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Sun R, Qian MG, Zhang X. T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics. MAbs 2024; 16:2324836. [PMID: 38512798 PMCID: PMC10962608 DOI: 10.1080/19420862.2024.2324836] [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: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.
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Affiliation(s)
- Ruoxuan Sun
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Mark G. Qian
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Xiaobin Zhang
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
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2
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Grąźlewska W, Holec-Gąsior L, Sołowińska K, Chmielewski T, Fiecek B, Contreras M. Epitope Mapping of BmpA and BBK32 Borrelia burgdorferi Sensu Stricto Antigens for the Design of Chimeric Proteins with Potential Diagnostic Value. ACS Infect Dis 2023; 9:2160-2172. [PMID: 37803965 PMCID: PMC10722512 DOI: 10.1021/acsinfecdis.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Indexed: 10/08/2023]
Abstract
Lyme disease is a tick-borne zoonosis caused by Gram-negative bacteria belonging to the Borrelia burgdorferi sensu lato (s.l.) group. In this study, IgM- and IgG-specific linear epitopes of two B. burgdorferi sensu stricto (s.s.) antigens BmpA and BBK32 were mapped using a polypeptide array. Subsequently, two chimeric proteins BmpA-BBK32-M and BmpA-BBK32-G were designed to validate the construction of chimeras using the identified epitopes for the detection of IgM and IgG, respectively, by ELISA. IgG-ELISA based on the BmpA-BBK32-G antigen showed 71% sensitivity and 95% specificity, whereas a slightly lower diagnostic utility was obtained for IgM-ELISA based on BmpA-BBK32-M, where the sensitivity was also 71% but the specificity decreased to 89%. The reactivity of chimeric proteins with nondedicated antibodies was much lower. These results suggest that the identified epitopes may be useful in the design of new forms of antigens to increase the effectiveness of Lyme disease serodiagnosis. It has also been proven that appropriate selection of epitopes enables the construction of chimeric proteins exhibiting reactivity with a specific antibody isotype.
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Affiliation(s)
- Weronika Grąźlewska
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
- SaBio,
Instituto de Investigación en Recursos Cinegéticos IREC−CSIC-UCLM-JCCM, 13005 Ciudad Real, Spain
| | - Lucyna Holec-Gąsior
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
| | - Karolina Sołowińska
- Department
of Molecular Biotechnology and Microbiology, Faculty of Chemistry, University of Gdańsk Technology, 80-233 Gdańsk, Poland
| | - Tomasz Chmielewski
- Department
of Parasitology and Diseases Transmitted by Vectors, National Institute of Public Health NIH - National Research Institute, 00-791 Warsaw, Poland
| | - Beata Fiecek
- Department
of Parasitology and Diseases Transmitted by Vectors, National Institute of Public Health NIH - National Research Institute, 00-791 Warsaw, Poland
| | - Marinela Contreras
- SaBio,
Instituto de Investigación en Recursos Cinegéticos IREC−CSIC-UCLM-JCCM, 13005 Ciudad Real, Spain
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3
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Lee ASE, Suprun M, Sampson H. Epitope-Based IgE Assays and Their Role in Providing Diagnosis and Prognosis of Food Allergy. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:2983-2988. [PMID: 37394177 DOI: 10.1016/j.jaip.2023.06.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
With advances in molecular and computational science, epitope-specific IgE antibody profiling has been developed and recently brought into clinical practice. Epitope-based testing detects IgE antibodies that directly bind to antigenic sites of an allergen, providing increased resolution specificity and fewer false-positive results for diagnosing food allergy. Epitope-binding profiles may also serve as prognostic markers of food allergy and help predict quantities of allergen that would provoke a reaction (ie, eliciting dose, possible severity of a reaction after allergen ingestion, and outcomes of treatment options such as oral immunotherapy [OIT]). Future studies are under way to discover additional applications of epitope-specific antibodies for multiple food allergens.
