Identification of the Molecular Mechanisms of non-response to Treatments, Relapses and Remission in Autoimmune, Inflammatory, and Allergic Conditions

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Deliverables

Report on the monitoring strategy adopted
Report on SOPs and templates

Project Website
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Publications

Plasma proteins elevated in severe asthma despite oral steroiduse and unrelated to Type-2 inflammation

Author(s): Maria Sparreman Mikus, Johan Kolmert, Lars I. Andersson, Jörgen Östling, Richard G. Knowles, Cristina Gómez, Magnus Ericsson, John-Olof Thörngren, Payam Emami Khoonsari, Barbro Dahlén, Maciej Kupczyk, Bertrand De Meulder, Charles Auffray, Per S. Bakke, Bianca Beghe, Elisabeth H. Bel, Massimo Caruso, Pascal Chanez, Bo Chawes, Stephen J. Fowler, Mina Gaga, Thomas Geiser, Mark Gjomarkaj, Ildikó
Published in: European Respiratory journal, Issue 13993003, 2022, ISSN 1399-3003
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00142-2021

A cluster of blood-based protein biomarkers associated with decreased cerebral blood flow relates to future cardiovascular events in patients with cardiovascular disease

Author(s): L Malin Overmars, Sanne Kuipers, Bram van Es, Jeroen de Bresser, Esther E Bron, Imo E Hoefer, Wouter W Van Solinge, L Jaap Kappelle, Matthias JP van Osch, Charlotte E Teunissen, Geert Jan Biessels, Saskia Haitjema, null null
Published in: Journal of Cerebral Blood Flow & Metabolism, Issue 43, 2024, Page(s) 2060-2071, ISSN 0271-678X
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1177/0271678x231195243

Novel IgG and IgA autoantibodies validated in two independent cohorts are associated with disease activity and determine organ manifestations in systemic lupus erythematosus: implications for anti-LIN28A, anti-HMGN5, anti-IRF5, and anti-TGIF1

Author(s): Julius Lindblom, Denis Lagutkin, Natalia Sherina, Helena Idborg, Lorenzo Beretta, Maria Orietta Borghi, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux, Anne-Lise Maudoux, Ana Tavares, Isabel Almeida, Miguel Angel Gonzalez-Gay Mantecón, Ricardo Blanco Alonso, Alfonso Corrales Martínez, Ignasi Rodríguez-Pintó, Gerard Espin
Published in: Annals of the Rheumatic Diseases, Issue 84, 2025, Page(s) 1164-1179, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1016/j.ard.2025.04.008

Development of Core Outcome Measures sets for paediatric and adult Severe Asthma (COMSA)

Author(s): Khaleva, Ekaterina; Rattu, Anna; Brightling, Chris; Bush, Andrew; Bossios, Apostolos; Bourdin, Arnaud; Chung, Kian Fan; Chaudhuri, Rekha; Coleman, Courtney; Dahlén, Sven Erik; Djukanovic, Ratko; Deschildre, Antoine; Fleming, Louise; Fowler, Stephen J.; Gupta, Atul; Hamelmann, Eckard; Hashimoto, Simone; Hedlin, Gunilla; Koppelman, Gerard H.; Melén, Erik; Murray, Clare S.; Pilette, Charles; Porsbj
Published in: EUROPEAN RESPIRATORY JOURNAL, Issue 5, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00606-2022

Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis

Author(s): Martin Kerick, Marialbert Acosta-Herrera, Carmen Pilar Simeón-Aznar, José Luis Callejas, Shervin Assassi, null null, P. Carreira, I. Castellvi, R. Ríos, R. García Portales, A. Fernández-Nebro, F. J. García-Hernández, M. A. Aguirre, B. Fernández-Gutiérrez, L. Rodríguez-Rodríguez, P. García de la Peña, E. Vicente, J. L. Andreu, M. Fernández de Castro, F. J. López-Longo, V. Fonollosa,
Published in: npj Genomic Medicine, Issue 7, 2023, ISSN 2056-7944
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41525-022-00327-8

Response to the letter ‘testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis’

Author(s): Daniel Toro-Domínguez, Jordi Martorell-Marugán, Manuel Martinez-Bueno, Raúl López-Domínguez, Elena Carnero-Montoro, Guillermo Barturen, Daniel Goldman, Michelle Petri, Pedro Carmona-Sáez, Marta E Alarcón-Riquelme
Published in: Briefings in Bioinformatics, Issue 25, 2023, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbad454

Distinct gene dysregulation patterns herald precision medicine potentiality in systemic lupus erythematosus

Author(s): Julius Lindblom, Daniel Toro-Domínguez, Elena Carnero-Montoro, Lorenzo Beretta, Maria Orietta Borghi, Jessica Castillo, Yvonne Enman, PRECISESADS Clinical Consortium, Chandra Mohan, Marta E. Alarcón-Riquelme, Guillermo Barturen, Ioannis Parodis
Published in: Journal of Autoimmunity Volume 136, April 2023, 103025, 2023, ISSN 1095-9157
Publisher: Elsevier
DOI: 10.1016/j.jaut.2023.103025

Predicting corticosteroid response in COPD using baseline bronchial biopsy DNA methylation

Author(s): Tessa E. Gillett, Corry-Anke Brandsma, Alen Faiz, Wim Timens, Gerard H. Koppelman, Martijn C. Nawijn, Maarten van den Berge
Published in: ERJ Open Research, Issue 11, 2025, Page(s) 00724-2024, ISSN 2312-0541
Publisher: European Respiratory Society (ERS)
DOI: 10.1183/23120541.00724-2024

New IgG and IgA autoantibody specificities against DNA-binding and RNA-binding proteins discriminate systemic lupus erythematosus from health and non-lupus autoimmunity–could anti-LIN28A enhance precision in diagnostics?

