Abstracts tagged "Bioinformatics"

Abstract Number: 2804 • 2018 ACR/ARHP Annual Meeting
Identifying Lupus Patients in Electronic Health Records: Development and Validation of Machine Learning Algorithms and Application of Rule-Based Algorithms
April Jorge¹, Victor M. Castro², April Barnado³, Vivian Gainer², Chuan Hong⁴, Tianxi Cai², Robert Carroll⁵, Leslie Crofford³, Karen Costenbader⁶, Katherine P. Liao⁷, Elizabeth Karlson⁶ and Candace H. Feldman⁶, ¹Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, ²Research Information Systems and Computing, Partners Healthcare, Boston, MA, ³Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, ⁴Harvard T.H. Chan School of Public Health, Boston, MA, ⁵Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, ⁶Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, ⁷Brigham and Women's Hospital, Boston, MA
Background/Purpose: To utilize electronic health records (EHR) to study SLE, phenotypic algorithms are needed to accurately identify these patients. We aimed to generate an EHR…
Abstract Number: 2903 • 2018 ACR/ARHP Annual Meeting
Single Cell Association Testing Identifies an Expanded Th1-Skewed Cytotoxic Effector CD4+ T Cell Subset in Rheumatoid Arthritis
Chamith Fonseka¹, Deepak Rao², Nikola Teslovich³, Ilya Korsunsky⁴, Susan Hannes⁵, Kamil Slowikowski¹, Michael Gurish⁶, Laura T. Donlin⁷, James A. Lederer⁸, Michael Weinblatt⁹, Elena Massarotti⁹, Jonathan Coblyn⁹, Simon Helfgott¹⁰, Derrick J. Todd¹¹, Vivian P. Bykerk¹², Elizabeth Karlson¹³, Joerg Ermann¹⁴, Yvonne C. Lee¹⁵, Michael Brenner¹⁶ and Soumya Raychaudhuri^1,17, ¹Divisions of Genetics and Rheumatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ²Human Immunology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ³Division of Genetics and Rheumatology, Department of Medicine, Harvard Medical School, Boston, MA, ⁴Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ⁵Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, ⁶Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ⁷Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, ⁸Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ⁹Brigham and Women's Hospital, Boston, MA, ¹⁰Division of Rheumatology, Brigham and Women’s Hospital, Boston, MA, ¹¹Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ¹²Deptartment of Rheumatology, Hospital for Special Surgery, New York, NY, ¹³Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ¹⁴Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, ¹⁵Northwestern University Feinberg School of Medicine, Chicago, IL, ¹⁶Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ¹⁷Program in Medical and Population Genetics, Broad Institute, Boston, MA
Background/Purpose: Defining the precise CD4+ T cell subsets that are dysregulated in RA patients is critical to deciphering pathogenesis. Here we present Mixed effects modeling…
Abstract Number: 583 • 2018 ACR/ARHP Annual Meeting
Identification of a Protein Profile Useful to Predict Response to Methotrexate in Early Rheumatoid Arthritis Patients
Cristina Ruiz-Romero¹, Florencia Picchi², Lucia González², Rebecca Hands³, Valentina Calamia², Patricia Fernández⁴, Maria Camacho², Rocío Paz², Conrad Bessant⁵, Costantino Pitzalis³ and Francisco J Blanco⁶, ¹Rheumatology Division, ProteoRed, PRB2-ISCIII. INIBIC-Hospital Universitario A Coruña, A Coruña, Spain, ²Rheumatology Research Group, Proteomics Unit-ProteoRed/ISCIII, INIBIC-CHUAC, A Coruña, Spain, ³Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London, School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom, ⁴Proteomics group, Rheumatology Division, ProteoRed, PRB2-ISCIII. INIBIC-Hospital Universitario A Coruña, La Coruña, Spain, ⁵School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom, ⁶Rheumatology Divison, INIBIC-Hospital Universitario A Coruña, A Coruña, Spain
