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Anna L Silverman, Madhumita Sushil, Balu Bhasuran, Dana Ludwig, James Buchanan, Rebecca Racz, Mahalakshmi Parakala, Samer El-Kamary, Ohenewaa Ahima, Artur Belov, Lauren Choi, Monisha Billings, Yan Li, Nadia Habal, Qi Liu, Jawahar Tiwari, Atul J Butte, Vivek A Rudrapatna
BACKGROUND AND AIMS: Outpatient clinical notes are a rich source of information regarding drug safety. However, data in these notes are currently underutilized for pharmacovigilance due to methodological limitations in text mining. Large language models (LLM) like BERT have shown progress in a range of natural language processing tasks but have not yet been evaluated on adverse event detection. METHODS: We adapted a new clinical LLM, UCSF BERT, to identify serious adverse events (SAEs) occurring after treatment with a non-steroid immunosuppressant for inflammatory bowel disease (IBD)...
September 8, 2023: medRxiv
#22
JOURNAL ARTICLE
Siavash Zamirpour, Alan E Hubbard, Jean Feng, Atul J Butte, Romain Pirracchio, Andrew Bishara
Acute kidney injury (AKI) is a major postoperative complication that lacks established intraoperative predictors. Our objective was to develop a prediction model using preoperative and high-frequency intraoperative data for postoperative AKI. In this retrospective cohort study, we evaluated 77,428 operative cases at a single academic center between 2016 and 2022. A total of 11,212 cases with serum creatinine (sCr) data were included in the analysis. Then, 8519 cases were randomly assigned to the training set and the remainder to the validation set...
August 5, 2023: Bioengineering
#23
JOURNAL ARTICLE
Atul J Butte
No abstract text is available yet for this article.
August 24, 2023: JAMA Oncology
#24
JOURNAL ARTICLE
Rohan Khera, Atul J Butte, Michael Berkwits, Yulin Hswen, Annette Flanagin, Hannah Park, Gregory Curfman, Kirsten Bibbins-Domingo
No abstract text is available yet for this article.
August 11, 2023: JAMA
#25
JOURNAL ARTICLE
Sanil Patel, Njeri Z R Sparman, Douglas Arneson, Alexandra Alvarsson, Luís C Santos, Samuel J Duesman, Alessia Centonze, Ephraim Hathaway, In Sook Ahn, Graciel Diamante, Ingrid Cely, Chung Hwan Cho, Noble Kumar Talari, Abha K Rajbhandari, Leigh Goedeke, Peng Wang, Atul J Butte, Cédric Blanpain, Karthickeyan Chella Krishnan, Aldons J Lusis, Sarah A Stanley, Xia Yang, Prashant Rajbhandari
Sympathetic activation during cold exposure increases adipocyte thermogenesis via the expression of mitochondrial protein uncoupling protein 1 (UCP1)1 . The propensity of adipocytes to express UCP1 is under a critical influence of the adipose microenvironment and varies between sexes and among various fat depots2-7 . Here we report that mammary gland ductal epithelial cells in the adipose niche regulate cold-induced adipocyte UCP1 expression in female mouse subcutaneous white adipose tissue (scWAT). Single-cell RNA sequencing shows that glandular luminal epithelium subtypes express transcripts that encode secretory factors controlling adipocyte UCP1 expression under cold conditions...
July 26, 2023: Nature
#26
JOURNAL ARTICLE
Lakshmi Radhakrishnan, Gundolf Schenk, Kathleen Muenzen, Boris Oskotsky, Habibeh Ashouri Choshali, Thomas Plunkett, Sharat Israni, Atul J Butte
OBJECTIVES: Clinical notes are a veritable treasure trove of information on a patient's disease progression, medical history, and treatment plans, yet are locked in secured databases accessible for research only after extensive ethics review. Removing personally identifying and protected health information (PII/PHI) from the records can reduce the need for additional Institutional Review Boards (IRB) reviews. In this project, our goals were to: (1) develop a robust and scalable clinical text de-identification pipeline that is compliant with the Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule for de-identification standards and (2) share routinely updated de-identified clinical notes with researchers...