Author(s): Ioannis Parodis, Denis Lagutkin, Julius Lindblom, Helena Idborg, Lorenzo Beretta, Maria Orietta Borghi, Janique M. Peyper, Guillermo Barturen, Per-Johan Jakobsson, Marta E. Alarcón-Riquelme, Natalia Sherina, Dionysis Nikolopoulos
Published in: Annals of the Rheumatic Diseases, Issue 84, 2025, Page(s) 1180-1194, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1016/j.ard.2025.04.003

Core outcome sets, developed collaboratively with patients, can improve the relevance and comparability of clinical trials

Author(s): Alexander G. Mathioudakis, Ekaterina Khaleva, Markus Fally, Paula R. Williamson, Jens-Ulrik Jensen, Tim W. Felton, Chris Brightling, Andrew Bush, Tonya Winders, John Linnell, Valeria Ramiconi, Courtney Coleman, Tobias Welte, Graham Roberts, Jørgen Vestbo
Published in: ERS Journal, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.02107-2022

Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease

Author(s): Alba Garrido-Trigo, Ana M. Corraliza, Marisol Veny, Isabella Dotti, Elisa Melón-Ardanaz, Aina Rill, Helena L. Crowell, Ángel Corbí, Victoria Gudiño, Miriam Esteller, Iris Álvarez-Teubel, Daniel Aguilar, M. Carme Masamunt, Emily Killingbeck, Youngmi Kim, Michael Leon, Sudha Visvanathan, Domenica Marchese, Ginevra Caratù, Albert Martin-Cardona, Maria Esteve, Ingrid Ordás, Julian Panés, Elena
Published in: Nature Communications, Issue 14, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-40156-6

FixNCut: single-cell genomics through reversible tissue fixation and dissociation

Author(s): Laura Jiménez-Gracia, Domenica Marchese, Juan C. Nieto, Ginevra Caratù, Elisa Melón-Ardanaz, Victoria Gudiño, Sara Roth, Kellie Wise, Natalie K. Ryan, Kirk B. Jensen, Xavier Hernando-Momblona, Joana P. Bernardes, Florian Tran, Laura Katharina Sievers, Stefan Schreiber, Maarten van den Berge, Tessa Kole, Petra L. van der Velde, Martijn C. Nawijn, Philip Rosenstiel, Eduard Batlle, Lisa M. Butler
Published in: Genome Biology, Issue 25, 2024, ISSN 1474-760X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13059-024-03219-5

Characterization of Inflammatory Bowel Disease Heterogeneity Using Serum Proteomics: A Multicenter Study

Author(s): Benita Salomon, Padhmanand Sudhakar, Daniel Bergemalm, Erik Andersson, Olle Grännö, Marie Carlson, Charlotte R H Hedin, Johan D Söderholm, Lena Öhman, null null, Ryan C Ungaro, Konrad Aden, Geert D’Haens, Mark S Silverberg, Sven Almer, Francesca Bresso, Adam Carstens, Mauro D’Amato, Carl Eriksson, Henrik Hjortswang, Åsa V Keita, Maria Ling Lundström, Maria K Magnusson, Jóhann P Hreinsso
Published in: Journal of Crohn's and Colitis, Issue 2024, XX, 1–12, 2024, ISSN 1873-9946
Publisher: Elsevier Science
DOI: 10.1093/ecco-jcc/jjae169

POS0030 Exploring the clinical and social determinants of multiple drug failures in refractory rheumatoid arthritis

Author(s): Y. Tan, M. Parkes, D. Plant, M. Buch
Published in: Annals of the Rheumatic Diseases, Issue 84, 2025, Page(s) 345, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1016/j.ard.2025.05.427

Characterization of the SPIRITAS: A Disposable Sampling Setup for Volatile Organic Compound Collection and Analysis

Author(s): David J. Mager, Yoni E. van Dijk, Özgü Varan, Susanne J. H. Vijverberg, Suzanne W. J. Terheggen-Lagro, Anke-Hilse Maitland-van der Zee, Hettie M. Janssens, Paul Brinkman
Published in: Separations, Issue 11, 2025, Page(s) 150, ISSN 2297-8739
Publisher: MDPI Open Access Journals
DOI: 10.3390/separations11050150

Transcription Factor Activity Inference in Systemic Lupus Erythematosus

Author(s): Raúl López-Domínguez, Daniel Toro-Domínguez, Jordi Martorell-Marugan, Adrian García-Moreno, Christian H. Holland, Julio Saez-Rodriguez, Daniel Goldman, Michelle Petri, Marta E. Alarcón-Riquelme and Pedro Carmona-Sáez
Published in: Life, Issue 20751729, 2021, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life11040299

<scp>CytoNorm</scp> 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls

Author(s): Katrien L. A. Quintelier, Marcella Willemsen, Victor Bosteels, Joachim G. J. V. Aerts, Yvan Saeys, Sofie Van Gassen
Published in: Cytometry Part A, Issue 107, 2025, Page(s) 69-87, ISSN 1552-4922
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24910

Reliability of serum neurofilament light and glial fibrillary acidic protein for detecting disease activity upon discontinuation of first-line disease-modifying therapy in stable multiple sclerosis (DOT-MS)