Background/Purpose: Among the best known disease-modifying antirheumatic drugs, Methotrexate (MTX) is one of the most effective and widely used medications. It is used as a…
Abstract Number: 836 • 2018 ACR/ARHP Annual Meeting
Genetic Risk Score Prediction in Ankylosing Spondylitis
Zhixiu Li¹, Erika De Guzman¹, Jessica Harris¹, Nurullah Akkoc², Mahdi Mahmoudi³, Maxime Breban⁴, Chung-Tei Chou⁵, Michael Weisman⁶, Lianne S. Gensler⁷, Michael Ward⁸, Mohammad H. Rahbar⁹, Laura A. Diekman¹⁰, Tae-Hwan Kim¹¹, Paul Leo¹, John D. Reveille¹⁰, Paul Wordsworth¹², Matthew Brown¹ and Huji Xu¹³, ¹Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia, Brisbane, Australia, ²Rheumatology, İzmir, Turkey, İzmir, Turkey, ³Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran, Tehran, Iran (Islamic Republic of), ⁴Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, Boulogne, France, Boulogne, France, ⁵Division of Allergy-Immunology-Rheumatology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, Taipei, Taiwan, ⁶Cedars-Sinai Medical Center, Los Angeles, CA, USA, Los Angeles, CA, ⁷University of California San Francisco, San Francisco, CA, ⁸National Institutes of Health, Bethesda, MD, USA, Bethesda, MD, ⁹Biostatistics/Epidemiology/Research Design (BERD) Core | Center for Clinical and Translational Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, USA, Houston, TX, ¹⁰Rheumatology, McGovern Medical School at the University of Texas Health Science Center at Houston, USA, Houston, TX, ¹¹Rheumatology, The Hospital for Rheumatic Diseases, Hanyang University, Seoul, Korea, Seoul, Korea, Republic of (South), ¹²Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK, Oxford, United Kingdom, ¹³School of Clinical Medicine, Tsinghua University, Beijing, China, Beijing, China
Background/Purpose: The diagnosis of ankylosing spondylitis (AS) is delayed by on average 8–11 years after the onset of symptoms, and there is increasing evidence that…
Abstract Number: 41 • 2017 ACR/ARHP Annual Meeting
A Fine Bioinformatical Analysis of Lymphocyte Distribution Predicts the Diagnosis of Systemic Autoimmune Diseases
Quentin Simon¹, Bénédicte Rouvière¹, Tifenn Martin¹, Lucas Le Lann¹, Alain Saraux¹, Valérie Devauchelle-Pensec¹, Concepcion Marañón², Nieves Varela Hernández², Aleksandra Dufour³, Carlo Chizzolini⁴, Ellen de Langhe⁵, Nuria Barbarroja⁶, Chary Lopez-Pedrera⁷, Velia Gerl⁸, Aurelie Degroof⁹, Julie Ducreux¹⁰, Elena Trombetta¹¹, Tianlu Li¹², Marta Alarcón-Riquelme¹³, Christophe Jamin¹ and Jacques-Olivier Pers¹, ¹U1227, Université de Brest, Inserm, Labex IGO, CHU de Brest, Brest, France, ²GENYO, Centre for Genomics and Oncological Research Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain, ³Immunology & Allergy, University Hospital and School of Medicine, Geneva, Switzerland, ⁴University hospital of Geneva, Geneva, Switzerland, ⁵Rheumatology, University Hospital KU Leuven, Leuven, Belgium, ⁶Rheumatology service, IMIBIC/Reina Sofia Hospital/University of Cordoba, Cordoba, Spain, ⁷IMIBIC/Reina Sofia Hospital/ University of Cordoba, Cordoba, Spain, ⁸Department of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, Germany, ⁹Pôle de Maladies Rhumatismales, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium, ¹⁰Pôle de pathologies rhumatismales inflammatoires et systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium, ¹¹Laboratorio di Analisi Chimico Cliniche e Microbiologia - Servizio di Citofluorimetria, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milano, Italy, ¹²Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain, ¹³GENYO. Center for Genomics and Oncological Research, Granada, Spain
