Improvement Strategies For Gene Prioritization With Large Language Models, Matthew B Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu Jan 2025

Survey And Improvement Strategies For Gene Prioritization With Large Language Models, Matthew B Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu

Duncan NRI Faculty and Staff Publications

Motivation: Rare diseases remain difficult to diagnose due to limited patient data and genetic diversity, with many cases remaining undiagnosed despite advances in variant prioritization tools. While large language models have shown promise in medical applications, their optimal application for trustworthy and accurate gene prioritization downstream of modern prioritization tools has not been systematically evaluated.

Results: We benchmarked various language models for gene prioritization using multi-agent and Human Phenotype Ontology classification approaches to categorize patient cases by phenotype-based solvability levels. To address language model limitations in ranking large gene sets, we implemented a divide-and-conquer strategy with mini-batching and token limiting …


Recurrent Carotid Paragangliomas In A Syndromic Patient With A Heterozygous Missense Variant In Dna Methyltransferase 3 Alpha, Ryan J German, Blake Vuocolo, Liesbeth Vossaert, Lisa Saba, Robin Fletcher, Matthew L Tedder, Bekim Sadikovic, Jennifer Kerkhof, Michael Wangler, Carlos A Bacino Jan 2025

Recurrent Carotid Paragangliomas In A Syndromic Patient With A Heterozygous Missense Variant In Dna Methyltransferase 3 Alpha, Ryan J German, Blake Vuocolo, Liesbeth Vossaert, Lisa Saba, Robin Fletcher, Matthew L Tedder, Bekim Sadikovic, Jennifer Kerkhof, Michael Wangler, Carlos A Bacino

Duncan NRI Faculty and Staff Publications

We report a 40-year-old African American female with a novel variant in exon 8 of DNA methyltransferase 3 alpha (DNMT3A), (NM_022552.4: c.905G>C, p.G302A) who presented with a history of recurrent carotid paragangliomas, mediastinal mass, intellectual disability, dysarthria, cholelithiasis, diabetes mellitus, hypertension, and dysmorphic features. We interpret this novel variant as likely pathogenic and causative for the patient's syndromic features of Heyn-Sproul-Jackson syndrome. Heyn-Sproul-Jackson syndrome is a condition caused by gain-of-function genetic changes in DNMT3A. Paragangliomas have also been observed in non-syndromic patients with genetic alterations in DNMT3A. We describe a patient with clinical features of Heyn-Sproul-Jackson syndrome such as …


Talking About Suffering In The Intensive Care Unit, Brent M Kious, Judith B Vick, Peter A Ubel, Olivia Sutton, Jennifer Blumenthal-Barby, Christopher E Cox, Deepshikha Ashana Jan 2025

Talking About Suffering In The Intensive Care Unit, Brent M Kious, Judith B Vick, Peter A Ubel, Olivia Sutton, Jennifer Blumenthal-Barby, Christopher E Cox, Deepshikha Ashana

Center for Medical Ethics and Health Policy Staff Publications

Background: Some have hypothesized that talk about suffering can be used by clinicians to motivate difficult decisions, especially to argue for reducing treatment at the end of life. We examined how talk about suffering is related to decision-making for critically ill patients, by evaluating transcripts of conversations between clinicians and patients' families.

Methods: We conducted a secondary qualitative content analysis of audio-recorded family meetings from a multicenter trial conducted in the adult intensive care units of five hospitals from 2012-2017 to look at how the term "suffering" and its variants were used. A coding guide was developed by consensus-oriented discussion …


Investigative Genetic Genealogy Practices Warranting Policy Attention: Results Of A Modified Policy Delphi, Christi J Guerrini, Louiza Kalokairinou, Jill O Robinson, Whitney Bash Brooks, Stephanie M Fullerton, Sara Huston, Jacklyn Dahlquist, Diana Madden, Norah Crossnohere, Nicola Campoamor, John F P Bridges, Amy L Mcguire Jan 2025

Investigative Genetic Genealogy Practices Warranting Policy Attention: Results Of A Modified Policy Delphi, Christi J Guerrini, Louiza Kalokairinou, Jill O Robinson, Whitney Bash Brooks, Stephanie M Fullerton, Sara Huston, Jacklyn Dahlquist, Diana Madden, Norah Crossnohere, Nicola Campoamor, John F P Bridges, Amy L Mcguire