October 2023: JAMIA Open
#27
JOURNAL ARTICLE
Michelle Wang, Shadera Slatter, Jesse Sussell, Chia-Wei Lin, Sarika Ogale, Debajyoti Datta, Atul J Butte, Lyudmila Bazhenova, Vivek A Rudrapatna
BACKGROUND: Randomized trials have demonstrated that anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) can be safe and efficacious treatments for patients with ALK-positive advanced non-small-cell lung cancer (aNSCLC). However, their safety, tolerability, effectiveness, and patterns of use in real-world patients remain understudied. OBJECTIVE: We sought to assess the overall treatment pattern characteristics, safety, and effectiveness outcomes of real-world patients with ALK-positive aNSCLC receiving ALK TKIs...
June 21, 2023: Targeted Oncology
#28
JOURNAL ARTICLE
Conor J Loy, Alicia Sotomayor-Gonzalez, Venice Servellita, Jenny Nguyen, Joan Lenz, Sanchita Bhattacharya, Meagan E Williams, Alexandre P Cheng, Andrew Bliss, Prachi Saldhi, Noah Brazer, Jessica Streithorst, William Suslovic, Charlotte J Hsieh, Burak Bahar, Nathan Wood, Abiodun Foresythe, Amelia Gliwa, Kushmita Bhakta, Maria A Perez, Laila Hussaini, Evan J Anderson, Ann Chahroudi, Meghan Delaney, Atul J Butte, Roberta L DeBiasi, Christina A Rostad, Iwijn De Vlaminck, Charles Y Chiu
Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here, we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with COVID-19 or MIS-C across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multiorgan involvement in MIS-C encompassing diverse cell types, including endothelial and neuronal cells, and an enrichment of pyroptosis-related genes...
April 21, 2023: Cell reports medicine
#29
JOURNAL ARTICLE
Michelle Wang, Gregory M Goldgof, Ayan Patel, Barbee Whitaker, Artur Belov, Brian Chan, Evan Phelps, Benjamin Rubin, Steven Anderson, Atul J Butte
BACKGROUND: Transfusion-associated circulatory overload (TACO) is a severe adverse reaction (AR) contributing to the leading cause of mortality associated with transfusions. As strategies to mitigate TACO have been increasingly adopted, an update of prevalence rates and risk factors associated with TACO using the growing sources of electronic health record (EHR) data can help understand transfusion safety. STUDY DESIGN AND METHODS: This retrospective study aimed to provide a timely and reproducible assessment of prevalence rates and risk factors associated with TACO...
May 29, 2023: Transfusion
#30
Shinwan Kany, Joel T Rämö, Cody Hou, Sean J Jurgens, Victor Nauffal, Jon Cunningham, Emily S Lau, Atul J Butte, Jennifer E Ho, Jeffrey E Olgin, Sammy Elmariah, Mark E Lindsay, Patrick T Ellinor, James P Pirruccello
Valvular heart disease is associated with a high global burden of disease. Even mild aortic stenosis confers increased morbidity and mortality, prompting interest in understanding normal variation in valvular function at scale. We developed a deep learning model to study velocity-encoded magnetic resonance imaging in 47,223 UK Biobank participants. We calculated eight traits, including peak velocity, mean gradient, aortic valve area, forward stroke volume, mitral and aortic regurgitant volume, greatest average velocity, and ascending aortic diameter...
May 1, 2023: medRxiv
#31
JOURNAL ARTICLE
Michelle Wang, Madhumita Sushil, Brenda Y Miao, Atul J Butte
OBJECTIVES: As the real-world electronic health record (EHR) data continue to grow exponentially, novel methodologies involving artificial intelligence (AI) are becoming increasingly applied to enable efficient data-driven learning and, ultimately, to advance healthcare. Our objective is to provide readers with an understanding of evolving computational methods and help in deciding on methods to pursue. TARGET AUDIENCE: The sheer diversity of existing methods presents a challenge for health scientists who are beginning to apply computational methods to their research...
