Digital Commons Network^™

Benchmarking Dna Foundation Models For Genomic And Genetic Tasks, Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu

Faculty, Staff and Student Publications

The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph, and GROVER) across diverse genomic and genetic tasks including sequence classification, gene expression prediction, variant effect quantification, and topologically associating domain (TAD) region recognition, using zero-shot embeddings. Our analysis reveals that mean token embedding consistently and significantly improves sequence classification performance, outperforming other pooling strategies. Model performance varies among tasks and datasets; while general purpose DNA foundation models showed competitive performance in pathogenic variant identification, they were less …

“I Missed My Other Oncologist”: Established Relationships As Barriers And Facilitators To Accessing Car-T And Autologous Transplantation, Zachary A. K. Frosch, Clark Meshack, Caitlin Meeker, Asya Varshavsky-Yanovsky, Rashmi Khanal, Michael Bromberg, Ashwin Chandar, Emmanuel Quien, Jordan Carter, Shazia K. Nakhoda, Marcus Messmer, Charissa Montgomery, Jason A. Incorvati, Nadia D. Ali, Michael J. Styler, Carolyn Y. Fang

Division of Gastroenterology and Hepatology Faculty Papers

BACKGROUND: Autologous stem cell transplantation (ASCT) and chimeric antigen receptor T-cell therapy (CAR-T) can provide significant clinical benefit, but are not equally available to all patients. Oncologist continuity and trust are important to patients, and may act as barriers to receipt of therapy. However, detailed data are lacking on the mechanism by which these might affect receipt of therapy, or how this barrier may be overcome.

METHODS: We conducted a qualitative interview study with patients with non-Hodgkin lymphoma (NHL), classic Hodgkin lymphoma (cHL) or multiple myeloma (MM) eligible for or treated with ASCT/CAR-T. Participants were recruited from a multi-site academic …

Investigating The Neuronal Role Of The Proteasomal Atpase Subunit Gene Psmc5 In Neurodevelopmental Proteasomopathies, Sébastien Küry, Janelle E Stanton, Geeske M Van Woerden, Amélie Bosc-Rosati, Tzung-Chien Hsieh, Lise Bray, Marielle Oloudé, Cory Rosenfelt, Marie Pier Scott-Boyer, Victoria Most, Tianyun Wang, Jonas J Papendorf, Charlotte De Konink, Wallid Deb, Virginie Vignard, Maja Studencka-Turski, Thomas Besnard, Anna M Hajdukowicz, Franziska G Thiel, Sophie Wolfgramm, Laëtitia Florenceau, Silvestre Cuinat, Sylvain Marsac, Yann Verrès, Audrey Dangoumau, Léa Poirier, Ingrid M Wentzensen, Annabelle Tuttle, Cara Forster, Johanna Striesow, Richard Golnik, Damara Ortiz, Laura Jenkins, Jill A Rosenfeld, Alban Ziegler, Clara Houdayer, Dominique Bonneau, Erin Torti, Amber Begtrup, Kristin G Monaghan, Sureni V Mullegama, Catharina M L Nienke Volker-Touw, Koen L I Van Gassen, Renske Oegema, Mirjam S De Pagter, Katharina Steindl, Anita Rauch, Ivan Ivanovski, Kimberly Mcdonald, Emily Boothe, Andrew Dauber, Janice Baker, Noelle Andrea V Fabie, Raphael A Bernier, Tychele N Turner, Siddharth Srivastava, Kira A Dies, Lindsay C Swanson, Carrie Costin, Alali Abdulrazak, Rebekah K Jobling, John Pappas, Rachel Rabin, Dmitriy Niyazov, Anne Chun-Hui Tsai, Karen Kovak, David B Beck, May Christine V Malicdan, David R Adams, Lynne Wolfe, Rebecca D Ganetzky, Colleen C Muraresku, Davit Babikyan, Zdeněk Sedláček, Miroslava Hančárová, Andrew T Timberlake, Hind Al Saif, Berkley Nestler, Kayla King, M J Hajianpour, Gregory Costain, D'Arcy Prendergast, Chumei Li, David Geneviève, Antonio Vitobello, Arthur Sorlin, Christophe Philippe, Tamar Harel, Ori Toker, Ataf Sabir, Derek Lim, Mark J Hamilton, Lisa J Bryson, Elaine Cleary, Sacha Weber, Trevor L Hoffman, Anna M Cueto-González, Eduardo F Tizzano, David Gómez-Andrés, Marta Codina-Solà, Athina Ververi, Efterpi Pavlidou, Alexandros Lambropoulos, Kyriakos Garganis, Marlène Rio, Jonathan Levy, Sarah J Langas, Anne M Mcrae, Mathieu K Lessard, Maria Daniela D'Agostino, Isabelle De Bie, Meret Wegler, Rami Abou Jamra, Susanne B Kamphausen, Viktoria Bothe, Lorraine Potocki, Eric Olinger, Yves Sznajer, Elsa Wiame, Michelle L Thompson, Molly C Schroeder, Catherine Gooch, Raphael A Smith, Arti Pandya, Larissa M Busch, Uwe Völker, Elke Hammer, Kristian Wende, Benjamin Cogné, Bertrand Isidor, Jens Meiler, Clémentine Ripoll, Stéphanie Bigou, Frédéric Laumonnier, Peter W Hildebrand, Evan E Eichler, Kirsty Mcwalter, Peter M Krawitz, Florence Roux-Dalvai, Ype Elgersma, Julien Marcoux, Marie-Pierre Bousquet, Arnaud Droit, Jeremie Poschmann, Andreas M Grabrucker, Francois V Bolduc, Stéphane Bézieau, Frédéric Ebstein, Elke Krüger

