Digital Commons Network^™

Adenovirus Disease Following Pediatric Liver Transplantation: 10-Year Experience From A Large Pediatric Transplant Program, Elizabeth A Moulton, Jeremy M Schraw, Kathleen Hosek, Dana Cerminara, Flor M Munoz, Krupa Mysore

Faculty, Staff and Students Publications

Background: Human adenovirus in immunocompromised patients can be life-threatening. We describe the prevalence, clinical presentation, and treatment of adenovirus after pediatric liver transplantation at a large transplant center.

Methods: We performed a retrospective cohort study of adenovirus infection in children from 2013 to 2022. We compared incidence, clinical characteristics, and outcomes of post-transplant children by adenovirus treatment status.

Results: Adenovirus disease developed in 26% (84/320) children after liver transplant. Median age at liver transplant was 17.5 months, 48% were female; 50% had biliary atresia. Fever (53%), gastrointestinal symptoms (48%), and hepatitis (41%) were the most common clinical presentations at diagnosis. …

Bortezomib And Vorinostat In Combination With Mitoxantrone, Dexamethasone, And Pegasparaginase During Induction And Reinduction For Infants With Acute Lymphoblastic Leukaemia: A Multicentre Single-Arm Phase 1/2 Study, Victor Lewis, Bill H Chang, Eric J Lowe, Jamie Frediani, Catherine Vezina, Bruno Michon, Michael Richards, Erin H Breese, Thai-Hoa Tran, Norman Lacayo, Christine Bolen, Sunil Desai, Jennifer L Pauley, Minxuan Huang, Emily Ashcraft, Cheng Cheng, Kirk R Schultz, Linda Stork, Krysta Schlis, Van T Huynh, Nathan Gossai, Yoav H Messinger, Henrique Bittencourt, Terzah M Horton, Uma Athale, Duncan Stearns, Deborah Schiff, Paul S Gaynon

Faculty, Staff and Students Publications

Background: Acute lymphoblastic leukaemia in infants remains a therapeutic challenge. In preclinical studies we previously identified bortezomib and vorinostat as active agents against KMT2A rearranged (KMT2Ar) leukaemia. The aim of this study was to determine the tolerability of incorporating bortezomib and vorinostat into an acute lymphoblastic leukaemia-chemotherapy backbone for newly diagnosed infants with acute lymphoblastic leukaemia both with and without KMT2Ar.

Methods: In this single-arm phase 1/2 study conducted at 18 hospitals in the USA and Canada, we enrolled patients aged 1 year or younger at the time of diagnosis with newly diagnosed acute lymphoblastic leukaemia or undifferentiated leukaemia (with …

Hes V2.0 Validation And Performance Compared To Galad And Asap In The Heds Cohort, K Rajender Reddy, Neehar Parikh, Amit G Singal, Jorge A Marrero, Aaron P Thrift, Jagpreet Chhatwal, Ziding Feng, Stephanie Page-Lester, Qingchun Jin, Nabihah Tayob, Fasiha Kanwal

Faculty, Staff and Students Publications

Background & aims: We previously developed HES V2.0, a biomarker panel (age, ALT, platelets, etiology, AFP, AFP-L3, DCP, and their 1-year gradients) for early detection of hepatocellular carcinoma (HCC) among patients with cirrhosis. We externally validated HES V2.0 and compared its performance with HES V1.0, GALAD, and ASAP.

Methods: We conducted a PRoBE (prospective specimen-collection, retrospective blinded-evaluation) cohort study in the HEDS (Hepatocellular Carcinoma Early Detection Strategy) cohort of 1,485 patients with cirrhosis, of whom 119 developed HCC. Patient- and test-level true positive rates (TPR) for HCC were calculated at 6, 12, and 24 months before diagnosis, using thresholds at …

Lonp1 Variants Are Associated With Clinically Diverse Phenotypes, David A Sweetser, Jessica L Waxler, Daryl A Scott, Tiana M Scott, Seema R Lalani, Mahshid S Azamian, Jill A Rosenfeld, Bret Bostwick, Lindsay C Burrage, Lance H Rodan, Bianca E Russell, Marina Dutra-Clarke, Michael Kruer, Somayeh Bakhtiarim, Hossein Darvish, David J Amor, Shamima Rahman, Karen Stals, Lisa Bradley, Susan Byrne, Leandra K Tolusso, Beatrix Wong, Laura Benedict, Kimberly Wallis, Kestutis Micke, Cindy Colson, Thomas Smol, Sabrina V Southwick, Kristen A Miller, Michelle L Kush, Odelia Chorin, Annick Rothschild, Wei Wang, Yufeng Shen, Wendy K Chung