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Affiliation(s)
- Ashley Sang Eun Lee
- Division of Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Maria Suprun
- Division of Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY; Janssen R&D, Spring House, Pa
| | - Hugh Sampson
- Division of Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY
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The Correlation between Subolesin-Reactive Epitopes and Vaccine Efficacy. Vaccines (Basel) 2022; 10:vaccines10081327. [PMID: 36016215 PMCID: PMC9414912 DOI: 10.3390/vaccines10081327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccination is an environmentally-friendly alternative for tick control. The tick antigen Subolesin (SUB) has shown protection in vaccines for the control of multiple tick species in cattle. Additionally, recent approaches in quantum vaccinomics have predicted SUB-protective epitopes and the peptide sequences involved in protein−protein interactions in this tick antigen. Therefore, the identification of B-cell−reactive epitopes by epitope mapping using a SUB peptide array could be essential as a novel strategy for vaccine development. Subolesin can be used as a model to evaluate the effectiveness of these approaches for the identification of protective epitopes related to vaccine protection and efficacy. In this study, the mapping of B-cell linear epitopes of SUB from three different tick species common in Uganda (Rhipicephalus appendiculatus, R. decoloratus, and Amblyomma variegatum) was conducted using serum samples from two cattle breeds immunized with SUB-based vaccines. The results showed that in cattle immunized with SUB from R. appendiculatus (SUBra) all the reactive peptides (Z-score > 2) recognized by IgG were also significant (Z-ratio > 1.96) when compared to the control group. Additionally, some of the reactive peptides recognized by IgG from the control group were also recognized in SUB cocktail−immunized groups. As a significant result, cattle groups that showed the highest vaccine efficacy were Bos indicus immunized with a SUB cocktail (92%), and crossbred cattle were immunized with SUBra (90%) against R. appendiculatus ticks; the IgG from these groups recognized overlapping epitopes from the peptide SPTGLSPGLSPVRDQPLFTFRQVGLICERMMKERESQIRDEYDHVLSAKLAEQYDTFVKFTYDQKRFEGATPSYLS (Z-ratio > 1.96), which partially corresponded to a Q38 peptide and the SUB protein interaction domain. These identified epitopes could be related to the protection and efficacy of the SUB-based vaccines, and new chimeras containing these protective epitopes could be designed using this new approach.
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Epitope Mapping of Allergenic Lipid Transfer Proteins. Methods Mol Biol 2021. [PMID: 34115355 DOI: 10.1007/978-1-0716-1562-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Food allergy is becoming a great problem in industrialized countries. Thus, there is the need for a robust understanding of all aspects characterizing IgE response to allergens. The epitope mapping of B-cell epitopes has the potential to become a fundamental tool for food allergy diagnosis and prognosis and to lead to a better understanding of the pathogenesis. Using this approach, we have worked on epitope mapping of the most important plant food allergens identified in the Mediterranean area. The final aim of this study is to define the immune response regarding B epitopes and its clinical relevance in LTP allergy. This chapter describes the protocol to produce microarrays using a library of overlapping peptides corresponding to the primary sequences of allergenic lipid transfer proteins.
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Foong RX, Santos AF. Biomarkers of diagnosis and resolution of food allergy. Pediatr Allergy Immunol 2021; 32:223-233. [PMID: 33020989 DOI: 10.1111/pai.13389] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/30/2020] [Accepted: 09/25/2020] [Indexed: 12/19/2022]
Abstract
Food allergy is increasing in prevalence, affecting up to 10% of children in developed countries. Food allergy can significantly affect the quality of life and well-being of patients and their families; therefore, an accurate diagnosis is of extreme importance. Some food allergies can spontaneously resolve in 50%-60% of cow's milk and egg-allergic, 20% of peanut-allergic and 9% of tree nut-allergic children by school age. For that reason, food-allergic status should be monitored over time to determine when to reintroduce the food back into the child's diet. The gold-standard to confirm the diagnosis and the resolution of food allergy is an oral food challenge; however, this involves the risk of causing an acute-allergic reaction and requires clinical experience and resources to treat allergic reactions of any degree of severity. In the clinical setting, biomarkers have been used and validated to enable an accurate diagnosis when combined with the clinical history, deferring the oral food challenge, whenever possible. In this review, we cover the tools available to support the diagnosis of food allergies and to predict food allergy resolution over time. We review the latest evidence on different testing modalities and how effective they are in guiding clinical decision making in practice. We also evaluate predictive test cut-offs for the more common food allergens to try and provide guidance on when challenges might be most successful in determining oral tolerance in children.