Faculty, Staff and Students Publications

Neurodevelopmental proteasomopathies are a group of disorders caused by variants in proteasome subunit genes, that disrupt protein homeostasis and brain development through poorly characterized mechanisms. Here, we report 26 distinct variants in PSMC5, encoding the AAA⁺ ATPase subunit PSMC5/RPT6, in individuals with syndromic neurodevelopmental conditions. Combining genetic, multi-omics and biochemical approaches across cellular models and Drosophila, we unveil the essential role of proteasomes in sustaining key cellular processes. Loss of PSMC5/RPT6 function impairs proteasome activity, leading to protein aggregation, disruption of mitochondrial homeostasis, and dysregulation of lipid metabolism and immune signaling. It also compromises synaptic balance, neuritogenesis, and neural progenitor …

Single-Cell Transcriptomic Analysis Of Peripheral Blood Mononuclear Cells Reveals Key Immune Responses In St-Segment Elevation Myocardial Infarction, Zheng Zhang, Shengfang Wang, Yahui Liu, Gaohan Li, Qianqian Cheng, Wei Yang, Gan-Xin Yan, Chuanyu Gao

Department of Medicine Faculty Papers

BACKGROUND: Inflammation plays a crucial role in the pathogenesis of ST-segment elevation myocardial infarction (STEMI). However, the precise immunological mechanisms remain incompletely understood. Single-cell RNA sequencing (scRNA-seq) provides a powerful approach to dissect immune cell heterogeneity and dynamic changes at single-cell resolution.

METHODS: Peripheral blood mononuclear cells (PBMCs) were collected from 7 STEMI patients (within 6h after primary percutaneous coronary intervention) and 3 healthy controls. Single-cell suspensions were prepared and subjected to scRNA-seq using the 10x Genomics Chromium platform and Illumina NovaSeq 6000. Data were processed using Cell Ranger and analyzed with Seurat for quality control, clustering, and annotation. Differentially …

Nivolumab Plus Ipilimumab Induce Hyper-Progression In Renal Medullary Carcinoma: Results Of A Phase Ii Trial And Preclinical Evidence, Melinda Soeung, Xinmiao Yan, Ciro Zanca, Jing Qian, Menuka Karki, Fei Duan, Hania Khan, Li Zhang, David H Peng, Mariah Williams, Rong He, Ziheng Chen, Luigi Perelli, Jianfeng Chen, Rebecca S Tidwell, Pankaj K Chauhan, Courtney N Le, Truong N A Lam, Nirjar Bhattacharya, Rutvi Shah, I-Lin Ho, Jason P Gay, Caroline C Carrillo, Ningping Feng, Kang Le, Guang Gao, Teresa L Perry, Faika Mseeh, Yongying Jiang, Quanyun A Xu, Niki Marie Zacharias, Rahul A Sheth, Tharakeswara K Bathala, Priya Rao, Najat C Daw, Durga N Tripathi, Cheryl L Walker, Mohammad M Mohammad, Jianhua Zhang, Guangchun Han, Yanshuo Chu, Ruiping Wang, Minghao Dang, Enyu Dai, Fuduan Peng, Yunhe Liu, Akshaya Jadhav, Wenhua Lang, Claudio A Arrechedera, Leticia Campos Clemente, Edwin R Parra, Hsinyi Lu, Cara L Haymaker, Ignacio I Wistuba, Andrew Futreal, Andrea Viale, Michael J Soth, Philip Jones, Joseph R Marszalek, Timothy Heffernan, Giulio F Draetta, Nizar M Tannir, Jianjun Gao, Linghua Wang, Giannicola Genovese, Pavlos Msaouel