Faculty, Staff and Students Publications

LONP1 encodes a mitochondrial protease essential for protein quality control and metabolism. Variants in LONP1 are associated with a diverse and expanding spectrum of disorders, including Cerebral, Ocular, Dental, Auricular, and Skeletal anomalies syndrome (CODAS), congenital diaphragmatic hernia (CDH), and neurodevelopmental disorders (NDD), with some individuals exhibiting features of mitochondrial encephalopathy. We report 16 novel LONP1 variants identified in 16 individuals (11 with NDD, 5 with CDH), further expanding the clinical spectrum. Structural mapping of disease-associated missense variants revealed phenotype-specific clustering, with CODAS variants enriched in the proteolytic chamber and NDD variants more broadly distributed. CODAS is caused by biallelic …

Lean On Me: Social Factors And Diabetes Outcomes Among Young Adults With Type 1 Diabetes Prior To Transitioning To Adult Care, Sarah K Lyons, Randi Streisand, Barbara J Anderson, Tricia S Tang, Siripoom Mckay, Katherine Gallagher, Sridevi Devaraj, Marisa E Hilliard

Faculty, Staff and Students Publications

Aims: Little is known about how different aspects of social relationships relate to diabetes self-management and glycaemic outcomes in young adults with type 1 diabetes (T1D). We examined relationships of general and diabetes-specific social variables with diabetes self-management and HbA1c. We hypothesized diabetes-specific factors would more strongly associate with self-management and HbA1c than general social factors.

Methods: We analysed baseline data from 100 young adults with T1D (Mage = 19.9 ± 1.3 years) enrolled in a randomized controlled trial of a paediatric to adult care transition intervention. We examined associations of self-reported general and diabetes-specific social factors with self-reported self-management …

Comparing Observed With Self-Reported Hand Hygiene Adherence Among Bedside Nurses And Physicians At Two Hospitals In The United States, Karen E Fowler, Serene Jacob, Laura Dillon, Michelle Espiritu, Nathan Houchens, Huberta T Cozart, Barbara W Trautner

Faculty, Staff and Students Publications

Background: Hand hygiene is a core component of infection prevention in healthcare settings. One potential reason for lack of adherence to recommended hand hygiene practices is erroneous self-perception. We aimed to compare perceptions about hand hygiene compliance with objective data.

Methods: Direct observations of hand hygiene performance by nurses and physicians during typical workflow in inpatient general medicine wards were conducted from 12 September 2022 to 27 October 2022 at two academic Veterans Affairs medical centers. Participants were surveyed regarding perceptions about their hand hygiene performance relative to recommended practices.

Results: Among nurses, hand hygiene was performed in 1,397/3,690 (37.9%) …

Application Of A Natural Language Processing Algorithm To Early Asthma Ascertainment For Adults In The Era Of Electronic Health Records, Sunghwan Sohn, Elham Sagheb, Bhavani Singh Agnikula Kshatriya, Shauna M Overgaard, Deepak K Sharma, Sungrim Moon, Elizabeth A Krusemark, Dave Watson, Sergio E Chiarella, Miguel A Park, Jason D Greenwood, Randy M Foss, Zhandong Liu, Meera Gupta, Carla M Davis, Wade Schulz, Hongfang Liu, Young J Juhn

Faculty, Staff and Students Publications

Background: The natural language processing (NLP) algorithm for predetermined asthma criteria (NLP-PAC) was successfully developed and validated for automatically ascertaining pediatric asthma from electronic health record (EHRs) systems. A scalable, efficient, and automated tool for ascertaining adult asthma status from EHRs remains nonexistent.

Objective: We validated NLP-PAC enabling ascertainment and early identification of adult asthma status in their EHRs.