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Affiliation(s)
- Ru-Xin Foong
- Department of Women and Children's Health (Paediatric Allergy), School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Children's Allergy Service, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Alexandra F Santos
- Department of Women and Children's Health (Paediatric Allergy), School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Children's Allergy Service, Guy's and St. Thomas' NHS Foundation Trust, London, UK.,Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK.,Asthma UK Centre for Allergic Mechanisms of Asthma, London, UK
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7
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Food allergy: epidemiology, pathogenesis, diagnosis, prevention, and treatment. Curr Opin Immunol 2020; 66:57-64. [DOI: 10.1016/j.coi.2020.03.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 02/06/2023]
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Santos AF, Barbosa‐Morais NL, Hurlburt BK, Ramaswamy S, Hemmings O, Kwok M, O’Rourke C, Bahnson HT, Cheng H, James L, Gould HJ, Sutton BJ, Maleki SJ, Lack G. IgE to epitopes of Ara h 2 enhance the diagnostic accuracy of Ara h 2-specific IgE. Allergy 2020; 75:2309-2318. [PMID: 32248566 DOI: 10.1111/all.14301] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Understanding the discrepancy between IgE sensitization and allergic reactions to peanut could facilitate diagnosis and lead to novel means of treating peanut allergy. OBJECTIVE To identify differences in IgE and IgG4 binding to peanut peptides between peanut-allergic (PA) and peanut-sensitized but tolerant (PS) children. METHODS PA (n = 56), PS (n = 42) and nonsensitized nonallergic (NA, n = 10) patients were studied. Synthetic overlapping 15-mer peptides of peanut allergens (Ara h 1-11) were spotted onto microarray slides, and patients' samples were tested for IgE and IgG4 binding using immunofluorescence. IgE and IgG4 levels to selected peptides were quantified using ImmunoCAP. Diagnostic model comparisons were performed using likelihood-ratio tests between each specified nominal logistic regression models. RESULTS Seven peptides on Ara h 1, Ara h 2, and Ara h 3 were bound more by IgE of PA compared to PS patients on the microarray. IgE binding to one peptide on Ara h 5 and IgG4 binding to one Ara h 9 peptide were greater in PS than in PA patients. Using ImmunoCAP, IgE to the Ara h 2 peptides enhanced the diagnostic accuracy of Ara h 2-specific IgE. Ratios of IgG4/IgE to 4 out of the 7 peptides were higher in PS than in PA subjects. CONCLUSIONS Ara h 2 peptide-specific IgE added diagnostic value to Ara h 2-specific IgE. Ability of peptide-specific IgG4 to surmount their IgE counterpart seems to be important in established peanut tolerance.