Faculty, Staff and Students Publications

Therapeutic options for patients with renal medullary carcinoma (RMC) are limited. Here we report the results of a phase II clinical trial (NCT03274258) of anti-PD1 nivolumab plus anti-CTLA4 ipilimumab in patients with RMC, with objective response rate as primary outcome. Enrollment was halted for futility at a prespecified interim analysis as all 10 treated patients experienced rapid disease progression. 5/10 met radiological criteria for hyperprogression and median progression-free survival (secondary outcome) was 1.38 months (95% confidence interval: 1.28, 1.60). In a post-hoc single-cell RNA sequencing analysis, data from patients with RMC before and after nivolumab plus ipilimumab treatment indicated that …

Turning Patients' Open-Ended Narratives Of Chronic Pain Into Quantitative Measures: Natural Language Processing Study, Raquel Norel, Jennifer Gewandter, Zhengwu Zhang, Anika Tahsin, Chadi G Abdallah, John Markman, Zhiyao Duan, Guillermo Cecchi, Paul Geha

Faculty, Staff and Students Publications

Background: Subjective report of pain remains the gold standard for assessing symptoms in patients with chronic pain and their response to analgesics. This subjectivity underscores the importance of understanding patients' personal narratives, as they offer an accurate representation of the illness experience.

Objective: In this pilot study involving 20 patients with chronic low back pain (CLBP), we applied emerging tools from natural language processing (NLP) to derive quantitative measures that captured patients' pain narratives.

Methods: Patients' narratives were collected during recorded semistructured interviews in which they spoke about their lives in general and their experiences with CLBP. Given that NLP …

Design And Refinement Of Cybercelltm, A Virtual Reality Health Education Program For Adolescents And Young Adults With Sickle Cell Disease, Aimee Hildenbrand, Melanie Pitone, Benjamin Bear, Corinna L. Schultz, Sherman Finch, Danielle Morley, Stephanie Hubbard, Alyssa Decino, Melissa A. Alderfer, Lori E. Crosby, Fredric Freeman

Department of Pediatrics Faculty Papers

For people living with sickle cell disease (SCD), the risk for disease complications and premature death rises sharply in adolescence and young adulthood, when chronic organ damage is compounded by reduced preventive care. To make informed health care decisions, adolescents and young adults (AYAs) require effective education about their health condition and treatment options. We aimed to systematically design and develop a user-centered, evidence-based virtual reality (VR) health education program to optimize the use of SCD therapies among AYAs with SCD. We engaged a diverse team including AYAs with SCD and their caregivers, multidisciplinary SCD clinicians and researchers, patient education …

Live-Cell Quantitative Monitoring Reveals Distinct, High-Affinity Gβγ Regulations Of Girk2 And Girk1/2 Channels, Reem Handklo-Jamal, Tal Keren Raifman, Boris Shalomov, Patrick Hofer, Uri Kahanovitch, Theres Friesacher, Galit Tabak, Vladimir Tsemakhovich, Haritha P Reddy, Orna Chomsky-Hecht, Debi Ranjan Tripathy, Kerstin Zuhlke, Carmen W Dessauer, Enno Klussmann, Yoni Haitin, Joel A Hirsch, Anna Stary-Weinzinger, Daniel Yakubovich, Nathan Dascal

Faculty, Staff and Student Publications

Gi/o protein-coupled receptors (GPCRs) inhibit cardiac and neuronal excitability via G protein-activated K+ channels (GIRK), assembled by combinations of GIRK1 - GIRK4 subunits. GIRKs are activated by direct binding of the Gβγ dimer of inhibitory Gi/o proteins. However, key aspects of this textbook signaling pathway remain debated. Recent studies suggested no Gi/o-GIRK pre-coupling and low (>250 µM) Gβγ-GIRK interaction affinity, contradicting earlier sub-µM estimates and implying low signaling efficiency. We show that Gγ prenylation, which mediates Gβγ membrane attachment required for GIRK activation, also contributes to the Gβγ-GIRK interaction, explaining the poor affinity obtained with non-prenylated Gβγ. Using quantitative …

Factfinders For Patient Safety: Minimizing Complications In Radiofrequency Neurotomy: Part I-Implantable Devices; Part Ii-Preprocedural Bvnrfn Imaging, David Hao, Gerald Yeung, Haewon Lee, Zheyan Chen, Ben Laplante, Paul Kitei, Reza Ehsanian, David Levi