Center for Medical Ethics and Health Policy Staff Publications

A technique known as investigative genetic genealogy (IGG) was first introduced to criminal investigations in 2018, and it has since been used by U.S. law enforcement to help identify hundreds of criminal perpetrators and unidentified human remains. As expertise in IGG grows, policymakers have shown interest in regulating it. To help inform these efforts and to promote coherence in IGG governance as it expands, we recruited experts representing a spectrum of IGG-relevant professions and perspectives to identify and prioritize IGG practices for policy attention and to develop policy options for addressing them. In two rounds of a modified policy Delphi, …


Survivorship From Pediatric And Adult Brain Tumors: The 2024 Brain Tumor Epidemiology Consortium Meeting Report, Scott L Coven, Roberta Mckean-Cowdin, Michael E Scheurer, Kimberly J Johnson, Luc Bauchet, Carol Kruchko, Ching C Lau, Quinn T Ostrom, John Villano, Yan Yuan, Friederike Erdmann Jan 2025

Survivorship From Pediatric And Adult Brain Tumors: The 2024 Brain Tumor Epidemiology Consortium Meeting Report, Scott L Coven, Roberta Mckean-Cowdin, Michael E Scheurer, Kimberly J Johnson, Luc Bauchet, Carol Kruchko, Ching C Lau, Quinn T Ostrom, John Villano, Yan Yuan, Friederike Erdmann

Center for Medical Ethics and Health Policy Staff Publications

The Brain Tumor Epidemiology Consortium (BTEC) is an international organization with membership of individuals from the scientific community with interests related to brain tumor epidemiology, including surveillance, classification, methodology, etiology, and factors associated with morbidity and survival. The 2024 annual BTEC meeting entitled “Survivorship from Pediatric and Adult Brain Tumors” was held in Mainz, Germany, USA, on May 15–17, 2024. The meeting gathered scientists from Africa, Australia, Europe, and North America and included 4 keynote sessions focusing on brain tumor survivorship across the age spectrum. The meeting included 3 abstract sessions, which also included scientific talks around brain …


On Minimizing Risk And Harm In The Use Of Psychedelics, Jules Evans, Marc Aixalà, Brian T Anderson, William Brennan, Rebecka Bremler, Joost J Breeksema, Lisa Burback, Abigail E Calder, Robin L Carhart-Harris, Katherine Cheung, Neşe Devenot, Ingmar Gorman, Jakub Greń, Peter S Hendricks, Brian Holoyda, Edward Jacobs, Joy Krecké, Daniel J Kruger, David Luke, Tomislav Majić, Amy L Mcguire, Nicky J Mehtani, David S Mathai, Kristin Nash, Tehseen Noorani, Roman Palitsky, Oliver C Robinson, Otto Simonsson, Elin Stahre, Michiel Van Elk, David B Yaden Jan 2025

On Minimizing Risk And Harm In The Use Of Psychedelics, Jules Evans, Marc Aixalà, Brian T Anderson, William Brennan, Rebecka Bremler, Joost J Breeksema, Lisa Burback, Abigail E Calder, Robin L Carhart-Harris, Katherine Cheung, Neşe Devenot, Ingmar Gorman, Jakub Greń, Peter S Hendricks, Brian Holoyda, Edward Jacobs, Joy Krecké, Daniel J Kruger, David Luke, Tomislav Majić, Amy L Mcguire, Nicky J Mehtani, David S Mathai, Kristin Nash, Tehseen Noorani, Roman Palitsky, Oliver C Robinson, Otto Simonsson, Elin Stahre, Michiel Van Elk, David B Yaden

Center for Medical Ethics and Health Policy Staff Publications

Objective: This article outlines recommendations from 30 psychedelic researchers on how to create a better psychedelic safety net.

Methods: A survey of 30 psychedelic researchers asked them to identify key critical research gaps around psychedelic harm and safety.

