A Systems medicine approach to chronic inflammatory disease

Risultati finali

Report on the maintenance of website, updating with project news, results, success information

A report on the maintenance of the Project Website including the updating with project news results and success Information will be submitted

Summer School on Systems Medicine

To disseminate knowledge and expertise also beyond SYSCID we will organize a summer school on Systems Medicine

Open access summary report

An open access questionnaire to assess each partners experiences with the process and their general opinion that has been developed by Eurice in direct collaboration with the infrastructure project OpenAIRE wwwopenaireeu will be used to collect partner feedback to be merged into an open access summary report at the end of the project

Final report on integrated analyses and model

This document will describe the machine learning methods employed for antigen prediction in the datasets integrated

Public project website

Eurice will be in charge of the set-up and maintenance of the public project website, which will serve as an additional showcase for presenting the project’s activities and achievements.

SYSCID movie

In addition to standard print materials such as project leaflets and posters, audio-visual material like a project movie will be produced to support dissemination to the interested public including patients.

Pubblicazioni

Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations

Autori: Degenhardt, F., G. Mayr, M. Wendorff, G. Boucher, E. Ellinghaus, D. Ellinghaus, H. ElAbd, E. Rosati, M. Hübenthal, S. Juzenas, S. Abedian, H. Vahedi, B. K. Thelma, S. K. Yang, B. D. Ye, J. H. Cheon, L. W. Datta, N. E. Daryani, P. Ellul, M. Esaki, Y. Fuyuno, D. P. B. McGovern, T. Haritunians, M. Hong, G. Juyal, E. S. Jung, M. Kubo, S. Kugathasan, T. L. Lenz, S. Leslie, R. Malekzadeh, V. Midha, A.
Pubblicato in: Human Molecular Genetics, 2021, ISSN 0964-6906
Editore: Oxford University Press
DOI: 10.1093/hmg/ddab017

Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation

Autori: Kevin Baßler, Wataru Fujii, Theodore S Kapellos, Erika Dudkin, Nico Reusch, Ari Horne, Benedikt Reiz Malte D Luecken, Collins Osei-Sarpong, Stefanie Warnat-Herresthal, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Allon Wagner, Patrick Günther, Carmen Pizarro, Tina Schreiber, Rainer Knoll, Lisa Holsten, Charlotte Kröger, Elena De Domenico, Matthias Becker, Kristian Händler, Christian T Wohnhaas
Pubblicato in: Frontiers in Immunology, Numero 16643224, 2022, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2022.917232

Demyelination with autoimmune features: a distinct clinical entity? Results from a longitudinal cohort

Autori: Dionysis Nikolopoulos, Dimitris Kitsos, Matilda Papathanasiou, Maria Chondrogianni, Aikaterini Theodorou, Panagiotis Garantziotis, Antigone Pieta, Triantafyllos Doskas, George Bertsias, Konstantinos Voumvourakis, Dimitrios T Boumpas, Antonis Fanouriakis
Pubblicato in: Rheumatology, Numero 14620324, 2021, ISSN 1462-0324
Editore: Oxford University Press
DOI: 10.1093/rheumatology/keaa902

Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis

Autori: Eleni Frangou, Panagiotis Garantziotis, Maria Grigoriou, Aggelos Banos, Dionysis Nikolopoulos, Antigone Pieta, Stavros A Doumas, Antonis Fanouriakis, Aikaterini Hatzioannou, Theodora Manolakou, Themis Alissafi, Panayotis Verginis, Emmanouil Athanasiadis, Emmanouil Dermitzakis, George Bertsias, Anastasia Filia, Dimitrios T Boumpas
Pubblicato in: Annals of the Rheumatic Diseases, Numero 00034967, 2022, ISSN 0003-4967
Editore: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2021-222069

Neutrophils in COVID-19

Autori: Nico Reusch, Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Kevin Baßler, Joachim L. Schultze, Anna C. Aschenbrenner
Pubblicato in: Frontiers in Immunology, Numero 12, 2021, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2021.652470

Distinct Longitudinal Changes in Immunoglobulin G N-Glycosylation Associate with Therapy Response in Chronic Inflammatory Diseases

Autori: Jerko Štambuk, Frano Vučković , Siniša Habazin, Maja Hanić, Mislav Novokmet, Susanna Nikolaus, Florian Tran, Stefan Schreiber, Andre Franke, Philip Rosenstiel, Gordan Lauc, Konrad Aden, Marija Pezer
Pubblicato in: International Journal of Molecular Sciences, Numero 14220067, 2022, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23158473