Moss-Magee Rehabilitation Papers

This series of FactFinders presents a brief summary of the evidence and outlines recommendations regarding minimizing risks with radiofrequency neurotomy procedures. The evidence in support of the following facts is presented: (1) While data on the safety of radiofrequency neurotomy in patients with implanted devices are limited, the procedure can likely be performed safely with careful adherence to best practices and manufacturer recommendations. (2) Basivertebral nerve radiofrequency neurotomy can be performed safely and effectively at the L3 through S1 vertebral levels. Scrutiny of preprocedural imaging may minimize risk. Although the transpedicular approach is preferred, patient anatomy may dictate a non-transpedicular …

Divergent Prefrontal Cortex Circuits Regulate Cued Food Seeking Under Distinct Metabolic Or Emotional States, Xu O Zhang, Guillermo Aquino-Miranda, Claire E Cho, Yongzhe Wang, Duy Hoang Ha, Nikita Elinson-Watson, Allen Dong, Caleb Kemere, Fabricio H Do-Monte

Faculty, Staff and Student Publications

Flexibly adjusting food-seeking behaviour in response to food-associated cues and internal states is crucial for animals' survival. However, the neural mechanisms that modulate cued food-seeking behaviour during varying metabolic (i.e., hungry vs. satiated) and emotional (i.e., safe vs. threatened) states remain elusive. Here, we show that the encoding of metabolic or threat states in projection-defined neurons in the prelimbic cortex (PL) mediates cued food-seeking responses in rats. Using microendoscopic imaging, we demonstrate that neural population dynamics in PL consistently represent food cues, task-relevant behaviours, and internal state changes by recruiting distinct subsets of cue-responsive neurons at each state. Single-unit recording …

Risk Factors For Unexpected Death In Patients Identified By A Communication And Resolution Program, Peter Lodato, Neal D. Goldstein, Alexandra M, Mapp, Adebayo Gbadebo, David A. Paul

Department of Pediatrics Faculty Papers

Many patients experience unexpected harm while receiving healthcare, with a lasting impact on patients, families, and caregivers. Communication and Resolution Programs are being adopted with increased frequency, as a more systematic, transparent, and equitable approach to these unexpected outcomes. The aim of this study was to identify whether demographic factors played a role in identifying patients with unexpected death, as managed in our CRP. This nested case-controlled compared 236 patients who experienced an unanticipated death with 2,360 controls who died expectedly over a 10-year period. Patients with unexpected death were more likely to be Black (AOR 2.18 95% CI 1.01-4.68), …

Shp2: A Redox-Sensitive Regulator Linking Immune Checkpoint Inhibitor Therapy To Cancer Treatment And Vascular Risk, Silvia Fernanda López Moreno, Stefania Assunto Lenz, Bernardo Casso-Chapa, Angelica Paniagua-Bojorges, Jung Hyun Kim, Nicolas L Palaskas, Kevin T Nead, Venkata S K Samanthapudi, Gilbert Mejia, Oanh Hoang, Jonghae Lee, Steven H Lin, Joerg Herrmann, Guangyu Wang, Syed Wamique Yusuf, Cezar A Iliescu, Noah I Beinart, Charlotte Manisty, Masuko Ushio-Fukai, Tohru Fukai, Pietro Ameri, Roza I Nurieva, Michelle A T Hildebrandt, Keri Schadler, Efstratios Koutroumpakis, Sivareddy Kotla, Nhat-Tu Le, Jun-Ichi Abe

Faculty, Staff and Student Publications

Src homology 2-domain containing protein tyrosine phosphatase 2 (SHP2), encoded by the Ptpn11 gene (Tyrosine-protein phosphatase non-receptor type 11), is a key downstream effector of PD-1/PD-L1 signaling and is likely important, in addition to immune modulation, in tumor development and vascular homeostasis. SHP2 conveys PD-1 mediated inhibitory signaling in T cells, and is emerging as a therapeutic target. Importantly, there is an association between immune checkpoint inhibitors (ICIs), immune-related adverse events (irAEs), and cardiovascular complications, underscoring the need to understand SHP2’s role in these processes. This review aims to summarize current knowledge on SHP2/PTPN11 biology, its role in immune …