Author(s): W. H. Fung, M. H. J. Wessels, E. M. E. Coerver, J. de Beukelaar, W. H. Bouvy, L. R. Canta, O. H. H. Gerlach, E. Hoitsma, E. L. J. Hoogervorst, B. A. de Jong, N. F. Kalkers, Z. L. E. van Kempen, H. Lövenich, C. E. P. van Munster, B. W. van Oosten, J. Smolders, A. Vennegoor, E. M. P. E. Zeinstra, M. Barrantes-Cepas, G. Kooij, M. M. Schoonheim, B. I. Lissenberg-Witte, B. Moraal, F. Barkhof, B. M. J.
Published in: Journal of Neurology, Issue 272, 2025, ISSN 0340-5354
Publisher: Dr. Dietrich Steinkopff Verlag
DOI: 10.1007/s00415-025-13231-9

Exploring the contribution of genetics on the clinical manifestations of systemic lupus erythematosus

Author(s): Ruth D. Rodríguez, Marta E. Alarcón-Riquelme
Published in: Best Practice & Research Clinical Rheumatology, Issue 38, 2024, Page(s) 101971, ISSN 1521-6942
Publisher: Bailliere Tindall And Cassell
DOI: 10.1016/j.berh.2024.101971

Reply: U-BIOPRED/BIOAIR proteins: inflammation or infection?

Author(s): Maria Sparreman Mikus, Johan Kolmert, Lars I. Andersson, Sven-Erik Dahlén, Anna James
Published in: European Respiratory Journal, Issue 60, 2025, Page(s) 2201795, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.01795-2022

Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients

Author(s): Elisa Melón-Ardanaz, Marisol Veny, Ana M Corraliza, Victoria Gudiño, Alba Garrido-Trigo, Ángela Sanzo-Machuca, Marc Buendia, Miriam Esteller, Lisseth Robbins-Moreno, Maite Rodrigo, M Carme Masamunt, Ángel Giner, Marta Gallego, Ingrid Ordás, Agnès Fernández-Clotet, Berta Caballol, Ángel Corbí, Bram Verstockt, Severine Vermeire, Julian Panés, Elena Ricart, Azucena Salas
Published in: Journal of Crohn's and Colitis, Issue 19, 2025, ISSN 1873-9946
Publisher: Elsevier Science
DOI: 10.1093/ecco-jcc/jjaf076

Urinary Leukotriene E 4 and Prostaglandin D 2 Metabolites Increase in Adult and Childhood Severe Asthma Characterized by Type 2 Inflammation. A Clinical Observational Study

Author(s): Johan Kolmert, Cristina Gómez, David Balgoma, Marcus Sjödin, Johan Bood, Jon R. Konradsen, Magnus Ericsson, John-Olof Thörngren, Anna James, Maria Mikus, Ana R. Sousa, John H. Riley, Stewart Bates, Per S. Bakke, Ioannis Pandis, Massimo Caruso, Pascal Chanez, Stephen J. Fowler, Thomas Geiser, Peter Howarth, Ildikó Horváth, Norbert Krug, Paolo Montuschi, Marek Sanak, Annelie Behndig, Dominick E
Published in: American Journal of Respiratory and Critical Care Medicine, Issue 203/1, 2021, Page(s) 37-53, ISSN 1073-449X
Publisher: American Thoracic Society
DOI: 10.1164/rccm.201909-1869oc

Molecular characterisation of lupus low disease activity state (LLDAS) and DORIS remission by whole-blood transcriptome-based pathways in a pan-European systemic lupus erythematosus cohort

Author(s): Ioannis Parodis, Julius Lindblom, Guillermo Barturen, Rafaela Ortega-Castro, Ricard Cervera, Jacques-Olivier Pers, Fernanda Genre, Falk Hiepe, Maria Gerosa, László Kovács, Ellen De Langhe, Silvia Piantoni , Georg Stummvoll, Carlos Vasconcelos, Barbara Vigone, Torsten Witte; PRECISESADS Clinical Consortium; Marta E Alarcón-Riquelme, Lorenzo Beretta
Published in: Annals of the Rheumatic Diseases, 2024, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/ard-2023-224795

Definitions of non-response and response to biological therapy for severe asthma: a systematic review

Author(s): Ekaterina Khaleva; Anna Rattu; Chris Brightling; Andrew Bush; Arnaud Bourdin; Apostolos Bossios; Kian Fan Chung; Rekha Chaudhuri; Courtney Coleman; Ratko Djukanovic; Sven-Erik Dahlén; Andrew Exley; Louise Fleming; Stephen J. Fowler; Atul Gupta; Eckard Hamelmann; Gerard H. Koppelman; Erik Melén; Vera Mahler; Paul Seddon; Florian Singer; Celeste Porsbjerg; Valeria Ramiconi; Franca Rusconi; Valenty
Published in: "ERJ Open Research, 2023, 9 (3), pp.00444-2022. ⟨10.1183/23120541.00444-2022⟩", Issue 3, 2023, ISSN 2312-0541
Publisher: European Respiratory Society
DOI: 10.1183/23120541.00444-2022

Serum profiling identifies CCL8, CXCL13, and IL-1RA as markers of active disease in patients with systemic lupus erythematosus

Author(s): Julius Lindblom, Lorenzo Beretta, Maria Orietta Borghi, and PRECISESADS Clinical Consortium, Marta E. Alarcón-Riquelme, Ioannis Parodis
Published in: Front Immunol, 2023, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2023.1257085

Risankizumab in severe asthma: A Phase IIa, placebo-controlled study

Author(s): Christopher E. Brightling, Parameswaran Nair, Renaud Louis, Dave Singh
Published in: The New England Journal of Medicine, 2021, ISSN 1533-4406
Publisher: Massachusetts Medical Society
DOI: 10.1056/nejmoa2030880

Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data

Author(s): Manuel Rueda, Ivo C Leist, Ivo G Gut
Published in: J Biomed Inform, 2024, ISSN 1532-0480
Publisher: Elsevier
DOI: 10.1016/j.jbi.2023.104558

Activating Transcription Factor 6 Mediates Inflammatory Signals in Intestinal Epithelial Cells Upon Endoplasmic Reticulum Stress

Author(s): Stephanie T. Stengel, Antonella Fazio, Simone Lipinski, Martin T. Jahn, Konrad Aden, Go Ito, Felix Wottawa, Jan W.P. Kuiper, Olivia I. Coleman, Florian Tran, Dora Bordoni, Joana P. Bernardes, Marlene Jentzsch, Anne Luzius, Sandra Bierwirth, Berith Messner, Anna Henning, Lina Welz, Nassim Kakavand, Maren Falk-Paulsen, Simon Imm, Finn Hinrichsen, Matthias Zilbauer, Stefan Schreiber, Arthur Kaser, Ri
Published in: Gastroenterology, Issue 159/4, 2020, Page(s) 1357-1374.e10, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2020.06.088

Serum glial fibrillary acidic protein in natalizumab-treated relapsing-remitting multiple sclerosis: An alternative to neurofilament light

Author(s): Mark HJ Wessels, Zoë YGJ Van Lierop, Samantha Noteboom, Eva MM Strijbis, Johannes A Heijst, Zoé LE Van Kempen, Bastiaan Moraal, Frederik Barkhof, Bernard MJ Uitdehaag, Menno M Schoonheim, Joep Killestein, Charlotte E Teunissen
Published in: Multiple Sclerosis Journal, Issue 29, 2025, Page(s) 1229-1239, ISSN 1352-4585
Publisher: SAGE Publications
DOI: 10.1177/13524585231188625

Current Insights on Biomarkers in Lupus Nephritis: A Systematic Review of the Literature

Author(s): Leonardo Palazzo, Julius Lindblom, Chandra Mohan, Ioannis Parodis
Published in: J. Clin. Med., 2022, ISSN 2077-0383
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/jcm11195759

Prospective trial of natalizumab personalised extended interval dosing by therapeutic drug monitoring in relapsing-remitting multiple sclerosis (NEXT-MS)

Author(s): Alyssa A Toorop, Zoë YGJ van Lierop, Liza MY Gelissen, Elske Hoitsma, Esther MPE Zeinstra, Luuk C van Rooij, Caspar EP van Munster, Anke Vennegoor, Jop P Mostert, Beatrijs HA Wokke, Nynke F Kalkers, Erwin LJ Hoogervorst, Jeroen JJ van Eijk, Christiaan M Roosendaal, Jolijn J Kragt, Marijke Eurelings, Jessie van Genugten, Jessica Nielsen, LGF Sinnige, Mark E Kloosterziel, Edo PJ Arnoldus, Gert W va
Published in: Journal of Neurology, Neurosurgery & Psychiatry, 2023, Page(s) jnnp-2023-332119, ISSN 0022-3050
Publisher: BMJ Publishing Group
DOI: 10.1136/jnnp-2023-332119

Impact of serum neurofilament light on clinical decisions in a tertiary multiple sclerosis clinic

Author(s): Zoë YGJ van Lierop, Mark HJ Wessels, Womei ML Lekranty, Bastiaan Moraal, Sam N Hof, Laura Hogenboom, Brigit A de Jong, Nandi Meijs, Liselore A Mensing, Bob W van Oosten, Nik Sol, Zoé LE van Kempen, Lisa Vermunt, Myrthe J Willems, Eva MM Strijbis, Bernard MJ Uitdehaag, Joep Killestein, Charlotte E Teunissen
Published in: Multiple Sclerosis Journal, Issue 30, 2025, Page(s) 1620-1629, ISSN 1352-4585
Publisher: SAGE Publications
DOI: 10.1177/13524585241277044

Diagnostic value of kappa free light chain index in patients with primary progressive multiple sclerosis – a multicentre study

Author(s): Harald Hegen, Klaus Berek, Paola Cavalla, Mikael Christiansen, Andreja Emeršič, Massimiliano Di Filippo, Lorenzo Gaetani, Michaela Hassler, Cyra Leurs, Dejan Milosavljevic, Vincent van Pesch, Thor Petersen, Stefan Presslauer, Igal Rosenstein, Uroš Rot, Christine Schnabl, Charlotte Teunissen, Domizia Vecchio, Marco Vercellino, Florian Deisenhammer
Published in: Frontiers in Immunology, Issue 14, 2023, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2023.1327947

DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon

Author(s): Antonella Fazio, Dora Bordoni, Jan W. P. Kuiper, Saskia Weber-Stiehl, Stephanie T. Stengel, Philipp Arnold, David Ellinghaus, Go Ito, Florian Tran, Berith Messner, Anna Henning, Joana P. Bernardes, Robert Häsler, Anne Luzius, Simon Imm, Finn Hinrichsen, Andre Franke, Samuel Huber, Susanna Nikolaus, Konrad Aden, Stefan Schreiber, Felix Sommer, Gioacchino Natoli, Neha Mishra & Philip Rosenstiel
Published in: Nature communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33844-2

Neurofilament-light and contactin-1 association with long-term brain atrophy in natalizumab-treated relapsing-remitting multiple sclerosis