Background/Purpose : We investigated 194 individuals with SADs (38 primary Sjögren’s syndrome (pSS), 47 rheumatoid arthritis (RA), 46 systemic lupus erythematosus (SLE), 42 systemic sclerosis…
Abstract Number: 177 • 2017 ACR/ARHP Annual Meeting
Intronic Variants of the B-Cell Proliferator RASGRP3 Affect Its Expression, and Might Contribute to Lupus Risk
Bhupinder Singh¹, Philip Borden², Julio Molineros³, Celi Sun³, Loren Looger² and Swapan Nath¹, ¹Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, OKlahoma City, OK, ²Howard Hughes Medical Institute, Ashburn, VA, ³Oklahoma Medical Research Foundation, OKlahoma City, OK
Background/Purpose: Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with complex genetic underpinnings. Variants from RASGRP3 (RAS Guanyl Releasing Protein 3) is one of…
Abstract Number: 183 • 2017 ACR/ARHP Annual Meeting
Allele-Dependent Binding of a Viral Protein to Autoimmune Disease-Associated Genetic Variants
Matthew Weirauch¹, Daniel Miller², Leah C. Kottyan³, Ignacio Ibarra⁴, Arthur Lynch², Sayeed Syed⁵, Xiaoting Chen², Erin Zoller², Connor Schroeder², Josh Lee², Albert Magnusen⁶, Ally Yang⁷, Timothy R. Hughes⁷, Joo-Seop Park⁸, Charles Vinson⁵ and John B. Harley^2,9, ¹Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ²Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ³Center for Autoimmune Genomics and Etiology (CAGE), Division of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ⁴Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany, ⁵NCI, Bethesda, MD, ⁶Center of Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ⁷University of Toronto, Toronto, ON, Canada, ⁸Divisions of Urology and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ⁹US Department of Veterans Affairs Medical Center, Cincinnati, OH
Background/Purpose: Risk factors are known for many diseases, but the etiologies of most autoimmune diseases remain unknown and are idiopathic. Pathogenesis of disease likely involves…
Abstract Number: 184 • 2017 ACR/ARHP Annual Meeting
An Epigenome-Guided Approach to Causal Variant Discovery in Autoimmune Disease
Richard C. Pelikan¹, Jennifer A. Kelly², Yao Fu², Caleb Lareau³, Graham B. Wiley¹, Stuart Glenn¹, Martin Aryee^3,4, Courtney Montgomery⁵ and Patrick Gaffney², ¹Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, ²Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, ³Department of Biostatistics, Harvard T.H. Chan School of Public Health, Charlestown, MA, ⁴Department of Pathology, Harvard Medical School, Boston, MA, ⁵Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
Background/Purpose: Genome-wide association studies have identified thousands of genetic associations with complex human diseases and traits. However, establishing the truly causal regions of risk haplotypes…
Abstract Number: 1334 • 2017 ACR/ARHP Annual Meeting
Identification of Key Regulators for Resolution of Chronic Inflammatory Arthritis through a Systems Approach
Jin-Sun Kong Sr.¹, Ji-Hwan park², Seung-Ah Yoo Sr.¹, Jung Hee Koh³, Daehee Hwang⁴ and Wan-Uk Kim Sr.⁵, ¹The Catholic University of Korea, Center for Integrative Rheumatoid Transcriptomics and Dynamics, seoul, Korea, Republic of (South), ²Center for Plant Aging Research, DGIST, Daegu 42988, South Korea, Daegu, Korea, Republic of (South), ³Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea, Republic of (South), ⁴Center for Plant Aging Research, DGIST, Daegu 42988, South Korea, Department of New Biology, DGIST, Daegu 42988, South Korea, Daegu, Korea, Republic of (South), ⁵The Catholic University of Korea, Department of Internal Medicine, seoul, Korea, Republic of (South)
