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Lourenço AA, Amaral PHR, Paim AAO, Marques GF, Gomes-de-Pontes L, da Mata CPSM, da Fonseca FG, Pérez JCG, Coelho-dos-Reis JGA. Algorithms for predicting COVID outcome using ready-to-use laboratorial and clinical data. Front Public Health 2024; 12:1347334. [PMID: 38807995 PMCID: PMC11130428 DOI: 10.3389/fpubh.2024.1347334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging crisis affecting the public health system. The clinical features of COVID-19 can range from an asymptomatic state to acute respiratory syndrome and multiple organ dysfunction. Although some hematological and biochemical parameters are altered during moderate and severe COVID-19, there is still a lack of tools to combine these parameters to predict the clinical outcome of a patient with COVID-19. Thus, this study aimed at employing hematological and biochemical parameters of patients diagnosed with COVID-19 in order to build machine learning algorithms for predicting COVID mortality or survival. Patients included in the study had a diagnosis of SARS-CoV-2 infection confirmed by RT-PCR and biochemical and hematological measurements were performed in three different time points upon hospital admission. Among the parameters evaluated, the ones that stand out the most are the important features of the T1 time point (urea, lymphocytes, glucose, basophils and age), which could be possible biomarkers for the severity of COVID-19 patients. This study shows that urea is the parameter that best classifies patient severity and rises over time, making it a crucial analyte to be used in machine learning algorithms to predict patient outcome. In this study optimal and medically interpretable machine learning algorithms for outcome prediction are presented for each time point. It was found that urea is the most paramount variable for outcome prediction over all three time points. However, the order of importance of other variables changes for each time point, demonstrating the importance of a dynamic approach for an effective patient's outcome prediction. All in all, the use of machine learning algorithms can be a defining tool for laboratory monitoring and clinical outcome prediction, which may bring benefits to public health in future pandemics with newly emerging and reemerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Alice Aparecida Lourenço
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Adriana Alves Oliveira Paim
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Geovane Ferreira Marques
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leticia Gomes-de-Pontes
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- CT Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juan Carlos González Pérez
- Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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2
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Narayanan SA, Jamison DA, Guarnieri JW, Zaksas V, Topper M, Koutnik AP, Park J, Clark KB, Enguita FJ, Leitão AL, Das S, Moraes-Vieira PM, Galeano D, Mason CE, Trovão NS, Schwartz RE, Schisler JC, Coelho-Dos-Reis JGA, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection. Eur J Hum Genet 2024; 32:10-20. [PMID: 37938797 PMCID: PMC10772081 DOI: 10.1038/s41431-023-01462-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 11/09/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.
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Affiliation(s)
- S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32301, USA.
| | - David A Jamison
- COVID-19 International Research Team, Medford, MA, 02155, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Michael Topper
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Departments of Oncology and Medicine and the Sidney Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andrew P Koutnik
- Human Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, FL, 32502, USA
- Sansum Diabetes Research Institute, Santa Barbara, CA, 93015, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 10065, USA
| | - Kevin B Clark
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Cures Within Reach, Chicago, IL, 60602, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation's Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), Philadelphia, PA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, 10016, USA
- Peace Innovation Institute, The Hague 2511, Netherlands and Stanford University, Palo Alto, 94305, CA, USA
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Saswati Das
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Mannohar Lohia Hospital, New Delhi, 110001, India
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC) and Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
| | - Diego Galeano
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA, 02155, USA
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jordana G A Coelho-Dos-Reis
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Basic and Applied Virology Lab, Department of Microbiology, Institute for Biological Sciences (ICB), Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Bioinformatics and Computational Biology Program, Center for Metabolomics, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Santa Clara, CA, 94035, USA.
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3
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Ferreira GM, Clarindo FA, Ribeiro ÁL, Gomes-de-Pontes L, de Carvalho LD, Martins-Filho OA, da Fonseca FG, Teixeira MM, Sabino ADP, Eapen MS, Morris DL, Valle SJ, Coelho-dos-Reis JGA. Taming the SARS-CoV-2-mediated proinflammatory response with BromAc ®. Front Immunol 2023; 14:1308477. [PMID: 38193087 PMCID: PMC10773902 DOI: 10.3389/fimmu.2023.1308477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction In the present study, the impact of BromAc®, a specific combination of bromelain and acetylcysteine, on the SARS-CoV-2-specific inflammatory response was evaluated. Methods An in vitro stimulation system was standardized using blood samples from 9 healthy donors, luminex assays and flow cytometry were performed. Results and discussion BromAc® demonstrated robust anti-inflammatory activity in human peripheral blood cells upon SARS-CoV-2 viral stimuli, reducing the cytokine storm, composed of chemokines, growth factors, and proinflammatory and regulatory cytokines produced after short-term in vitro culture with the inactivated virus (iSARS-CoV-2). A combined reduction in vascular endothelial growth factor (VEGF) induced by SARS-CoV-2, in addition to steady-state levels of platelet recruitment-associated growth factor-PDGFbb, was observed, indicating that BromAc® may be important to reduce thromboembolism in COVID-19. The immunophenotypic analysis of the impact of BromAc® on leukocytes upon viral stimuli showed that BromAc® was able to downmodulate the populations of CD16+ neutrophils and CD14+ monocytes observed after stimulation with iSARS-CoV-2. Conversely, BromAc® treatment increased steady-state HLA-DR expression in CD14+ monocytes and preserved this activation marker in this subset upon iSARS-CoV-2 stimuli, indicating improved monocyte activation upon BromAc® treatment. Additionally, BromAc® downmodulated the iSARS-CoV-2-induced production of TNF-a by the CD19+ B-cells. System biology approaches, utilizing comprehensive correlation matrices and networks, showed distinct patterns of connectivity in groups treated with BromAc®, suggesting loss of connections promoted by the compound and by iSARS-CoV-2 stimuli. Negative correlations amongst proinflammatory axis and other soluble and cellular factors were observed in the iSARS-CoV-2 group treated with BromAc® as compared to the untreated group, demonstrating that BromAc® disengages proinflammatory responses and their interactions with other soluble factors and the axis orchestrated by SARS-CoV-2. Conclusion These results give new insights into the mechanisms for the robust anti-inflammatory effect of BromAc® in the steady state and SARS-CoV-2-specific immune leukocyte responses, indicating its potential as a therapeutic strategy for COVID-19.