Methods: We applied the validated NLP-PAC to EHRs of a convenient sample (adult cohorts who participated in our previous population-based studies) in which a reference standard (ie, asthma status defined by manual chart review) is available. The performance of NLP-PAC was …

Validation Of Longitudinal Biomarker Screening Algorithms For Hcc Detection In Patients With Cirrhosis, Neehar D Parikh, Anna S Lok, Camden Lopez, Stephanie Page-Lester, Lewis R Roberts, Rajender Reddy, Michelle Luster, Saira Khaderi, Sumeet K Asrani, Hashem B El-Serag, Fasiha Kanwal, Ziding Feng, Nabihah Tayob

Faculty, Staff and Students Publications

Background: Blood-based biomarker panels, including GALAD, have been proposed as an alternative to abdominal ultrasound for hepatocellular carcinoma (HCC) surveillance. Studies suggest longitudinal evaluation of biomarkers can improve test performance; however, no large studies have validated these findings.

Methods: We leveraged the HCC Early Detection Strategy (HEDS) study (n=1019 patients with cirrhosis; 99 incident HCC) and Texas HCC Consortium (THCCC) (n=2345 patients with cirrhosis; 126 incident HCC) to compare the performance of fixed-threshold GALAD (cutoff of -1.36), and 4 longitudinal algorithms: longitudinal GALAD, PALAD, mFB-ALAD, and mPEB-ALAD. The HEDS cohort was used to derive longitudinal algorithms, and external validation was …

Risk Factors For Acute Rejection In Pediatric Lung Transplantation And Its Impact On Graft Failure, Selena Li, Abbas Rana

Faculty, Staff and Students Publications

Background: Although acute rejection is a common complication of lung transplantation, few studies have analyzed risk factors for acute rejection in pediatric lung transplant patients. The purpose of this study was to examine risk and protective factors for acute rejection in pediatric lung transplantation and its impact on graft failure.

Methods: A retrospective analysis was performed on lung transplant data for a cohort of 906 pediatric patients from the Organ Procurement and Transplantation Network (OPTN) Database between October 1, 1987, and June 30, 2023. Multivariable logistic regression was conducted to identify risk and protective factors for acute rejection, adjusting for …

Rural-Urban Differences In Use Of Mental Health Care For Serious Mental Illness At The Veterans Health Administration: A Retrospective Cohort Analysis, Liang Chen, Amy K Cuellar, Giselle Day, Alexandra Zingg, Julianna Hogan, Jan A Lindsay

Faculty, Staff and Students Publications

PURPOSE: Rural Veterans with serious mental illness (SMI) encounter significant barriers to accessing mental health care, related to SMI symptoms and rurality. A 2023 Government Accountability Office report found that rural Veterans used Veterans Health Administration (VHA) intensive mental health care for SMI less than urban Veterans relative to their population distributions. Our purpose was to deepen understanding of rural-urban differences in use of VHA mental health care among Veterans with SMI.

METHODS: Using VHA databases, we conducted a retrospective cohort analysis of 387,477 Veterans diagnosed with SMI, examining rurality as a predictor of intensive care for SMI and other …

External Validation Of Calculator For Cesarean Delivery During Induction Of Labor, Estefania Guthrie, Ipsita Ghose, Hector Mendez-Figueroa, Suneet P Chauhan

Faculty, Staff and Students Publications

Objective: To validate a published risk calculator to predict cesarean delivery (CD) among singletons undergoing induction of labor.

Methods: Our retrospective cohort study included singletons undergoing induction of labor. A predicted CD score was calculated for each individual based on a previously developed calculator. External validation of the calculator was assessed by the discriminative power of the model by using the area under the receiver operating characteristic curve, and by a calibration curve. The score was categorized as less than 10%, 10% to less than 30%, and 30% or greater. The primary outcome was CD. The secondary outcomes were a …

Toward Scientific Rigor: Setting Standards For Indirect Calorimetry Analysis And Reporting

Faculty, Staff and Students Publications

Indirect calorimetry determines energy expenditure by measuring respiratory gas exchange. The approach is based on the principle that nutrient metabolism consumes O2 and produces CO2 and water in predictable ratios that can be compared with heat production. Due to the impracticality and high cost of direct calorimetry, indirect calorimetry is the major approach for modern metabolic studies in preclinical models. Despite the broad adoption of this method in rodent phenotyping, the field has lacked standardized methods for analyzing, representing, and sharing these data, limiting scientific progress. The recent review in Nature Metabolism by the International Indirect Calorimetry Consensus Committee (IICCC) …

Living Evidence-Informed Guideline On The Early Detection Of Oral Squamous Cell Carcinoma And Potentially Malignant Disorders: Cytology Adjuncts To Determine The Need For Biopsy, Version 2026 1.0, James C Melville, Anita S H Patel, Alessandro Villa, Michael Glick, Mark W Lingen

Faculty, Staff and Student Publications

Background: Early detection of oral potentially malignant disorders and oral cavity cancer can improve patient prognosis. The guideline panel addressed the use of cytology adjuncts to screen adults without mucosal abnormalities and determine the need for biopsy among adults with mucosal abnormalities.