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Affiliation(s)
- Alexandra F. Santos
- Department of Women and Children’s Health (Paediatric Allergy) School of Life Course Sciences Faculty of Life Sciences and Medicine King’s College London London UK
- Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine King’s College London London UK
- Children’s Allergy ServiceEvelina London Children's Hospital, Guy’s and St Thomas’ Hospital London UK
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
| | - Nuno L. Barbosa‐Morais
- Faculdade de Medicina Instituto de Medicina Molecular João Lobo Antunes Universidade de Lisboa Lisbon Portugal
| | - Barry K. Hurlburt
- US Department of Agriculture Southern Regional Research Center New Orleans LA USA
| | - Sneha Ramaswamy
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
- Randall Centre for Cell & Molecular Biophysics King’s College London London UK
| | - Oliver Hemmings
- Department of Women and Children’s Health (Paediatric Allergy) School of Life Course Sciences Faculty of Life Sciences and Medicine King’s College London London UK
- Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine King’s College London London UK
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
| | - Matthew Kwok
- Department of Women and Children’s Health (Paediatric Allergy) School of Life Course Sciences Faculty of Life Sciences and Medicine King’s College London London UK
- Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine King’s College London London UK
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
| | | | | | - Hsiaopo Cheng
- US Department of Agriculture Southern Regional Research Center New Orleans LA USA
| | - Louisa James
- Blizard Institute Queen Mary University of London London UK
| | - Hannah J. Gould
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
- Randall Centre for Cell & Molecular Biophysics King’s College London London UK
| | - Brian J. Sutton
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
- Randall Centre for Cell & Molecular Biophysics King’s College London London UK
| | - Soheila J. Maleki
- US Department of Agriculture Southern Regional Research Center New Orleans LA USA
| | - Gideon Lack
- Department of Women and Children’s Health (Paediatric Allergy) School of Life Course Sciences Faculty of Life Sciences and Medicine King’s College London London UK
- Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine King’s College London London UK
- Children’s Allergy ServiceEvelina London Children's Hospital, Guy’s and St Thomas’ Hospital London UK
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
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Novel Bead-Based Epitope Assay is a sensitive and reliable tool for profiling epitope-specific antibody repertoire in food allergy. Sci Rep 2019; 9:18425. [PMID: 31804555 PMCID: PMC6895130 DOI: 10.1038/s41598-019-54868-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/09/2019] [Indexed: 12/16/2022] Open
Abstract
Identification of allergenic IgE epitopes is instrumental for the development of novel diagnostic and prognostic methods in food allergy. In this work, we present the quantification and validation of a Bead-Based Epitope Assay (BBEA) that through multiplexing of epitopes and multiple sample processing enables completion of large experiments in a short period of time, using minimal quantities of patients’ blood. Peptides that are uniquely coupled to beads are incubated with serum or plasma samples, and after a secondary fluorophore-labeled antibody is added, the level of fluorescence is quantified with a Luminex reader. The signal is then normalized and converted to epitope-specific antibody binding values. We show that the effect of technical artifacts, i.e. well position or reading order, is minimal; and batch effects - different individual microplate runs - can be easily estimated and eliminated from the data. Epitope-specific antibody binding quantified with BBEA is highly reliable, reproducible and has greater sensitivity of epitope detection compared to peptide microarrays. IgE directed at allergenic epitopes is a sensitive biomarker of food allergy and can be used to predict allergy severity and phenotypes; and quantification of the relationship between epitope-specific IgE and IgG4 can further improve our understanding of the immune mechanisms behind allergic sensitization.
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10
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Ehlers AM, Blankestijn MA, Knulst AC, Klinge M, Otten HG. Can alternative epitope mapping approaches increase the impact of B-cell epitopes in food allergy diagnostics? Clin Exp Allergy 2018; 49:17-26. [PMID: 30294841 PMCID: PMC7380004 DOI: 10.1111/cea.13291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023]
Abstract
In vitro allergy diagnostics are currently based on the detection of specific IgE binding on intact allergens or a mixture thereof. This approach has drawbacks as it may yield false‐negative and/or false‐positive results. Thus, we reviewed the impact of known B‐cell epitopes of food allergens to predict transience or persistence, tolerance or allergy and the severity of an allergic reaction and to examine new epitope mapping strategies meant to improve serum‐based allergy diagnostics. Recent epitope mapping approaches have been worthwhile in epitope identification and may increase the specificity of allergy diagnostics by using epitopes predominately recognized by allergic patients in some cases. However, these approaches did not lead to discrimination between clinically relevant and irrelevant epitopes so far, since the polyclonal serum IgE‐binding epitope spectrum seems to be too individual, independent of the disease status of the patients. New epitope mapping strategies are necessary to overcome these obstacles. The use of patient‐derived monoclonal antibodies instead of patient sera for functional characterization of clinically relevant and irrelevant epitope combinations, distinguished by their ability to induce degranulation, might be a promising approach to gain more insight into the allergic reaction and to improve serum‐based allergy diagnostics.
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Affiliation(s)
- Anna M Ehlers
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark A Blankestijn
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Andre C Knulst
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Henny G Otten
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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