Nirsevimab Effectiveness Against Intensive Care Unit Admission For Respiratory Syncytial Virus In Infants - 24 States, December 2024-April 2025., Laura D. Zambrano, Regina M. Simeone, Margaret M. Newhams, Amanda B. Payne, Natasha B. Halasa, Amber O. Orzel-Lockwood, Jemima M. Calixte, Satoshi Kamidani, Hillary Crandall, Melissa A. Cameron, Jennifer E. Schuster, Aline B. Maddux, Kathleen Chiotos, Katherine Irby, Steven L. Shein, Mary Allen Staat, Lora M. Martin, Samina S. Bhumbra, Ryan A. Nofziger, Jigar C. Chauhan, Danielle M. Zerr, Shira J. Gertz, Judith A. Guzman-Cottrill, Michele Kong, Janet R. Hume, Bria M. Coates, Kelly N. Michelson, Emily R. Levy, Tamara T. Bradford, Stephanie P. Schwartz, Tracie C. Walker, Melissa S. Stockwell, Austin Biggs, Alexander H. Hogan, Katherine Lindsey, Angela P. Campbell, Adrienne G. Randolph, Overcoming Rsv Investigators

Manuscripts, Articles, Book Chapters and Other Papers

Respiratory syncytial virus (RSV) is a leading cause of intensive care unit (ICU) admission and respiratory failure among infants (children aged < 1 year) in the United States. In August 2023, CDC's Advisory Committee on Immunization Practices recommended nirsevimab, a long-acting monoclonal antibody, to protect against RSV-associated lower respiratory tract infection among all infants aged < 8 months born during or entering their first RSV season. Following licensure, nirsevimab effectiveness has been demonstrated against RSV-associated infant hospitalization, but evidence regarding effectiveness against RSV-associated critical illness is limited. In a 27-hospital case-control investigation, nirsevimab effectiveness against both RSV-associated infant ICU admission and acute respiratory failure (illness requiring continuous positive airway pressure, bilevel positive airway pressure, or invasive mechanical ventilation) after hospital admission was evaluated during December 1, 2024-April 15, 2025. Among 457 case-patients who received a positive RSV test result and 302 control patients who received a negative RSV test result admitted to an ICU with respiratory symptoms, 14% and 45%, respectively, had received nirsevimab ≥7 days before symptom onset. Nirsevimab was 80% effective (95% CI = 70%-86%) against RSV-associated ICU admission and 83% effective (95% CI = 74%-90%) against acute respiratory failure when received a median of 52 days (IQR = 32-89 days) and 50 days (IQR = 32-86 days) before onset for each respective endpoint. These estimates support the recommendation for use of nirsevimab as a prevention strategy to protect infants against severe outcomes from RSV infection.

Single Cell Long Read Whole Genome Sequencing Reveals Somatic Transposon Activity In Human Brain, Michal B Izydorczyk, Ester Kalef-Ezra, Dominic W Horner, Xinchang Zheng, Nadine Holmes, Marco Toffoli, Zeliha Sahin, Yi Han, Heer H Mehta, Sonja W Scholz, Clifton L Dalgard, Donna M Muzny, Adam Ameur, Fritz J Sedlazeck, Christos Proukakis

Faculty, Staff and Students Publications

The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover previously uncharacterized genomic dynamics in 18 cells from three human brains utilizing single cell long-read whole genome sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements, but requires validation in larger studies.

Ultra-Low-Field Portable Magnetic Resonance Imaging Feasibility And Safety In Pediatric And Neonatal Extracorporeal Membrane Oxygenation: A Single-Center Year-Long Experience., Jessica S. Wallisch, Asdis Finnsdottir Wagner, John M. Daniel Iv, Allison Taber, Maura Sien, Sarah Foster, Nathan S. Artz, Timothy Zinkus, Hung-Wen Yeh, Jose A. Pineda, Patrick M. Kochanek, Sherwin S. Chan

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Despite improving outcomes, extracorporeal membrane oxygenation (ECMO) remains associated with high rates of acute brain injury, impacting survival and outcomes. Clinical imaging modalities, including computed tomography and standard-field magnetic resonance imaging (≥1.5 Tesla), have either limited early detection of ischemic-type injuries or are incompatible with ECMO, causing diagnostic delays. A Food and Drug Administration-cleared ultra-low-field portable magnetic resonance imaging (pMRI; 0.064 Tesla) has shown promise in acute brain injury detection and use with MRI-unsafe equipment, but pediatric ECMO data are limited.

METHODS: This institutional review board-approved, single-center study was conducted at a quaternary children's hospital. Neonatal and pediatric patients …

Hypertensive Remodelling: When Bigger Body Means Bigger Problems, Eric Lazartigues

School of Medicine Faculty Publications

No abstract provided.