Background/Purpose: Collagen-induced arthritis(CIA), a representative animal model of chronic inflammatory arthritis, follows phases of induction, peak of inflammation and resolution. This study aims to identify…
Abstract Number: 2405 • 2017 ACR/ARHP Annual Meeting
Biological Function Integrated Prediction of Severe Radiographic Progression in Rheumatoid Arthritis: A Nested Case Control Study
Young Bin Joo¹, Yul Kim², Youngho Park³, Kwangwoo Kim⁴, Jeong Ah Ryu⁵, Seunghun Lee⁶, So-Young Bang⁷, Hye-Soon Lee⁸, Gwan-Su Yi⁹ and Sang-Cheol Bae⁷, ¹Internal Medicine, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea, Republic of (South), ²Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea, Republic of (South), ³Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea, Republic of (South), ⁴4Department of Biology, Kyung Hee University, Seoul, Korea, Republic of (South), ⁵Department of Radiology, Hanyang University Hospital, Seoul, Korea, Republic of (South), ⁶17 Haengdang-Dong, Seongdong-G, Hanyang University Hospital, Seoul, Korea, Republic of (South), ⁷Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea, Republic of (South), ⁸Hanyang University Guri Hospital, Gyeonggi-do, Korea, Republic of (South), ⁹Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea, Republic of (South)
Background/Purpose: Radiographic progression is reported to be highly heritable in rheumatoid arthritis (RA). However, previous study using genetic loci showed an insufficient accuracy of prediction…
Abstract Number: 2931 • 2017 ACR/ARHP Annual Meeting
Multi-Organ RNA-Sequencing of Patients with Systemic Sclerosis (SSc) Finds That Intrinsic Subsets Are Conserved across Organ Systems
Bhaven K. Mehta¹, Jennifer Franks², Guoshuai Cai², Diana Toledo³, Tammara A. Wood², Kimberly A. Archambault¹, Noelle Kosarek¹, Kathleen Kolstad⁴, Marianna Stark⁵, Antonia Valenzuela⁶, David Fiorentino⁷, Nielsen Fernandez-Becker⁸, Laren Becker⁸, Linda Nguyen⁸, John Clarke⁹, Francesco Boin¹⁰, Paul Wolters¹¹, Lorinda Chung¹² and Michael L. Whitfield¹, ¹Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, ²Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, ³Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, ⁴Rheumatology, Stanford University Medical Center, Stanford, CA, ⁵Stanford University, Stanford, CA, ⁶Stanford University School of Medicine, Stanford, CA, ⁷Department of Dermatology, Stanford University School of Medicine, Palo Alto, CA, ⁸Gastroenterology & Hepatology, Stanford University School of Medicine, Palo Alto, CA, ⁹Medicine/Gastroenterology, Stanford University, Stanford, CA, ¹⁰Rheumatology, University California, San Francisco, San Francisco, CA, ¹¹Pulmonary Division, Department of Medicine, University of California, San Francisco, San Francisco, CA, ¹²Rheumatology, Stanford University Medical Center, Palo Alto, CA
Background/Purpose: While skin fibrosis is a hallmark of systemic sclerosis (SSc), internal organ involvement is the primary cause of morbidity and mortality, often related to…
Abstract Number: 1201 • 2016 ACR/ARHP Annual Meeting
Deconvolution of Immune Cell Proportions from Whole Blood RNA Using Next-Generation Sequencing