Types of studies reviewed: The guideline panel used the Grading of Recommendations Assessment, Development and Evaluation Evidence to Decision framework to formulate recommendations. The authors conducted reviews to assess the benefits and harms of cytology adjuncts and people and clinician values and preferences as they relate to adjunct tests and biopsy of mucosal abnormalities. As part of the …

Histologic Analysis Of Peri-Implant Soft Tissue Around External Hexagon And Morse Taper Implant Connections

Faculty, Staff and Student Publications

Background: Twenty patients rehabilitated with screw-retained full-arch implant-supported prostheses functioning for at least one year were included.

Material and methods: This clinical study included 20 patients rehabilitated with screw-retained full-arch implant-supported prostheses in function for at least 1 year. Participants were allocated into two groups according to the implant-abutment connection design: external hexagon (EH; n = 10) and Morse taper (MT; n = 10). One peri-implant soft tissue biopsy specimen was obtained from each patient and processed for hematoxylin-eosin staining. Histological evaluation assessed epithelial hyperplasia, epithelial organization, inflammatory infiltrate intensity, and connective tissue fibrosis. Data normality was assessed using the …

A Comprehensive Biomechanical Material Characterization Of The Human Breast Fibro-Structural Support System, Aroj Bhattarai, Gregory P Reece, Kristy K Brock, Krishnaswamy Ravi-Chandar

Faculty, Staff and Student Publications

Breast surgery for aesthetic purposes, such as breast augmentation or breast reduction, and breast reconstruction after cancer treatment require an accurate structural (anatomical) and mechanical (functional) understanding of the breast components, including the fascial-ligamentous support system of the breast, to achieve optimal results. This paper aims to provide a comprehensive description of the mechanical behavior of the ligamentous and fascial connective tissues of the human female breast. Fasciae and ligaments obtained from 17 patients between 35 and 85 years of age who were undergoing mastectomy and three female cadavers were tested. Uniaxial tensile tests were conducted, and three constitutive models …

Optimizing Feasibility And Acceptability Of An Online Expressive Writing Intervention For Survivors Of Adolescent And Young Adult Cancer: A Pilot Randomized Trial Of Iterative Modifications And Outcomes, Eunju Choi, Yusi Aveva Xu, Celia Cy Wong-Meli, Michael E Roth, Yisheng Li

Faculty, Staff and Student Publications

Objective: To evaluate the feasibility of an online expressive writing (EW) intervention for survivors of adolescent and young adult (AYA) cancer and determine whether iterative, theory-driven modifications can enhance response, adherence, and completion rates.

Methods: In this randomized pilot trial, survivors of AYA cancer were recruited through a hospital-based AYA oncology clinic and an online community. Forty participants were randomly assigned to the EW intervention or control group. To improve on lower-than-expected adherence and completion rates in a previous cohort, the protocol was iteratively revised using the Framework for Reporting Adaptations and Modifications to Evidence-based Implementation Strategies (FRAME-IS). Modifications included …

Pharmacokinetic Modeling Strategies For Dynamic Hyperpolarized Urea Imaging, Keith A Michel, Collin J Harlan, Christopher M Walker, Matthew E Merritt, Yunyun Chen, James A Bankson

Faculty, Staff and Student Publications

Purpose: To evaluate pharmacokinetic modeling methods for quantification of tissue perfusion/permeability with hyperpolarized 13C urea.

Methods: Three models for quantitative analysis of dynamic HP urea imaging data were proposed and evaluated in numerical simulations and a thyroid cancer mouse model. A multicompartment model resembling the extended Tofts model for DCE-MRI (Model I) and two simplified models were used. The simplified models each eliminate a volume parameter representing vascular (Model II) or impermeable cellular space (Model III). Signal curves were generated from Model I, and models were fit to these synthetic data to quantify the effects of acquisition settings, bias in …

Defining A Quantitative Threshold For Adaptive Re-Planning Using A Percentile-Based Scoring System, Alexandra O Leone, Christine B Peterson, Anna Lee, Adam S Garden, G Brandon Gunn, Amy C Moreno, C David Fuller, Jay P Reddy, Karen Hoffman, Ivan Vazquez, Ming Yang, Joshua S Niedzielski, Laurence E Court, Thomas J Whitaker

Faculty, Staff and Student Publications

Background: Despite the frequent need for adaptive planning in head and neck proton therapy, no quantitative indicators have been identified to determine when a plan should be adapted. Here, we aimed to determine a quantitative threshold for the change in plan quality between the primary treatment plan and verification plans that correlates with the physician's decision to adapt.