Results: The critical research gaps identified by the authors included defining the main types of psychedelic harm, the predictors of those harms, and the most effective way to treat those harms. They also call for better support for those experiencing post-psychedelic difficulties, including better online information, peer support groups, affordable therapy, and psychiatric consultation and medication. Finally, the authors call for better …


A Landscape Analysis Of Psychedelic Retreat Organizations Advertising Online, Logan Neitzke-Spruill, Caroline S Beit, Jill Oliver Robinson, Nikita Singh, Srijith Kambala, Rishi Ramesh, Amy L Mcguire Jan 2025

A Landscape Analysis Of Psychedelic Retreat Organizations Advertising Online, Logan Neitzke-Spruill, Caroline S Beit, Jill Oliver Robinson, Nikita Singh, Srijith Kambala, Rishi Ramesh, Amy L Mcguire

Center for Medical Ethics and Health Policy Staff Publications

Research into psychedelics' clinical potential has corresponded to a growth in public interest and adult use. One common pathway to accessing psychedelics is through psychedelic retreats. While individual retreats have been characterized in the anthropological literature, no systematic evaluation of the psychedelic retreat industry exists. Assessing the characteristics of the psychedelic retreat industry is critical to understanding the associated ethical, legal, and social implications and ensuring consumer safety. To this end, we conducted a landscape analysis of online, publicly available information to capture and characterize a broad range of organizations offering psychedelic retreats and marketing to English-speaking consumers. From July …


Reframing Stigma In Tourette Syndrome: An Updated Scoping Review, Kelly Pring, Melina Malli, Brandy W Hardy, Stephen R Rapp, Eric A Storch, Jonathan W Mink, Jaclyn M Martindale Jan 2025

Reframing Stigma In Tourette Syndrome: An Updated Scoping Review, Kelly Pring, Melina Malli, Brandy W Hardy, Stephen R Rapp, Eric A Storch, Jonathan W Mink, Jaclyn M Martindale

Center for Medical Ethics and Health Policy Staff Publications

Persistent tic disorders (PTD) such as Tourette's syndrome (TS) are common childhood-onset neurodevelopmental disorders. Stigmatization of individuals with these disorders remains an ongoing problem. The purpose of this scoping review is to serve as an updated review of the research regarding stigmatization in youth with PTD since the publication of the original systematic review about this topic in 2016. The electronic databases Embase, Web of Science, PubMed, PsycINFO, and CINAHL were searched. Of the 4751 initial articles screened after removing duplications, 47 studies met the inclusion criteria. The studies were examined under the social-ecological stigmatization model, which helps categorize stigmatization …


Patient-Centric Federated Learning: Automating Meaningful Consent To Health Data Sharing With Smart Contracts, Kristin M Kostick-Quenet, Marcelo Corrales Compagnucci, Mateo Aboy, Timo Minssen Jan 2025

Patient-Centric Federated Learning: Automating Meaningful Consent To Health Data Sharing With Smart Contracts, Kristin M Kostick-Quenet, Marcelo Corrales Compagnucci, Mateo Aboy, Timo Minssen

Center for Medical Ethics and Health Policy Staff Publications

Federated Learning (FL) promises to enhance data-driven health research by enabling collaborative machine learning across distributed datasets without direct data exchange. However, current FL implementations primarily reflect the data-sharing interests of institutional controllers rather than those of individual patients whose data are at stake. Existing consent mechanisms-like broad consent under HIPAA or explicit consent under the GDPR-fail to provide patients with control over how their data is used. This article explores the integration of smart contracts (SCs) into FL as a mechanism for automating, enforcing, and documenting consent in data transactions. SCs, encoded in decentralized ledger technologies, can ensure that …


Advancing Medical Applications Of Cancer Nanotechnology: Highlighting Two Decades Of The Nci's Nanotechnology Characterization Laboratory Service To The Research Community, Rachael M Crist, Yechezkel Barenholz, Ahuva Cern, Kate N Clark, Pieter R Cullis, Cheryl Dean, Neil Desai, Mauro Ferrari, Matthieu Germain, Carmen A Giacomantonio, Emma Grabarnik, Piotr Grodzinski, Atara Hod, Barry E Kennedy, Ruvanthi N Kularatne, Glen S Kwon, Emmanuel Loeb, Erin B Noftall, Len Pagliaro, Morteza Rasoulianboroujeni, Alexander Roth, Darren Rowles, Kulbir Singh, Nicole F Steinmetz, Zhanna Yehtina, Yao Zhang, Daniel Zilbersheid, Jeffrey D Clogston, Stephan T Stern, Marina A Dobrovolskaia Jan 2025