Author(s): Zoë YGJ van Lierop, Samantha Noteboom, Martijn D Steenwijk, Maureen van Dam, Alyssa A Toorop, Zoé LE van Kempen, Bastiaan Moraal, Frederik Barkhof, Bernard MJ Uitdehaag, Menno M Schoonheim, Charlotte E Teunissen, Joep Killestein
Published in: Multiple Sclerosis Journal, Issue 28, 2025, Page(s) 2231-2242, ISSN 1352-4585
Publisher: SAGE Publications
DOI: 10.1177/13524585221118676

Single-cell microbiota phenotyping reveals distinct disease and therapy-associated signatures in Crohn’s disease

Author(s): Lisa Budzinski, Gi-Ung Kang, René Riedel, Toni Sempert, Leonie Lietz, René Maier, Janine Büttner, Bettina Bochow, Marcell T. Tordai, Aayushi Shah, Amro Abbas, Tanisha Momtaz, Jannike L. Krause, Robin Kempkens, Katrin Lehman, Gitta A. Heinz, Anne E. Benken, Stefanie Bartsch, Kathleen Necke, Ute Hoffmann, Mir-Farzin Mashreghi, Robert Biesen, Tilmann Kallinich, Tobias Alexander, Bosse Jessen, Carl
Published in: Gut Microbes, Issue 17, 2025, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2025.2452250

Tezepelumab and Mucus Plugs in Patients with Moderate-to-Severe Asthma

Author(s): Lars H. Nordenmark, Ph.D., Åsa Hellqvist, M.Sc., Claire Emson, Ph.D., Sarah Diver, M.D., Celeste Porsbjerg, M.D., Ph.D., Janet M. Griffiths, Ph.D., John D. Newell, Jr, M.D., +5, and Christopher E. Brightling, F.Med.Sci.
Published in: NEJM Evidence, 2023, ISSN 2766-5526
Publisher: NEJM group
DOI: 10.1056/evidoa2300135

Glycosylation Alterations in Multiple Sclerosis Show Increased Proinflammatory Potential

Author(s): Ana Cvetko, Domagoj Kifer, Olga Gornik, Lucija Klarić, Elizabeth Visser, Gordan Lauc, James F. Wilson, Tamara Štambuk
Published in: Biomedicines, Issue 8/10, 2020, Page(s) 410, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines8100410

Author(s): Morell M., Pérez-Cózar F, Marañón C.
Published in: International Journal of Molecular Science, Issue 14220067, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22137143

Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies

Author(s): Paulina Rybakowska, Catalina Burbano, Sofie Van Gassen, Nieves Varela, Rocío Aguilar‐Quesada, Yvan Saeys, Marta E. Alarcón‐Riquelme, Concepción Marañón
Published in: Cytometry Part A, 2020, ISSN 1552-4922
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24241

PeacoQC: Peak-based selection of high quality cytometry data

Author(s): Annelies Emmaneel, Katrien Quintelier, Dorine Sichien, Paulina Rybakowska, Concepción Marañón, Marta E. Alarcón-Riquelme, Gert Van Isterdael, Sofie Van Gassen, Yvan Saeys
Published in: Cytometry Part A, Issue 15524930, 2021, Page(s) 325-338, ISSN 1552-4930
Publisher: International Society for Advancement of Cytometry
DOI: 10.1002/cyto.a.24501

YOUPI: Your powerful and intelligent tool for segmenting cells from imaging mass cytometry data

Author(s): Yvonne Scuiller, Patrice Hemon, Marion Le Rochais, Jacques-Olivier Pers, Christophe Jamin, Nathan Foulquier
Published in: Frontiers in Immunology, Issue 14, 2023, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2023.1072118

Interferon and B-cell Signatures Inform Precision Medicine in Lupus Nephritis

Author(s): Ioannis Parodis, Julius Lindblom, Daniel Toro-Domínguez, Lorenzo Beretta, Maria O. Borghi, Jessica Castillo, Elena Carnero-Montoro, Yvonne Enman, Chandra Mohan, Marta E. Alarcón-Riquelme, Guillermo Barturen, Dionysis Nikolopoulos, Lorenzo Beretta, Barbara Vigone, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Divi Cornec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux,
Published in: Kidney International Reports, Issue 9, 2024, Page(s) 1817-1835, ISSN 2468-0249
Publisher: Elsevier Inc.
DOI: 10.1016/j.ekir.2024.03.014

Molecular subtypes explain lupus epigenomic heterogeneity unveiling new regulatory genetic risk variants

Author(s): Olivia Castellini-Pérez, Elena Povedano, Guillermo Barturen, Manuel Martínez-Bueno, Andrii Iakovliev, Martin Kerick, Raúl López-Domínguez, Concepción Marañón, Javier Martín, Esteban Ballestar, PRECISEADS Clinical Consortium, PRECISEADS Flow Cytometry Study Group, María Orietta Borghi, Weiliang Qiu, Cheng Zhu, Srinivas Shankara, Athina Spiliopoulou, Emanuele de Rinaldis, Elena Carnero-Mon
Published in: npj Genomic Medicine, Issue 9, 38, 2024, ISSN 2056-7944
Publisher: Springer Nature
DOI: 10.1038/s41525-024-00420-0

Identifying Predictive Biomarkers of Response in Patients With Rheumatoid Arthritis Treated With Adalimumab Using Machine Learning Analysis of Whole‐Blood Transcriptomics Data

Author(s): Chuan Fu Yap, Nisha Nair, Ann W. Morgan, John D. Isaacs, Anthony G. Wilson, Kimme Hyrich, Guillermo Barturen, María Riva‐Torrubia, Marta Gut, Ivo Gut, Marta E. Alarcón Riquelme, Anne Barton, Darren Plant
Published in: Arthritis & Rheumatology, 2025, ISSN 2326-5191
Publisher: Wiley
DOI: 10.1002/art.43255

Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond

Author(s): Ivo C. Leist, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Guillermo Barturen, PRECISESADS Clinical Consortium, Ivo G. Gut, Manuel Rueda
Published in: BMC Bioinformatics, Issue 25, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-024-05993-2

Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis

Author(s): Lisa Budzinski, Toni Sempert, Leonie Lietz, René Maier, Gi-Ung Kang, Anne Sae Lim von Stuckrad, Carl Christoph Goetzke, Maria Roth, Aayushi Shah, Amro Abbas, Katrin Lehman, Kathleen Necke, Stefanie Bartsch, Ute Hoffmann, Mir-Farzin Mashreghi, Robert Biesen, Tilmann Kallinich, Hyun-Dong Chang
Published in: Molecular and Cellular Pediatrics, Issue 11, 2024, ISSN 2194-7791
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s40348-024-00186-6

9-HODE associates with thalamic atrophy and predicts white matter damage in multiple sclerosis

Author(s): Wing Hee Fung, Marike R. van Lingen, Jelle Y. Broos, Ka-Hoo Lam, Maureen van Dam, Wing Ka Fung, Samantha Noteboom, Ismail Koubiyr, Helga E. de Vries, Bas Jasperse, Charlotte E. Teunissen, Martin Giera, Joep Killestein, Hanneke E. Hulst, Eva M.M. Strijbis, Menno M. Schoonheim, Gijs Kooij
Published in: Multiple Sclerosis and Related Disorders, Issue 92, 2025, Page(s) 105946, ISSN 2211-0348
Publisher: Elsevier
DOI: 10.1016/j.msard.2024.105946

Cerebrospinal fluid kappa free light chains for the diagnosis of multiple sclerosis

Author(s): Hegen, Harald; Arrambide, Georgina||; Gnanapavan, Sharmilee||; Kaplan, Batia; Khalil, Michael||; Saadeh, Ruba; Teunissen, Charlotte E||; Tumani, Hayrettin||; Villar, Luisa Maria; Willrich, Maria Alice V; Zetterberg, Henrik||; Deisenhammer, Florian||
Published in: Multiple Sclerosis Journal, 2022, ISSN 1477-0970
Publisher: Sage Publications
DOI: 10.1177/135245852211342

HLA-DRB1 and HLA-DQA1 associated with immunogenicity to adalimumab therapy in patients with rheumatoid arthritis

Author(s): Chuan Fu Yap, Nisha Nair, Annick de Vries, Floris C Loeff, Ann W Morgan, John D Isaacs, Anthony G Wilson, Kimme L Hyrich, Anne Barton, Darren Plant
Published in: Ann Rheum Dis., 2024, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/ard-2023-223955

Why Is Multiple Sclerosis More Frequent in Women? Role of the Immune System and of Oral and Gut Microbiota

Author(s): Marianna D’Anca, Francesca R. Buccellato, Gianluca Martino Tartaglia, Massimo Del Fabbro, Paola Muti, Elio Scarpini, Daniela Galimberti, Laura Ghezzi
Published in: Applied Sciences, Issue 13, 2025, Page(s) 5881, ISSN 2076-3417
Publisher: MDPI AG
DOI: 10.3390/app13105881

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Author(s): Neha Mishra, Konrad Aden, Johanna I. Blase, Nathan Baran, Dora Bordoni, Florian Tran, Claudio Conrad, Diana Avalos, Charlot Jaeckel, Michael Scherer, Signe B. Sørensen, Silja H. Overgaard, Berenice Schulte, Susanna Nikolaus, Guillaume Rey, Gilles Gasparoni, Paul A. Lyons, Joachim L. Schultze, Jörn Walter, Vibeke Andersen, SYSCID Consortium, Emmanouil T. Dermitzakis, Stefan Schreiber & Philip Ros
Published in: Genome Medicine, 2022, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-022-01112-z

Rare Variants in Systemic Lupus Erythematosus: From Monogenic to Polygenic Disease

Author(s): Ruth D. Rodríguez, Marta E. Alarcón-Riquelme
Published in: Medical Research Archives, 2023, ISSN 2375-1916
Publisher: European Society of Medicine
DOI: 10.18103/mra.v11i10.4363

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression

Author(s): Daniel Toro-Domínguez, Jordi Martorell-Marugán, Manuel Martinez-Bueno, Raúl López-Domínguez, Elena Carnero-Montoro, Guillermo Barturen, Daniel Goldman, Michelle Petri, Pedro Carmona-Sáez, Marta E Alarcón-Riquelme
Published in: Briefings in Bioinformatics, Issue 14774054, 2022, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbac332

Differential molecular signatures in response to CD19-CAR T cell therapy compared with conventional pharmacotherapy in systemic lupus erythematosus

Author(s): Panagiotis Garantziotis, Lorenzo Beretta, Julius Lindblom, Georgia-Savina Moysidou, Dionysis Nikolopoulos, Ricardo Grieshaber-Bouyer, Melanie Hagen, Christina Bergmann, Andreas Wirsching, Aline Bozec, Matthias Schneider, Guillermo Barturen, George Bertsias, Dimitrios T Boumpas, Marta E Alarcón-Riquelme, Andreas Mackensen, Georg Schett, Ioannis Parodis
Published in: Annals of the Rheumatic Diseases, 2025, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1016/j.ard.2025.06.2132

Narrative review to capture patients’ perceptions and opinions about non-response and response to biological therapy for severe asthma