Methods: Primary treatment and verification plans were extracted from the clinical treatment planning system for 167 patients who underwent intensity-modulated proton therapy for base of tongue, tonsillar, or oropharyngeal cancers, with and without nodal involvement, between 2016 and 2021. All plans were …

Analysis Of Patients With Monocytic And Monocytic-Like Acute Myeloid Leukemia, Including Aml-M4 And Aml-M5, Treated With Venetoclax Plus Azacitidine, Marina Konopleva, Courtney D Dinardo, Yan Sun, Paul Jung, Sanam Loghavi, Monique Dail, Daniel A Pollyea

Faculty, Staff and Student Publications

No abstract provided.

Barriers To Occupational And Physical Therapy Utilization For Children With Cancer, Maria C Swartz, Shiming Zhang, Donna Kelly, Clark R Andersen, Keri Schadler, Eduardo Gonzalez Villarreal, Amy Heaton, Karen Moody

Faculty, Staff and Student Publications

Introduction: Occupational and physical therapy (OT/PT) referrals and utilization barriers for childhood cancer patients have not been adequately examined. The current study investigated factors influencing referrals to and utilization of OT/PT services among children with cancer at an NIH-designated cancer center.

Methods: This retrospective cohort study included pediatric cancer patients (up to 18.99 years) presenting to the center over a 33.5-month period. Variables that could influence referrals to OT/PT were extracted from the electronic medical record (EMR) including OT and PT referrals (inpatient and outpatient), OT and PT consult completion, age at diagnosis, cancer type, sex, race/ethnicity, insurance, cancer treatment, …

Impact Of Mutational Landscape And Burden On Rbc Transfusion Response In Patients With Lower-Risk Myelodysplastic Syndromes (Lr-Mds) In The Commands Study, Rami S Komrokji, Sheida Hayati, Manuel Ugidos, Guillermo Garcia-Manero, Matteo Giovanni Della Porta, Valeria Santini, Anita K Gandhi, Rajasekhar N V S Suragani

Faculty, Staff and Student Publications

The COMMANDS trial established luspatercept as a first‐line treatment for anemia in transfusion‐dependent lower‐risk (LR) myelodysplastic syndromes (MDS). Here we report red blood cell (RBC) transfusion response analysis based on somatic mutations profile and disease risk for patients treated with luspatercept or epoetin alfa in the COMMANDS trial. Of 350 evaluable patients, 238 (68.0%) had MDS with multiple lineage dysplasia and ring sideroblasts (RS) according to World Health Organization 2016 criteria, and 320 (91.4%) had somatic mutations in ≥ 1 gene (median, 2) with median variant allele frequencies (VAF) of 2%–59%. Mutation profiles were similar in the treatment groups. Luspatercept …

Segmental Tracheal Resection For Thyroid Cancer: Perioperative Morbidity, Locoregional Control, And Survival, Anastasios Maniakas, David C Wilde, Isabelle Fournier, Emily K Hyde, Li Xu, Neil D Gross, Victoria Banuchi, Naifa L Busaidy, Maria E Cabanillas, Priyanka Iyer, Ramona Dadu, Steven G Waguespack, Mimi I Hu, G Brandon Gunn, Michael Kwon, Salmaan Ahmed, Michelle D Williams, Mark E Zafereo

Faculty, Staff and Student Publications

Background: Segmental tracheal resection is rarely needed for advanced thyroid cancer but is among the most complex, high-risk thyroid surgeries.

Methods: Retrospective study of patients undergoing segmental tracheal resection for thyroid cancer at MD Anderson Cancer Center (2005-2024).