Apathy Self-Awareness And Its Neural Correlates In Parkinson’S Disease, Hannah Conn, Hideo Suzuki, Zekai Jin, Ana Marin, Xi Zhu, Seonjoo Lee, Edward Huey, Ratko Radakovic, Sarah R Heilbronner, Nora Vanegas-Arroyave

Faculty, Staff and Students Publications

Apathy is a prevalent non-motor symptom in Parkinson's disease (PD) that negatively impacts quality of life. Impaired self-awareness of apathy (ISA-a) further impacts patient care by limiting engagement. While apathy has been associated with reduced fronto-striatal functional connectivity (FC), the neural basis of ISA-a remains unclear. We examined ISA-a in 52 individuals and the neural basis of ISA-a in 35 individuals with PD using a dimensional approach (i.e., initiation, executive, and emotional apathy) and resting-state fMRI (3T scanner). Apathetic PD patients (42%) showed poorer self-awareness than non-apathetic peers. Apathetic PD patients showed a trend towards reduced FC between the left …

Be Faster Community Of Practice To Increase Rapid Initiation Of Antiretroviral Therapy In Houston, Texas: A Pre-Post Intervention Study, Naomi Sequeira, Bich N Dang, Melanie Goebel, Monisha Arya, Avishek Ghosh-Hajra, Kathryn Fergus, Shital M Patel

Faculty, Staff and Students Publications

Background: Rapid initiation of antiretroviral therapy (Rapid ART) is a key strategy of the Ending the HIV Epidemic (EHE) initiative. The Baylor College of Medicine Extension for Community Healthcare Outcomes (ECHO) Facilitating Antiretroviral Start Earlier (BE FASTER) program was developed to address this call-to-action. The program uses the ProjectECHO tele-mentoring model as an implementation tool in Harris County, a priority EHE jurisdiction. The authors present results on the acceptability and feasibility of the BE FASTER program.

Methods: Multidisciplinary health professionals from 5 Ryan White Part A funded agencies formed the community of practice. The BE FASTER program included 9 monthly …

Elastic Cytomatrix Dynamics Influences Metabolic Rate And Tumor Microenvironment Formation, Tattym E Shaiken, Tulendy T Nurkenov, Meruyert S Kurmanbayeva, David Y Graham

Faculty, Staff and Students Publications

In healthy cells, the cytomatrix mechanics utilize mitochondrial respiration to control cytosolic motion and fine-tune the chemical processes. In cancer, the cytosolic motion is energized by glycolytic fermentation (the Warburg effect), which provides additional energy to supply the needs of the cytomatrix. Here, we describe the physical and chemical processes of the integrated and cooperative cytomatrix cytoarchitecture, in which structure and function are inseparable. The extracellular matrix is interconnected with the intracellular cytomatrix and functions as two integrated elastic solid phases. This finding led us to propose mechanisms of tumor microenvironment formation resulting from the mutational burden, in which altered …

From Nicu To Neighborhood: Supporting Premature Patients Beyond The Hospital, Bob Underwood, Jermine Harriet Romald

Pediatrics in Practice: A CME Podcast

In this episode, we chat with neonatologist Harriet Romald, MD, FAAP, to explore the critical role pediatricians play in the long-term care of premature infants. From NICU discharge to developmental milestones, we discuss how pediatricians and neonatologists collaborate to ensure continuity of care, monitor common health challenges and navigate social determinants that impact outcomes. Whether you're new to caring for former NICU patients or looking to deepen your understanding, this conversation offers practical insights and the latest updates in neonatal follow-up care.

Click here to stream the podcast episode.

Cordmilk: Umbilical Cord Milking Versus Early Cord Clamping On Short-And Long-Term Outcomes In Neonates Who Are Non-Vigorous At Birth-Study Protocol Of A Multi-Center, Cluster-Randomized, Crossover-Controlled Trial, S. Yogeshkumar, Sunil S. Vernekar, Sangappa M. Dhaded, Kiran Talekar, Benjamin E Leiby, Rebecca Hartman, Yvonne Vaucher, Nitin Chouthai, Meenakshi Girish, Manish Jain, Shuchi Jain, Seema Parvekar, Vinita Jain, Alka Patankar, Milind Suryawanshi, Manish Tiwari, Manjushri Waikar, Nidhi Nashine, Deepali Ambike, Mahesh Asalkar, Rajesh Kulkarni, Sandhya Haribhaktha, Hemraj Narkhede, Sudha Chaudhari, Milind Kamble, Deepti Shrirame, Balchandra Falke, Seema Mehta, Asha Verma, Sunil Gothwal, Shivaprasad S. Goudar, Richard Derman, Anup Katheria, Zubair H. Aghai