Author(s): Courtney Coleman; Ekaterina Khaleva; Anna Rattu; Betty Frankemölle; Hanna Nielsen; Graham Roberts; Clare Williams
Published in: Crossref, Issue 6, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00837-2022

Data processing workflow for large-scale immune monitoring studies by mass cytometry

Author(s): Paulina Rybakowska, Sofie Van Gassen, Katrien Quintelier, Yvan Saeys, Marta E. Alarcón-Riquelme, Concepción Marañón
Published in: Computational and Structural Biotechnology Journal, Issue 19, 2021, Page(s) 3160-3175, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2021.05.032

Predictors of Response to Biologics for Severe Asthma: A Systematic Review and Meta‐Analysis

Author(s): Anna Rattu, Piers Dixey, David Charles, Chris Brightling, Kian Fan Chung, Apostolos Bossios, Arnaud Bourdin, Ratko Djukanovic, Sven‐Erik Dahlén, Louise Fleming, Rekha Chaudhuri, Erik Melén, Antoine Deschildre, Charles Pilette, Gerard H. Koppelman, Andrew Exley, Freja Anckers, Sarah Miller, Hanna Nielsen, Clare Williams, Ekaterina Khaleva, Graham Roberts, null null
Published in: Allergy, 2025, ISSN 0105-4538
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/all.70031

The Potential of Computational Modeling to Predict Disease Course and Treatment Response in Patients with Relapsing Multiple Sclerosis

Author(s): Francesco Pappalardo, Giulia Russo, Marzio Pennisi, Giuseppe Alessandro Parasiliti Palumbo, Giuseppe Sgroi, Santo Motta, Davide Maimone
Published in: Cells, Issue 9/3, 2020, Page(s) 586, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells9030586

Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline

Author(s): Paulina Rybakowska, Sofie Van Gassen, Jordi Martorell Marugán, Katrien Quintelier, Yvan Saeys, Marta E. Alarcón-Riquelme, Concepción Marañón
Published in: STAR Protocols, Issue 3, 2024, Page(s) 101697, ISSN 2666-1667
Publisher: Elsevier BV
DOI: 10.1016/j.xpro.2022.101697

Real-world efficacy of treatment with benralizumab, dupilumab, mepolizumab and reslizumab for severe asthma: A systematic review and meta-analysis

Author(s): David Charles, Jemma Shanley, Sasha-Nicole Temple, Anna Rattu, Ekaterina Khaleva, Graham Roberts
Published in: Clinical & Experimental Allergy, Issue 13652222, 2022, Page(s) 616-627, ISSN 1365-2222
Publisher: Britisch Society for Allergy & Clinical Immunology
DOI: 10.1111/cea.14112

Optimized network inference for immune diseased single cells

Author(s): Elena Merino Tejero, Dwain Jude Vaz, Guillermo Barturen, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Walter Kolch, David Matallanas
Published in: Frontiers in Immunology, Issue 16, 2025, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2025.1597862

Identifying and appraising outcome measures for severe asthma: a systematic review

Author(s): Anna Rattu, Ekaterina Khaleva, Chris Brightling, Sven-Erik Dahlén, Apostolos Bossios, Louise Fleming, Kian Fan Chung, Erik Melén, Ratko Djukanovic, Rekha Chaudhuri, Andrew Exley, Gerard H. Koppelman, Arnaud Bourdin, Franca Rusconi, Celeste Porsbjerg, Courtney Coleman, Clare Williams, Hanna Nielsen, Elizabeth Davin, Phil Taverner, Sofia Romagosa Vilarnau, Graham Roberts on behalf of the 3TR Conso
Published in: ERS Journal, 2023, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.01231-2022

Patient Reported Outcomes in Chronic Inflammatory Diseases: Current State, Limitations and Perspectives

Author(s): Florian Tran, Jan Henrik Schirmer, Ilka Ratjen, Wolfgang Lieb, Philip Helliwell, Johan Burisch, Juliane Schulz, Florian Schrinner, Charlot Jaeckel, Ulf Müller-Ladner, Stefan Schreiber, Bimba F. Hoyer
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.614653

Identification of urinary bacterial genes as biomarkers for non-invasive diagnosis of renal lupus

Author(s): Virginia Pérez-Carrasco, Ana Soriano-Lerma, Cinzia Guzzi, María Luisa García-Martín, María J. Tello, Ángel Linde-Rodríguez, Victoria Sánchez-Martín, Matilde Ortiz-González, null null, Lorenzo Beretta, Barbara Vigone, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Divi Cornec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux, Anne-Lise Maudoux, Carlos Vasconcelos,
Published in: Biomarker Research, Issue 13, 2025, ISSN 2050-7771
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s40364-025-00828-5

Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples

Author(s): Fabienne K. Roessler, Birke J. Benedikter, Bernd Schmeck, Nadav Bar
Published in: Scientific Reports, Issue 11, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-89762-8

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Author(s): Joana P Bernardes 1, Neha Mishra 1, Florian Tran 2, Thomas Bahmer 3, Lena Best 4, Johanna I Blase 1, Dora Bordoni 1, Jeanette Franzenburg 5, Ulf Geisen 6, Jonathan Josephs-Spaulding 4, Philipp Köhler 7, Axel Künstner 8, Elisa Rosati 1, Anna C Aschenbrenner 9, Petra Bacher 10, Nathan Baran 1, Teide Boysen 1, Burkhard Brandt 11, Niklas Bruse 12, Jonathan Dörr 6, Andreas Dräger 13, Gunnar Elke 14
Published in: Immunity, Issue 10747613, 2020, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2020.11.017

Stem Cells and Organoid Technology in Precision Medicine in Inflammation: Are We There Yet?