Results: We identified 120 patients with a median follow-up of 4.6 years (range 0.02-16.38). Papillary thyroid cancer was most common (68%). The median number of tracheal rings resected was 4 (range 1-9). Seventeen (14%) patients had a new tracheostomy placed at the time of surgery, with 11 (9%) remaining trach-dependent at last follow-up. Twenty-six (22%) patients had a return to the operating …

Intraoperative Ultrasound Imaging Features Guiding Surgical Strategy In Spinal Cord Ependymoma Resection, Esteban Ramirez-Ferrer, Ian E Mccutcheon, Gil Kimchi, Behrang Amini, Romulo Andrade Almeida, Juan Pablo Zuluaga-Garcia, Christopher A Alvarez-Breckenridge, Jeffrey S Weinberg, Laurence D Rhines, Claudio E Tatsui

Faculty, Staff and Student Publications

Background and objectives: Preoperative imaging provides surgeons with an initial estimate of tumor infiltration and the likelihood of achieving an en-bloc resection in spinal cord ependymomas, yet the definitive decision is made intraoperatively. This study characterizes the intraoperative ultrasound (iUS) features that guide real-time surgical strategy and are associated with successful en-bloc removal.

Methods: A retrospective review of iUS images obtained during resection of spinal cord ependymomas was performed. The presence of a peritumoral halo representing the transition zone between the tumor and the spinal cord, the dorsal sagittal area of the spinal cord overlying the tumoral poles, the presence …

Physical Activity In Osteosarcoma Patients During And Post Therapy: A Single Site Prospective Observational Study, Elysia R Cohen, Clark Andersen, Karen Moody, Maria C Swartz, Michael C Robertson, Theresa Honey, Grace Waterman, Keri Schadler

Faculty, Staff and Student Publications

PURPOSE: Osteosarcoma is the most common primary bone tumor in childhood and adolescence. Many patients face long-term impairments in their mobility and function after treatment, leading to a decrease in their quality of life. Exercise has been shown to improve functional recovery and improve quality of life in patients with cancer, though data specific to children with osteosarcoma are sparse. Exercise has also been shown to be feasible in patients undergoing chemotherapy, with numerous potential benefits to health and quality of life. To design the most effective exercise interventions for children and adolescents with osteosarcoma, we must first understand the …

Clemastine Ameliorates Cognitive Deficits In An Experimental Rat Model Of Chronic Cerebral Hypoperfusion, Xuemei Zong, Zhihai Huang, Fanfei Kong, Yu Feng, Yulan Zhang, Hung Wen Lin, Quanguang Zhang

Faculty, Staff and Student Publications

Chronic cerebral hypoperfusion (CCH) profoundly affects patient well-being and has been proposed as a risk factor for cognitive impairment and dementia. However, due to the limited understanding of the pathophysiology of CCH, there are currently no effective preventive or therapeutic approaches for CCH-associated cognitive impairment. Therefore, identifying new targets for CCH is essential to bridge this knowledge gap. In this study, we sought to determine whether enhanced myelination could prevent cognitive impairment associated with CCH. Experimental CCH was induced via bilateral common carotid artery occlusion (BCCAO) in rats, and clemastine, a well-established pro-myelinating agent, was administered to boost myelin renewal. …

Trends And Challenges: A 15-Year Review Of Imaging And Radiation Oncology Core Anthropomorphic Phantom Audits For Proton Therapy, Lian Duan, Hunter S Mehrens, Stephen F Kry, Jessica R L Lowenstein, Nadia Hernandez, Paige A Taylor

Faculty, Staff and Student Publications

Purpose: This study aims to analyze the trends in institutional performance on Imaging and Radiation Oncology Core (IROC) proton phantoms and to investigate the impact of treatment parameters on proton therapy delivery accuracy.

Materials and methods: We analyzed 402 IROC anthropomorphic phantom audits performed by 57 institutions worldwide between 2009 and 2024, including brain, head and neck (H&N), spine, prostate, lung, and liver phantoms. Dosimetric assessments included thermoluminescent dosimeters (TLDs) for dose comparison and gamma analysis of radiochromic film. The lung and liver phantoms were irradiated with simulated motion. Univariate analysis was performed to evaluate the relationships between treatment parameters …

Information Extraction From Clinical Notes: Are We Ready To Switch To Large Language Models?, Jimin Huang, Vipina K Keloth, Vincent J Zhang, Ruey-Ling Weng, Cathy Shyr, Qingyu Chen, Xiaoqian Jiang, Kirk E Roberts, Hua Xu

Faculty, Staff and Student Publications

Objectives: To assess the performance, generalizability, and computational efficiency of instruction-tuned Large Language Model Meta AI (LLaMA)-2 and LLaMA-3 models compared to bidirectional encoder representations from transformers (BERT) for clinical information extraction (IE) tasks, specifically named entity recognition (NER) and relation extraction (RE).

