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Keet C, Sicherer SH, Bunyavanich S, Visness C, Fulkerson PC, Togias A, Davidson W, Perry S, Hamrah S, Calatroni A, Robinson K, Dunaway L, Davis CM, Anvari S, Leong-Kee SM, Hershey GK, DeFranco E, Devonshire A, Kim H, Joseph C, Davidson B, Strong NK, Tsuang AJ, Groetch M, Wang J, Dantzer J, Mudd K, Aina A, Shreffler W, Yuan Q, Simmons V, Leung DY, Hui-Beckman J, Ramos JA, Chinthrajah S, Winn V, Sindher T, Jones SM, Manning NA, Scurlock AM, Kim E, Stuebe A, Gern JE, Singh AM, Krupp J, Wood RA. The SunBEAm birth cohort: Protocol design. J Allergy Clin Immunol Glob 2023; 2:100124. [PMID: 37771674 PMCID: PMC10509956 DOI: 10.1016/j.jacig.2023.100124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 09/30/2023]
Abstract
Background Food allergy (FA) and atopic dermatitis (AD) are common conditions that often present in the first year of life. Identification of underlying mechanisms and environmental determinants of FA and AD is essential to develop and implement effective prevention and treatment strategies. Objectives: We sought to describe the design of the Systems Biology of Early Atopy (SunBEAm) birth cohort. Methods Funded by the National Institute of Allergy and Infectious Diseases (NIAID) and administered through the Consortium for Food Allergy Research (CoFAR), SunBEAm is a US population-based, multicenter birth cohort that enrolls pregnant mothers, fathers, and their newborns and follows them to 3 years. Questionnaire and biosampling strategies were developed to apply a systems biology approach to identify environmental, immunologic, and multiomic determinants of AD, FA, and other allergic outcomes. Results Enrollment is currently underway. On the basis of an estimated FA prevalence of 6%, the enrollment goal is 2500 infants. AD is defined on the basis of questionnaire and assessment, and FA is defined by an algorithm combining history and testing. Although any FA will be recorded, we focus on the diagnosis of egg, milk, and peanut at 5 months, adding wheat, soy, cashew, hazelnut, walnut, codfish, shrimp, and sesame starting at 12 months. Sampling includes blood, hair, stool, dust, water, tape strips, skin swabs, nasal secretions, nasal swabs, saliva, urine, functional aspects of the skin, and maternal breast milk and vaginal swabs. Conclusions The SunBEAm birth cohort will provide a rich repository of data and specimens to interrogate mechanisms and determinants of early allergic outcomes, with an emphasis on FA, AD, and systems biology.
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Affiliation(s)
- Corinne Keet
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | | | | | | | - Patricia C. Fulkerson
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alkis Togias
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Wendy Davidson
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Susan Perry
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sanaz Hamrah
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Lars Dunaway
- Rho Inc, Federal Research Operations, Durham, NC
| | - Carla M. Davis
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Sara Anvari
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Susan M. Leong-Kee
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Tex
| | | | | | | | | | | | | | | | | | | | - Julie Wang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer Dantzer
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Kim Mudd
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Abimbola Aina
- Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine, Baltimore, Md
| | | | - Qian Yuan
- Massachusetts General Hospital, Newton-Wellesley Hospital, Newton, Mass
| | - Virginia Simmons
- Massachusetts General Hospital, Newton-Wellesley Hospital, Newton, Mass
| | | | | | | | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, Calif
| | - Virginia Winn
- Division Maternal Fetal Medicine and Obstetrics, Stanford University, Palo Alto, Calif
| | - Tina Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, Calif
| | - Stacie M. Jones
- University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, Ark
| | | | - Amy M. Scurlock
- University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, Ark
| | - Edwin Kim
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | - Alison Stuebe
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wis
| | | | - Jennifer Krupp
- Maternal and Fetal Medicine, Obstetrics and Gynecology, SSM Health, Madison, Wis
| | - Robert A. Wood
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Md