Department of Radiology Faculty Papers

BACKGROUND: Facilitating placental transfusion-the transfer of blood from the placenta to the newborn-via delayed cord clamping (DCC) or umbilical cord milking (UCM) at birth has been shown to improve iron stores in healthy term infants and may positively impact long-term neurodevelopmental outcomes. Infants who are non-vigorous at birth and at risk of developing hypoxic-ischemic encephalopathy (HIE) are particularly likely to benefit from placental transfusion. This process may offer neuroprotection by enhancing cardiopulmonary transition, supporting cardiac preload, improving systemic and cerebral perfusion, delivering stem cells and neurotrophic factors, and preventing iron deficiency. While DCC is not currently recommended for non-vigorous term …

Multiomic Analysis Reveals A Key Bcat1 Role In Mtor Activation By B Cell Receptor And Tlr9, Rui Guo, Yizhe Sun, Matthew Y Lim, Hardik Shah, Joao A Paulo, Rahaman A Ahmed, Weixing Li, Yuchen Zhang, Haopeng Yang, Liang Wei Wang, Daniel Strebinger, Nicholas A Smith, Meng Li, Merrin Man Long Leong, Michael Lutchenkov, Jin Hua Liang, Zhixuan Li, Yin Wang, Rishi Puri, Ari Melnick, Michael R Green, John M Asara, Adonia E Papathanassiu, Duane R Wesemann, Steven P Gygi, Vamsi K Mootha, Benjamin E Gewurz

Faculty, Staff and Student Publications

B lymphocytes play major adaptive immune roles, producing antibodies and driving T cell responses. However, how immunometabolism networks support B cell activation and differentiation in response to distinct receptor stimuli remains incompletely understood. To gain insights, we systematically investigated acute primary human B cell transcriptional, translational, and metabolomic responses to B cell receptor (BCR), TLR9, CD40-ligand (CD40L), IL-4, or combinations thereof. T cell-independent BCR/TLR9 costimulation, which drives malignant and autoimmune B cell states, highly induced transaminase branched chain amino acid transaminase 1 (BCAT1), which localized to lysosomal membranes to support branched chain amino acid synthesis and mTORC1 activation. BCAT1 inhibition …

Disinhibited Behavior Associated With Rapid Clinical Response To Deep Brain Stimulation For Obsessive-Compulsive Disorder: Illustrative Cases, Sarah S Soubra, Tommy B Liu, Zain U Naqvi, Thomas Hamre, Danika L Paulo, Kalman A Katlowitz, Nisha Giridharan, Katie Van Arsdel, Jonathan H Bentley, Kasra A Mansourian, Davin Devara, Eric A Storch, Sarah R Heilbronner, Sameer A Sheth, Wayne Goodman, Nicole R Provenza

Faculty, Staff and Students Publications

Background: Deep brain stimulation (DBS) of the ventral capsule/ventral striatum (VC/VS) can alleviate symptoms of obsessive-compulsive disorder (OCD) refractory to conventional therapies. Overstimulation, however, can elicit pathological behaviors marked by disinhibition and recklessness.

Observations: Two patients with OCD underwent DBS of the VC/VS region and met responder status within 1 month of stimulation onset, as evidenced by a ≥ 35% reduction in their Yale-Brown Obsessive Compulsive Scale score. Notably, both patients exhibited signs of disinhibited behavior soon after DBS activation, including gambling, sleep disruption, and interpersonal relationship volatility. Through careful management, responder status persisted stably beyond the transient period of …

Describing The Determinants Of Fluid Prescribing And Fluid Balance Optimization In The Pediatric Intensive Care Unit: A Qualitative Study At A Community Hospital, Salvador Roland Maffei, Graciela Sanabria, Matthew Pesek, Ayse Akcan-Arikan, Satid Thammasitboon, Patrick G Lyons

Faculty, Staff and Students Publications

Background: Critically ill children tend to receive fluid volumes exceeding physiologic requirements despite evidence demonstrating harm with increasing net positive fluid balance. However, interventions aimed at optimizing fluid balance have yet to demonstrate significant clinical benefit, likely because there are multiple drivers of this complex problem. In this study, we used qualitative inquiry to describe the current practice at a community pediatric intensive care unit and discover potential barriers and facilitators to clinical practice change.