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Affiliation(s)
- Geovane Marques Ferreira
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe Alves Clarindo
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ágata Lopes Ribeiro
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Letícia Gomes-de-Pontes
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luciana Debortoli de Carvalho
- Departamento de Biologia e Biotecnologia de Microrganismos, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Olindo Assis Martins-Filho
- Grupo Integrado de Pesquisas em Biomarcadores, Rene Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico de Belo Horizonte, Belo Horizonte, Brazil
| | - Mauro Martins Teixeira
- CT Terapias Avançadas e Inovadoras (CT-Terapias), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriano de Paula Sabino
- Laboratório de Hematologia Clínica, Experimental e Molecular, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathew Suji Eapen
- Research & Development Department, Mucpharm Pty Ltd, Sydney, NSW, Australia
| | - David L. Morris
- Research & Development Department, Mucpharm Pty Ltd, Sydney, NSW, Australia
- St George and Sutherland Hospital Clinical School, University of New South Wales, Sydney, NSW, Australia
- Department of Surgery, St George Hospital, Sydney, NSW, Australia
| | - Sarah J. Valle
- Research & Development Department, Mucpharm Pty Ltd, Sydney, NSW, Australia
- St George and Sutherland Hospital Clinical School, University of New South Wales, Sydney, NSW, Australia
- Intensive Care Unit, St George Hospital, Sydney, NSW, Australia
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- CT Terapias Avançadas e Inovadoras (CT-Terapias), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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4
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Santiago L, Gonçalves-Pereira MH, Vieira MS, Gómez Ravetti C, Vassallo PF, Silva e Castro R, Costa Pimenta PP, de Andrade MVM, Santiago HDC, Nobre V. Compartmentalized Regulation of Pulmonary and Systemic Inflammation in Critical COVID-19 Patients. Viruses 2023; 15:1704. [PMID: 37632046 PMCID: PMC10458965 DOI: 10.3390/v15081704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Critical COVID-19 has been associated with altered patterns of cytokines. Distinct inflammatory processes in systemic and pulmonary sites have been reported, but studies comparing these two sites are still scarce. We aimed to evaluate the profile of pulmonary and systemic cytokines and chemokines in critically ill COVID-19 patients. Levels of cytokines and chemokines were measured in plasma samples and minibronchoalveolar lavage of critical COVID-19 patients within 48 h and 5-8 days after intubation. Distinct inflammatory processes were observed in the lungs and blood, which were regulated separately. Survivor patients showed higher lung cytokine levels including IFN-γ, IL-2, IL-4, G-CSF, and CCL4, while nonsurvivors displayed higher levels in the blood, which included IL-6, CXCL8, CXCL10, CCL2, and CCL4. Furthermore, our findings indicate that high TNF and CXCL8 levels in the mini-BAL were associated with better lung oxygen exchange capacity, whereas high levels of IFN-γ in plasma were associated with worse lung function, as measured using the PaO2/FiO2 ratio. These results suggest that a robust and localized inflammatory response in the lungs is protective and associated with survival, whereas a systemic inflammatory response is detrimental and associated with mortality in critical COVID-19.
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Affiliation(s)
- Luciana Santiago
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, MG, Brazil;
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.H.G.-P.); (M.S.V.)
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
| | - Marcela Helena Gonçalves-Pereira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.H.G.-P.); (M.S.V.)
| | - Mariana Sousa Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.H.G.-P.); (M.S.V.)
| | - Cecilia Gómez Ravetti
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, MG, Brazil;
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
| | - Paula Frizera Vassallo
- Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, MG, Brazil;
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
| | - Rafael Silva e Castro
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
| | - Pedro Pires Costa Pimenta
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
| | - Marcus Vinícius Melo de Andrade
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, MG, Brazil;
| | - Helton da Costa Santiago
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.H.G.-P.); (M.S.V.)
| | - Vandack Nobre
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.S.); (C.G.R.); (R.S.e.C.); (P.P.C.P.); (M.V.M.d.A.)
- Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, MG, Brazil;
- Núcleo Interdisciplinar de Investigação em Medicina Intensiva (NIIMI), Belo Horizonte 31270-901, MG, Brazil
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