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Liu EG, Zhang B, Martin V, Anthonypillai J, Kraft M, Grishin A, Grishina G, Catanzaro JR, Chinthrajah S, Sindher T, Manohar M, Quake AZ, Nadeau K, Burks AW, Kim EH, Kulis MD, Henning AK, Jones SM, Leung DYM, Sicherer SH, Wood RA, Yuan Q, Shreffler W, Sampson H, Shabanova V, Eisenbarth SC. Food-specific immunoglobulin A does not correlate with natural tolerance to peanut or egg allergens. Sci Transl Med 2022; 14:eabq0599. [PMID: 36383680 PMCID: PMC10219469 DOI: 10.1126/scitranslmed.abq0599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ImmunoglobulinA (IgA) is the predominant antibody isotype in the gut, where it regulates commensal flora and neutralizes toxins and pathogens. The function of food-specific IgA in the gut is unknown but is presumed to protect from food allergy. Specifically, it has been hypothesized that food-specific IgA binds ingested allergens and promotes tolerance by immune exclusion; however, the evidence to support this hypothesis is indirect and mixed. Although it is known that healthy adults have peanut-specific IgA in the gut, it is unclear whether children also have gut peanut-specific IgA. We found in a cohort of non-food-allergic infants (n = 112) that there is detectable stool peanut-specific IgA that is similar to adult quantities of gut peanut-specific IgA. To investigate whether this peanut-specific IgA is associated with peanut tolerance, we examined a separate cohort of atopic children (n = 441) and found that gut peanut-specific IgA does not predict protection from development of future peanut allergy in infants nor does it correlate with concurrent oral tolerance of peanut in older children. We observed higher plasma peanut-specific IgA in those with peanut allergy. Similarly, egg white-specific IgA was detectable in infant stools and did not predict egg tolerance or outgrowth of egg allergy. Bead-based epitope assay analysis of gut peanut-specific IgA revealed similar epitope specificity between children with peanut allergy and those without; however, gut peanut-specific IgA and plasma peanut-specific IgE had different epitope specificities. These findings call into question the presumed protective role of food-specific IgA in food allergy.
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Affiliation(s)
- Elise G. Liu
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
- Department of Medicine, Section of Rheumatology, Allergy, and Immunology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Biyan Zhang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore 138648, Singapore
| | - Victoria Martin
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Food Allergy Center, Massachusetts General Hospital, MGH Professional Office Building, Suite 530, 275 Cambridge Street, Boston, MA 02114, USA
- Food Allergy Science Initiative, Broad Institute, Cambridge, MA 02142, USA
| | - John Anthonypillai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
- Department of Medicine, Section of Rheumatology, Allergy, and Immunology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Magdalena Kraft
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Alexander Grishin
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Galina Grishina
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jason R. Catanzaro
- Section of Pulmonology, Allergy, Immunology, and Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94040, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tina Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94040, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94040, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Antonia Zoe Quake
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94040, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94040, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - A. Wesley Burks
- University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Edwin H. Kim
- University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Michael D. Kulis
- University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Stacie M. Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, AR 72205, USA
| | - Donald Y. M. Leung
- Department of Pediatrics, Division of Pediatric Allergy-Immunology, National Jewish Health, Denver, CO 80206, USA
| | - Scott H. Sicherer
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert A. Wood
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Qian Yuan
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Food Allergy Center, Massachusetts General Hospital, MGH Professional Office Building, Suite 530, 275 Cambridge Street, Boston, MA 02114, USA
- Food Allergy Science Initiative, Broad Institute, Cambridge, MA 02142, USA
- Pediatrics at Newton Wellesley, Newton, MA 02462, USA
| | - Wayne Shreffler
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Food Allergy Center, Massachusetts General Hospital, MGH Professional Office Building, Suite 530, 275 Cambridge Street, Boston, MA 02114, USA