Methods: We designed a semi-structured interview guide informed by the consolidated framework in implementation research (CFIR) and conducted interviews with attending physicians, dietitians, nurses, nurse …

Exploring Generation Z Student Satisfaction In Radiography Programs Within A Southern State: Development And Application Of A Survey Instrument For Leadership Use, Brittany Seruntine Smith

Doctoral Dissertations

This dissertation employed a sequential exploratory mixed-methods design to examine the extent to which Generation Z students in radiography programs within a southern state perceive that their needs and expectations are being fulfilled. Additionally, the study examined how program leaders perceived and plan to utilize the survey and its findings within the cycle of continuous program improvement and accreditation readiness. A Likert-scale survey instrument was constructed by cross-referencing Generation Z’s characteristics, needs, and expectations with JRCERT standards. Items were refined through target population focus groups and validated using Lawshe’s Content Validity Ratio. The validated instrument was then administered to Generation …

Severe Myocarditis In The Pediatric Patient: A Simulation For Emergency Department Management, Prayerna Uppal, Anita Thomas, Robyn Wing, Lauren Kinneman, Cassandra Koid Jia Shin, Daisy Ciener, Jean I. Pearce, Claire Smith, Jennifer Reid, Kimberly Stone, Katina Summerford, Katherine Wolpert

School of Medicine Faculty Publications

Myocarditis in a pediatric patient can present with a variety of signs and symptoms, leading to a broad differential diagnosis. Delays in the correct identification of myocarditis and the initiation of appropriate interventions can have a detrimental impact on patient outcomes. In this case, a simulated five-year-old patient with myocarditis and secondary cardiogenic shock presents to the emergency department (ED). The goals of this simulation curriculum were to familiarize trainees and ED providers with the often nonspecific presentation of pediatric myocarditis, educate the care team about crucial interventions that positively or negatively impact the patient's stabilization course, and reinforce the …

The American Dermatological Association And The Story Of American Dermatology, Thomas N. Helm, Lawrence C. Parish, Amy S. Paller, David M. Pariser

Department of Dermatology and Cutaneous Biology Faculty Papers

No abstract provided.

Vaping And Substance Abuse Warning Signs, Bob Underwood, Thuylinh Pham, Addisyn Davis

Pediatrics in Practice: A CME Podcast

In this episode, Dr. Bob Underwood hosts Dr. Thuylinh Pham, an urgent care pediatrician, and Addisyn Davis, a youth advocate, to explore the complexities of vaping among teens. Understand the significant health risks associated with vaping, the misconceptions that persist, and how to identify warning signs of substance abuse. Tune in to equip yourself with essential knowledge to support the youth in your life. Don't miss out on this informative discussion!

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‘In Texas, Everybody Wants Antibiotics’: Reducing Inappropriate Antibiotic Expectations And Use With A Provider-Patient Communication Tool In Primary Care, Ashley Collazo, Paige Wermuth, Johanan Luna Rodriguez, Kiara Olmeda, Azalia Mancera, Fabrizia Faustinella, Michael K Paasche-Orlow, Roger Zoorob, Barbara Wells Trautner, Larissa Grigoryan

Faculty, Staff and Students Publications

Background/objective: Patients often expect antibiotics for self-limiting diseases, pressuring providers to prescribe antibiotics unnecessarily. These expectations also contribute to the unsafe practice of taking antibiotics without a prescription (non-prescription use), such as pills retained from prior prescriptions or antibiotics from non-medical sources. Previous work shows that non-prescription use is due to strong, widely held misconceptions regarding the curative power of antibiotics. To reduce unnecessary use of antibiotics, we developed and pilot-tested a patient-focused, bilingual (English and Spanish) educational tool with patient and provider stakeholder input. The tool, a trifold brochure, included information on safe antibiotic use, potential antibiotic harms and …

Development Of A Targeted Bioprotac Degrader Selective For Misfolded Sod1, Christen G Chisholm, Rachael Bartlett, Mikayla L Brown, Emma-Jayne Proctor, Natalie E Farrawell, Jody Gorman, Fabien Delerue, Lars M Ittner, Kara L Vine-Perrow, Heath Ecroyd, Neil R Cashman, Darren N Saunders, Luke Mcalary, Jeremy S Lum, Justin J Yerbury

Faculty, Staff and Student Publications

The accumulation of misfolded proteins underlies a broad range of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Due to their dynamic nature, these misfolded proteins have proven challenging to target therapeutically. Here, we specifically target misfolded disease variants of the ALS-associated protein superoxide dismutase 1 (SOD1), using a biological proteolysis targeting chimera (BioPROTAC) composed of a SOD1-specific intrabody and an E3 ubiquitin ligase. Screening of intrabodies and E3 ligases for optimal BioPROTAC construction reveals a candidate capable of degrading multiple disease variants of SOD1, preventing their aggregation in cells. Using CRISPR/Cas9 technology to develop a BioPROTAC transgenic mouse line, we …