Omar Jabado¹, Sarah Hu², Julie Carman³, Suzanne Suchard³, Deborah Lee⁴, Zhenhao Qi⁵, Stefan Kirov⁶, Ryan Golhar⁷, Aiqing He⁷, Cate Speake⁸, Peter S. Linsley⁸, Steven G. Nadler⁹ and Somnath Bandyopadhyay², ¹3551 Lawrenceville Princeton, Bristol-Myers Squibb, Princeton, NJ, ²Bristol-Myers Squibb, Princeton, NJ, ³Discovery Translational Sciences Group, Bristol-Myers Squibb, Princeton, NJ, ⁴Discovery Immunoscience, Bristol-Myers Squibb, Princeton, NJ, ⁵Exploratory Clinical and Translational Research, Bristol-Myers Squibb, Princeton, NJ, ⁶Genetically Defined Diseased & Genomics, Bristol-Myers Squibb, Princeton, NJ, ⁷Genetically Defined Diseases & Genomics, Bristol-Myers Squibb, Princeton, NJ, ⁸Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, ⁹Immunosciences Translational Research, Bristol-Myers Squibb, Princeton, NJ
Background/Purpose: Measurements of immune cell proportions from whole blood can be used to detect pharmacodynamic effects, as a marker for prognosis and to aid in…
Abstract Number: 1207 • 2016 ACR/ARHP Annual Meeting
Design of a Multiplex Serum Proteome Assay to Monitor Biologic Drug Response in Rheumatoid Arthritis Patients
Niamh Callan¹, Aisha Butt¹, Stephen R. Pennington², Cathy McGeough³, Philip Gardiner⁴, Gary Wright⁵, Tony Bjourson³ and David S. Gibson⁶, ¹Proteome Research Centre, Conway Institute, University College Dublin, Dublin, Ireland, ²Proteome Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland, ³Northern Ireland Centre for Stratified Medicine, Ulster University, Londonderry, United Kingdom, ⁴Rheumatology, Altnagelvin Hospital, Londonderry, United Kingdom, ⁵Rheumatology, Musgrave Park Hospital, BELFAST, United Kingdom, ⁶Inflammatory Disease Research Group, Northern ireland Centre for Stratified Medicine, Ulster University, Londonderry, United Kingdom
Background/Purpose: Biologic drugs have revolutionised the treatment of Rheumatoid Arthritis (RA), however these therapies are expensive and exhibit a high non–response rate (30%). Currently there…
Abstract Number: 1208 • 2016 ACR/ARHP Annual Meeting
High-Throughput Screening Discovers Multiple Novel Autoantibodies in Rheumatoid Arthritis, Systemic Lupus, Systemic Sclerosis and Sjogrens Syndrome
Peter Schulz-Knappe¹, Hans-Dieter Zucht¹, Petra Budde¹, Heike Göhler¹, Daniel Wirtz¹, Johannes Schulte-Pelkum¹, Stefan Vordenbäumen², Torsten Witte³ and Prof. Dr. Matthias Schneider⁴, ¹Protagen AG, Dortmund, Germany, ²Rheumatology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany, ³Department of Clinical Immunology and Rheumatology, Hannover Medical School, Hannover, Germany, ⁴Department of Rheumatology & Hiller Research Unit, Heinrich-Heine University, Düsseldorf, Germany
Background/Purpose: Diagnostic biomarkers are decision-making tools in clinical lab routine and are of growing importance for clinical management of patients. In autoimmune diseases, one important…
Abstract Number: 1211 • 2016 ACR/ARHP Annual Meeting
Allele-Dependent Binding of a Viral Protein to Autoimmune Disease-Associated Genetic Variants
Matthew T. Weirauch¹, Daniel Miller¹, Leah C. Kottyan², Ignacio Ibarra³, Sayeed Syed⁴, Xiaoting Chen¹, Erin Zoller¹, Arthur Lynch¹, Connor Schroeder¹, Josh Lee¹, Albert Magnussen¹, Ally Yang⁵, Timothy R. Hughes⁵, Joo-Seop Park¹, Charles Vinson⁴ and John B. Harley^6,7, ¹Cincinnati Childrens Hospital, Cincinnati, OH, ²Center for Autoimmune Genomics and Etiology, Cincinnati Childrens Hospital, Cincinnati, OH, ³EMBL, Heidelberg, Germany, ⁴NCI, Bethesda, MD, ⁵University of Toronto, Toronto, ON, Canada, ⁶US Department of Veterans Affairs Medical Center, Cincinnati, OH, ⁷Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Childrens Hospital, Cincinnati, OH
Methods: We tested the hypothesis that some autoimmune variants might act by altering the binding of the EBV-encoded transcription factor ZTA, consequently resulting in downstream…

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