- Food Allergy Science Initiative, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hugh Sampson
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Veronika Shabanova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
- Department of Medicine, Section of Rheumatology, Allergy, and Immunology, Yale University School of Medicine, New Haven, CT 06519, USA
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Sullivan L, Schumacher C, Martinez K, Collins W, Fast K, Chinthrajah S, Sindher T, Cao S. Improvement of Quality of Life and Positive Feedback in Long-Term Follow-Up Study in Food Allergic Participants with Oral Immunotherapy Treatment. J Allergy Clin Immunol 2022. [DOI: 10.1016/j.jaci.2021.12.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Kepner K, Parsons E, Kost L, Nadeau K, Andorf S, Chinthrajah RS, Sindher T. Age and Successful Food Allergy Desensitization in Children. J Allergy Clin Immunol 2022. [DOI: 10.1016/j.jaci.2021.12.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Arunachalam PS, Scott MKD, Hagan T, Li C, Feng Y, Wimmers F, Grigoryan L, Trisal M, Edara VV, Lai L, Chang SE, Feng A, Dhingra S, Shah M, Lee AS, Chinthrajah S, Sindher T, Mallajosyula V, Gao F, Sigal N, Kowli S, Gupta S, Pellegrini K, Tharp G, Maysel-Auslender S, Bosinger S, Maecker HT, Boyd SD, Davis MM, Utz PJ, Suthar MS, Khatri P, Nadeau KC, Pulendran B. Systems biological assessment of human immunity to BNT162b2 mRNA vaccination. Res Sq 2021:rs.3.rs-438662. [PMID: 34013244 PMCID: PMC8132234 DOI: 10.21203/rs.3.rs-438662/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The emergency use authorization of two COVID-19 mRNA vaccines in less than a year since the emergence of SARS-CoV-2, represents a landmark in vaccinology1,2. Yet, how mRNA vaccines stimulate the immune system to elicit protective immune responses is unknown. Here we used a systems biological approach to comprehensively profile the innate and adaptive immune responses in 56 healthy volunteers vaccinated with the Pfizer-BioNTech mRNA vaccine. Vaccination resulted in robust production of neutralizing antibodies (nAbs) against the parent strain and the variant of concern, B.1.351, but no induction of autoantibodies, and significant increases in antigen-specific polyfunctional CD4 and CD8 T cells after the second dose. The innate response induced within the first 2 days of booster vaccination was profoundly increased, relative to the response at corresponding times after priming. Thus, there was a striking increase in the: (i) frequency of CD14+CD16+ inflammatory monocytes; (ii) concentration of IFN- y in the plasma, which correlated with enhanced pSTAT3 and pSTAT1 levels in monocytes and T cells; and (iii) transcriptional signatures of innate responses characteristic of antiviral vaccine responses against pandemic influenza, HIV and Ebola, within 2 days following booster vaccination compared to primary vaccination. Consistent with these observations, single-cell transcriptomics analysis of 242,479 leukocytes demonstrated a ~100-fold increase in the frequency of a myeloid cluster, enriched in a signature of interferon-response transcription factors (TFs) and reduced in AP-1 TFs, one day after secondary immunization, at day 21. Finally, we delineated distinct molecular pathways of innate activation that correlate with CD8 T cell and nAb responses and identified an early monocyte-related signature that was associated with the breadth of the nAb response against the B1.351 variant strain. Collectively, these data provide insights into the immune responses induced by mRNA vaccines and demonstrate their capacity to stimulate an enhanced innate response following booster immunization.
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Affiliation(s)
- Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Madeleine K. D. Scott
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Lilit Grigoryan
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Lilin Lai
- Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Sarah Esther Chang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaurya Dhingra
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mihir Shah
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
| | - Allie Skye Lee
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
| | | | - Tina Sindher
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Fei Gao
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sheena Gupta
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Sofia Maysel-Auslender
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Steven Bosinger
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Scott D. Boyd
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehul S. Suthar
- Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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