Materials and methods: We developed a comprehensive annotated corpus of 1588 clinical notes from 4 data sources-UT Physicians (UTP) (1342 notes), Transcribed Medical Transcription Sample Reports and Examples (MTSamples) (146), Medical Information Mart for Intensive Care (MIMIC)-III (50), and Informatics for Integrating Biology and the Bedside (i2b2) (50), capturing 4 clinical entities (problems, tests, medications, other treatments) …

Large Language Models For Bioinformatics, Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yao Lu, Yue Wang, Peilong Wang, Lin Zhao, Tao Wang, Yufang Liu, Luyang Fang, Ziyu Liu, Zhengliang Liu, Yiwei Li, Zihao Wu, Junhao Chen, Hanqi Jiang, Yi Pan, Zhenyuan Yang, Jingyuan Chen, Shizhe Liang, Wei Zhang, Terry Ma, Yuan Dou, Jianli Zhang, Xinyu Gong, Qi Gan, Yusong Zou, Zebang Chen, Yuanxin Qian, Shuo Yu, Jin Lu, Kenan Song, Xianqiao Wang, Andrea Sikora, Gang Li, Xiang Li, Quanzheng Li, Yingfeng Wang, Lu Zhang, Yohannes Abate, Lifang He, Wenxuan Zhong, Rongjie Liu, Chao Huang, Wei Liu, Ye Shen, Ping Ma, Hongtu Zhu, Yajun Yan, Dajiang Zhu, Tianming Liu

Faculty, Staff and Student Publications

With the rapid advancements in large language model technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and …

Influence Of Pullback Pressure Gradient On Residual Angina At One Year, Takuya Mizukami, Kazumasa Ikeda, Daniel Munhoz, Koshiro Sakai, Jeroen Sonck, Hitoshi Matsuo, Toshiro Shinke, Hirohiko Ando, Brian Ko, Simone Biscaglia, Fernando Rivero, Thomas Engstrøm, Antonio Maria Leone, Lokien X Van Nunen, William F Fearon, Evald Høj Christiansen, Stephane Fournier, Liyew Desta, Andy Yong, Julien Adjedj, Javier Escaned, Masafumi Nakayama, Ashkan Eftekhari, Frederik M Zimmermann, Tatyana Storozhenko, Frédéric Bouisset, Domenico Galante, Bruno R Da Costa, Gianluca Campo, Colin Berry, Damien Collison, Tetsuya Amano, Divaka Perera, Allen Jeremias, Ziad A Ali, Ethan Korngold, Eric Wyffels, Adriaan Wilgenhof, Nico Pijls, Bernard De Bruyne, Nils P Johnson, Carlos Collet

Faculty, Staff and Student Publications

Background: The pullback pressure gradient (PPG) is a novel physiological metric that quantifies coronary artery disease patterns as focal or diffuse on a scale from 0 to 1. This study assessed the relationship between PPG and residual angina at 1 year.

Methods: PPG Global is a prospective, investigator-initiated, single-arm, multicenter study that enrolled patients with at least 1 lesion with a fractional flow reserve ≤0.80 intended to be treated with percutaneous coronary intervention. After the PPG calculation, physicians could revise treatment assignment to medical therapy or coronary artery bypass graft surgery instead of percutaneous coronary intervention. Focal and diffuse disease …

An Artificial Intelligence Model For Electrocardiogram Detection Of Occlusion Myocardial Infarction: A Retrospective Study To Reduce False-Positive Cath Lab Activations, Benjamin L Cooper, Evan A Genova, Carrie A Bakunas, Catherine E Reynolds, Benjamin Karfunkle, Nils P Johnson

Faculty, Staff and Student Publications

Aims: Existing ST-segment elevation myocardial infarction (STEMI) alert pathways that rely on traditional STEMI criteria perform suboptimally. We aimed to evaluate the diagnostic performance of an artificial intelligence (AI) model to detect acute occlusion myocardial infarction (OMI) from the routine 12-lead electrocardiogram (ECG) and, specifically, its potential to reduce false-positive activations.

Methods and results: Consecutive adults managed via the STEMI pathway were included from a tertiary academic medical centre between January 2022 and December 2023. Cases without an available ECG for review, death prior to catheterization, or alternative reasons for activation (i.e. electrical instability or urgent interventions) were excluded. Pre-coronary …