May 15, 2023: Journal of the American Medical Informatics Association: JAMIA
#32
JOURNAL ARTICLE
M Binvignat, P Emond, F Mifsud, B Miao, A Courties, A Lefèvre, E Maheu, M D Crema, D Klatzmann, M Kloppenburg, P Richette, A J Butte, E Mariotti-Ferrandiz, F Berenbaum, H Sokol, J Sellam
OBJECTIVE: To investigate host and gut-microbiota related Tryptophan metabolism in hand osteoarthritis (HOA). METHODS: The baseline serum concentration of 20 Tryptophan metabolites was measured in 416 HOA patients in a cross-sectional analysis of the DIGICOD cohort. Tryptophan metabolites levels, metabolite-ratios and metabolism pathway activation were compared between erosive (N = 141) and non-erosive HOA (N = 275) by multiple logistic regressions adjusted on age, BMI and sex...
August 2023: Osteoarthritis and Cartilage
#33
JOURNAL ARTICLE
Erica A Voss, Azza Shoaibi, Lana Yin Hui Lai, Clair Blacketer, Thamir Alshammari, Rupa Makadia, Kevin Haynes, Anthony G Sena, Gowtham Rao, Sebastiaan van Sandijk, Clement Fraboulet, Laurent Boyer, Tanguy Le Carrour, Scott Horban, Daniel R Morales, Jordi Martínez Roldán, Juan Manuel Ramírez-Anguita, Miguel A Mayer, Marcel de Wilde, Luis H John, Talita Duarte-Salles, Elena Roel, Andrea Pistillo, Raivo Kolde, Filip Maljković, Spiros Denaxas, Vaclav Papez, Michael G Kahn, Karthik Natarajan, Christian Reich, Alex Secora, Evan P Minty, Nigam H Shah, Jose D Posada, Maria Teresa Garcia Morales, Diego Bosca, Honorio Cadenas Juanino, Antonio Diaz Holgado, Miguel Pedrera Jiménez, Pablo Serrano Balazote, Noelia García Barrio, Selçuk Şen, Ali Yağız Üresin, Baris Erdogan, Luc Belmans, Geert Byttebier, Manu L N G Malbrain, Daniel J Dedman, Zara Cuccu, Rohit Vashisht, Atul J Butte, Ayan Patel, Lisa Dahm, Cora Han, Fan Bu, Faaizah Arshad, Anna Ostropolets, Fredrik Nyberg, George Hripcsak, Marc A Suchard, Dani Prieto-Alhambra, Peter R Rijnbeek, Martijn J Schuemie, Patrick B Ryan
BACKGROUND: Adverse events of special interest (AESIs) were pre-specified to be monitored for the COVID-19 vaccines. Some AESIs are not only associated with the vaccines, but with COVID-19. Our aim was to characterise the incidence rates of AESIs following SARS-CoV-2 infection in patients and compare these to historical rates in the general population. METHODS: A multi-national cohort study with data from primary care, electronic health records, and insurance claims mapped to a common data model...
April 2023: EClinicalMedicine
#34
JOURNAL ARTICLE
Travis Zack, Kurt P Losert, Samantha M Maisel, Jennifer Wild, Amin Yaqubie, Michael Herman, Jennifer J Knox, Robert J Mayer, Alan P Venook, Atul Butte, Allison F O'Neill, Ghassan K Abou-Alfa, John D Gordan
The incidence and biochemical consequences of rare tumor subtypes are often hard to study. Fibrolamellar liver cancer (FLC) is a rare malignancy affecting adolescents and young adults. To better characterize the incidence and biochemical consequences of this disease, we combined a comprehensive analysis of the electronic medical record and national payer data and found that FLC incidence is likely five to eight times higher than previous estimates. By employing unsupervised learning on clinical laboratory data from patients with hyperammonemia, we find that FLC-associated hyperammonemia mirrors metabolic dysregulation in urea cycle disorders...
March 23, 2023: NPJ Precision Oncology
#35
LETTER
Erica Farrand, Oksana Gologorskaya, Hunter Mills, Lakshmi Radhakrishnan, Harold R Collard, Atul J Butte
No abstract text is available yet for this article.