Author(s): Florian Tran, Christine Klein, Alexander Arlt, Simon Imm, Evelyn Knappe, Alison Simmons, Philip Rosenstiel, Philip Seibler
Published in: Frontiers in Immunology, Issue 16643224, 2020, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2020.573562

Tryptophan degradation as a systems phenomenon in inflammation - an analysis across 13 chronic inflammatory diseases

Author(s): Danielle M M Harris, Silke Szymczak, Sven Schuchardt, Johannes Labrenz, Florian Tran, Lina Welz, Hanna Graßhoff, Henner Zirpel, Melike Sümbül, Mhmd Oumari, Nils Engelbogen, Ralf Junker, Claudio Conrad, Diamant Thaçi, Norbert Frey, Andre Franke, Stephan Weidinger, Bimba Hoyer, Philip Rosenstiel, Silvio Waschina, Stefan Schreiber, Konrad Aden
Published in: EBio Medicine, 2024, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105056

OP0231 MASS CYTOMETRY DATA RECLASSIFY SYSTEMIC AUTOIMMUNE DISEASE PATIENTS IN PHENOTYPICALLY DISTINCTIVE GROUPS

Author(s): P. Rybakowska, S. van Gassen, C. Perez-Sanchez, A. Ibañez-Costa, N. Varela, R. Ortega Castro, C. Fernández-Roldán, I. Jiménez-Moleón, N. Ortego, E. Raya, R. Aguilar Quesada, C. Lopez-Pedrera, E. Collantes Estevez, Y. Saeys, M. Alarcon-Riquelme, C. Marañón
Published in: Annals of the Rheumatic Diseases, Issue 81, 2025, Page(s) 152-153, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2022-eular.1123

3TR: a pan-European cross-disease research consortium aimed at improving personalised biological treatment of asthma and COPD.

Author(s): Celeste Porsbjerg; Anke H. Maitland-van der Zee; Guy Brusselle; Giorgio Walter Canonica; Alvar Agusti; Rosa Faner; Claus Vogelmeier; Martijn C. Nawijn; Maarten van den Berge; Franca Rusconi; Charles Pilette; Valeria Ramiconi; Courtney Coleman; Rekha Chaudhuri; Kian Fan Chung; Jadwiga A. Wedzicha; Sejla Saglani; Marc P. van der Schee; Liam G Heaney; Arnaud Bourdin; Graham Roberts; Graham Roberts; G
Published in: European Respiratory Journal, 58(4):2102168. EUROPEAN RESPIRATORY SOC JOURNALS LTD, Issue 7, 2021, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.02168-2021

Dysregulation of innate and adaptive lymphoid immunity may have implications for symptom attribution and predict responses to targeted therapies in neuropsychiatric systemic lupus erythematosus

Author(s): Julius Lindblom, Guillermo Barturen, Lorenzo Beretta, Daniel Toro-Domínguez, Elena Carnero-Montoro, Maria Orietta Borghi, Jessica Castillo, Ellen Iacobaeus, Yvonne Enman, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux, Anne-Lise Maudoux, Ana Tavares, Isabel Almeida, Miguel Angel Gonzalez-Gay Mantecón, Ricardo Blanco Alonso
Published in: Journal of Translational Autoimmunity, Issue 11, 2025, Page(s) 100296, ISSN 2589-9090
Publisher: Elsevier BV
DOI: 10.1016/j.jtauto.2025.100296

Patient-centred composite scores as tools for assessment of response to biological therapy for paediatric and adult severe asthma

Author(s): Ekaterina Khaleva, Chris Brightling, Thomas Eiwegger, Alan Altraja, Philippe Bégin, Katharina Blumchen, Apostolos Bossios, Arnaud Bourdin, Anneke Ten Brinke, Guy Brusselle, Roxana Silvia Bumbacea, Andrew Bush, Thomas B. Casale, Graham W. Clarke, Rekha Chaudhuri, Kian Fan Chung, Courtney Coleman, Jonathan Corren, Sven-Erik Dahlén, Antoine Deschildre, Ratko Djukanovic, Katrien Eger, Andrew Exley,
Published in: European Respiratory Journal, Issue 65, 2025, Page(s) 2400691, ISSN 0903-1936
Publisher: European Respiratory Society
DOI: 10.1183/13993003.00691-2024

Risankizumab in severe asthma: A Phase IIa, placebo-controlled study

Author(s): Brightling, Christopher E.; Nair, Parameswaran; Louis, Renaud; Singh, Dave
Published in: Airway pharmacology and treatment, Issue 1, 2020
Publisher: European Respiratory Society
DOI: 10.1183/13993003.congress-2020.3699

Adapting asthma clinical trials in response to the COVID-19 pandemic - the BenRex study design

Author(s): Smith SJ, Gillespie L, Heaney LG, Brightling CE , McConnachie A¬, Siddiqui S, Mistry V4, Brown V , Jackson DJ, Lee NW, Fowler SJ, Mansur AH, Burhan H, Saralaya D, Kurukulaaratchy R, Nasser S, Pfeffer P, Brown T, Lordan J, Pavord ID, Chaudhuri R.
Published in: European Respiratory Journal, 2021, ISSN 1399-3003
Publisher: European Respiratory Society
DOI: 10.1183/13993003.congress-2021.pa1108

Outcome measures and predictors of response to biological treatments for severe asthma

Author(s): Anna Rattu
Published in: 2024
Publisher: n/a

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