Advancing Medical Applications Of Cancer Nanotechnology: Highlighting Two Decades Of The Nci's Nanotechnology Characterization Laboratory Service To The Research Community, Rachael M Crist, Yechezkel Barenholz, Ahuva Cern, Kate N Clark, Pieter R Cullis, Cheryl Dean, Neil Desai, Mauro Ferrari, Matthieu Germain, Carmen A Giacomantonio, Emma Grabarnik, Piotr Grodzinski, Atara Hod, Barry E Kennedy, Ruvanthi N Kularatne, Glen S Kwon, Emmanuel Loeb, Erin B Noftall, Len Pagliaro, Morteza Rasoulianboroujeni, Alexander Roth, Darren Rowles, Kulbir Singh, Nicole F Steinmetz, Zhanna Yehtina, Yao Zhang, Daniel Zilbersheid, Jeffrey D Clogston, Stephan T Stern, Marina A Dobrovolskaia

Center for Medical Ethics and Health Policy Staff Publications

The Nanotechnology Characterization Laboratory (NCL) is a US federally funded resource providing characterization and expertise to the cancer nanomedicine research community. Founded as a formal partnership among the US National Cancer Institute (NCI), the US Food and Drug Administration (FDA), and the US National Institute of Standards and Technology (NIST), the NCL has spent two decades developing a one-of-a-kind service with broad multidisciplinary expertise to meet the needs of a rapidly evolving drug development field. To mark the 20th anniversary of the lab's founding, the NCL hosted a symposium to highlight the achievements of the cancer nanomedicine field, showcase novel, …


Examining Treatment Options In Youth With Major Depressive Disorder: Observations From The Tx-Ydsrn Registry Study, Emine Rabia Ayvaci, Karabi Nandy, Ryan Becker, Laura Stone, Abu Minhajuddin, Holli Slater, Lynnel C Goodman, Sarah M Wakefield, Eric A Storch, Joseph C Blader, Cesar A Soutullo, Graham J Emslie, Madhukar H Trivedi Jan 2025

Examining Treatment Options In Youth With Major Depressive Disorder: Observations From The Tx-Ydsrn Registry Study, Emine Rabia Ayvaci, Karabi Nandy, Ryan Becker, Laura Stone, Abu Minhajuddin, Holli Slater, Lynnel C Goodman, Sarah M Wakefield, Eric A Storch, Joseph C Blader, Cesar A Soutullo, Graham J Emslie, Madhukar H Trivedi

Center for Medical Ethics and Health Policy Staff Publications

Objective: Treatment decisions for depression are a complex process, influenced by factors such as clinical characteristics, socioeconomic factors, and patient/caregiver preferences. This study examines the characteristics of treatment options during the first month of enrollment among depressed youth.

Methods: Data for 646 depressed youth were extracted from the Texas Youth Depression and Suicide Research Network study. Participants' treatments during the first month were categorized as no treatment (NT), psychotherapy only (THER), pharmacotherapy only (MED), or a combination of psychotherapy and pharmacotherapy (COMB). Sociodemographic and clinical features were compared across these treatment types.

Results: 7% were on NT, 5% on THER, …


Adolescent And Caregiver Preparation For Legal Changes At Age 18, Blanca Sanchez-Fournier, Jordyn Babla, Mary Majumder, Beth H Garland, Constance M Wiemann, Albert C Hergenroeder Jan 2025

Adolescent And Caregiver Preparation For Legal Changes At Age 18, Blanca Sanchez-Fournier, Jordyn Babla, Mary Majumder, Beth H Garland, Constance M Wiemann, Albert C Hergenroeder

Center for Medical Ethics and Health Policy Staff Publications

Background: Most adolescents with special healthcare needs (ASHCN) will assume legal responsibility for making decisions about their medical treatment at age 18. Simultaneously, parents or other legal representatives (Caregivers) will lose ASHCN medical record access. This study examined ASHCN and Caregiver knowledge of, satisfaction with, and suggestions for improvement in preparing for these changes.

Methods: Eighty-three dyads (18-year-old ASHCN and Caregivers) completed an assessment to evaluate their knowledge about changes in responsibility for decision making with a focus on consent, satisfaction with the preparation received, and recommendations for improved preparation. Descriptive statistics and mean comparisons were used. Responses to open-ended …