May 15, 2023: American Journal of Respiratory and Critical Care Medicine
#36
Gregory M Goldgof, Shenghuan Sun, Jacob Van Cleave, Linlin Wang, Fabienne Lucas, Laura Brown, Jacob D Spector, Leonardo Boiocchi, Jeeyeon Baik, Menglei Zhu, Orly Ardon, Chuanyi M Lu, Ahmet Dogan, Dmitry B Goldgof, Iain Carmichael, Sonam Prakash, Atul J Butte
Morphology-based classification of cells in the bone marrow aspirate (BMA) is a key step in the diagnosis and management of hematologic malignancies. However, it is time-intensive and must be performed by expert hematopathologists and laboratory professionals. We curated a large, high-quality dataset of 41,595 hematopathologist consensus-annotated single-cell images extracted from BMA whole slide images (WSIs) containing 23 morphologic classes from the clinical archives of the University of California, San Francisco...
February 21, 2023: bioRxiv
#37
JOURNAL ARTICLE
Vivek A Rudrapatna, Yao-Wen Cheng, Colin Feuille, Arman Mosenia, Jonathan Shih, Yongmei Shi, Olivia Roberson, Benjamin Rubin, Atul J Butte, Uma Mahadevan, Nicholas Skomrock, Ngozi Erondu, Christel Chehoud, Saquib Rahim, David Apfel, Mark Curran, Najat S Khan, Christopher O'Brien, Natalie Terry, Benjamin D Martini
BACKGROUND: Randomized trials are the gold-standard for clinical evidence generation, but they can sometimes be limited by infeasibility and unclear generalizability to real-world practice. External control arm (ECA) studies may help address this evidence gaps by constructing retrospective cohorts that closely emulate prospective ones. Experience in constructing these outside the context of rare diseases or cancer is limited. We piloted an approach for developing an ECA in Crohn's disease using electronic health records (EHR) data...
2023: PloS One
#38
EDITORIAL
Howard Bauchner, Mary M McDermott, Atul J Butte
No abstract text is available yet for this article.
February 28, 2023: Annals of Internal Medicine
#39
JOURNAL ARTICLE
Aaron E Kornblith, Chandan Singh, Gabriel Devlin, Newton Addo, Christian J Streck, James F Holmes, Nathan Kuppermann, Jacqueline Grupp-Phelan, Jeffrey Fineman, Atul J Butte, Bin Yu
OBJECTIVE: The Pediatric Emergency Care Applied Research Network (PECARN) has developed a clinical-decision instrument (CDI) to identify children at very low risk of intra-abdominal injury. However, the CDI has not been externally validated. We sought to vet the PECARN CDI with the Predictability Computability Stability (PCS) data science framework, potentially increasing its chance of a successful external validation. MATERIALS & METHODS: We performed a secondary analysis of two prospectively collected datasets: PECARN (12,044 children from 20 emergency departments) and an independent external validation dataset from the Pediatric Surgical Research Collaborative (PedSRC; 2,188 children from 14 emergency departments)...
August 2022: PLOS Digit Health
#40
JOURNAL ARTICLE
Carla V Rodriguez-Watson, Natalie E Sheils, Anthony M Louder, Elizabeth H Eldridge, Nancy D Lin, Benjamin D Pollock, Jennifer L Gatz, Shaun J Grannis, Rohit Vashisht, Kanwal Ghauri, Gina Valo, Aloka G Chakravarty, Tamar Lasky, Mary Jung, Stephen L Lovell, Jacqueline M Major, Carly Kabelac, Camille Knepper, Sandy Leonard, Peter J Embi, William G Jenkinson, Reyna Klesh, Omai B Garner, Ayan Patel, Lisa Dahm, Aiden Barin, Dan M Cooper, Tom Andriola, Carrie L Byington, Bridgit O Crews, Atul J Butte, Jeff Allen
BACKGROUND: As diagnostic tests for COVID-19 were broadly deployed under Emergency Use Authorization, there emerged a need to understand the real-world utilization and performance of serological testing across the United States. METHODS: Six health systems contributed electronic health records and/or claims data, jointly developed a master protocol, and used it to execute the analysis in parallel. We used descriptive statistics to examine demographic, clinical, and geographic characteristics of serology testing among patients with RNA positive for SARS-CoV-2...
2023: PloS One
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