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Autori: Benjamin Krämer, Rainer Knoll, Lorenzo Bonaguro, Michael To Vinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, Kim Melanie Kaiser, Gereon J. Rieke, Jenny Bischoff, Malte B. Monin, Christoph Hoffmeister, Stefan Schlabe, Elena De Domenico, Nico Reusch Kristian Händler, Gary Reynolds, Nils Blüthgen, Gudrun Hack, Claudia Finnemann, Hans D. Nischalke, Christian P. Strassburg, Em
Pubblicato in: Immunity, Numero 00928674, 2021, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.immuni.2021.09.002

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

Autori: Michael Scherer; Gilles Gasparoni; Souad Rahmouni; Tatiana I. Shashkova; Marion Arnoux; Edouard Louis; Arina Nostaeva; Diana Avalos; Emmanouil T. Dermitzakis; Emmanouil T. Dermitzakis; Yurii S. Aulchenko; Thomas Lengauer; Paul A. Lyons; Michel Georges; Jörn Walter
Pubblicato in: Epigenetics & Chromatin, Vol 14, Iss 1, Pp 1-17 (2021), Numero 17568935, 2021, ISSN 1756-8935
Editore: BioMed Central
DOI: 10.17863/cam.77053

Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state

Autori: Caterina Carraro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Arik Horne, Marie Oestreich, Stefanie Warnat-Herresthal, Tim Helbing, Michele De Franco, Kristian Haendler, Sach Mukherjee, Thomas Ulas, Valentina Gandin, Richard Goettlich, Anna C Aschenbrenner, Joachim L Schultze, and Barbara Gatto
Pubblicato in: eLife, Numero 2050084X, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.78012

Swarm Learning for decentralized and confidential clinical machine learning

Autori: Stefanie Warnat-Herresthal, Hartmut Schultze, Krishnaprasad Lingadahalli Shastry, Sathyanarayanan Manamohan, Saikat Mukherjee, Vishesh Garg, Ravi Sarveswara, Kristian Händler, Peter Pickkers, N. Ahmad Aziz, Sofia Ktena, Florian Tran, Michael Bitzer, Stephan Ossowski, Nicolas Casadei, Christian Herr, Daniel Petersheim, Uta Behrends, Fabian Kern, Tobias Fehlmann, Philipp Schommers, Clara Lehmann, M
Pubblicato in: Nature, Numero 594/7862, 2021, Pagina/e 265-270, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-021-03583-3

Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19

Autori: Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Matthias Becker, Kristian Händler, Joachim L. Schultze
Pubblicato in: STAR Protocols, Numero 1/3, 2020, Pagina/e 100233, ISSN 2666-1667
Editore: ScienceDirect
DOI: 10.1016/j.xpro.2020.100233

Differential associations between a priori diet quality scores and markers of cardiovascular health in women: cross-sectional analyses from TwinsUK

Autori: Olatz Mompeo, Sarah E. Berry, Tim D. Spector, Cristina Menni, Massimo Mangino, Rachel Gibson
Pubblicato in: British Journal of Nutrition, 2020, Pagina/e 1-11, ISSN 0007-1145
Editore: CABI Publishing
DOI: 10.1017/s000711452000495x

Molecular Taxonomy of Systemic Lupus Erythematosus Through Data-Driven Patient Stratification: Molecular Endotypes and Cluster-Tailored Drugs

Autori: Panagiotis Garantziotis, Dimitrios Nikolakis, Stavros Doumas, Eleni Frangou, George Sentis, Anastasia Filia, Antonis Fanouriakis, George Bertsias and Dimitrios T. Boumpas
Pubblicato in: Frontiers in Immunology, Numero 16643224, 2022, ISSN 1664-3224
Editore: Froniters Media S.A.
DOI: 10.3389/fimmu.2022.860726

The Relation between Red Meat and Whole-Grain Intake and the Colonic Mucosal Barrier: A Cross-Sectional Study

Autori: Mohamad Jawhara, Signe Bek Sørensen, Berit Lilienthal Heitmann, Þórhallur Ingi Halldórsson, Andreas Kristian Pedersen, Vibeke Andersen
Pubblicato in: Nutrients, Numero 12/6, 2020, Pagina/e 1765, ISSN 2072-6643
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu12061765

Association Between Human Gut Microbiome and N-Glycan Composition of Total Plasma Proteome

Autori: Vyacheslav A Petrov , Sodbo Zh Sharapov, Lev Shagam, Arina V Nostaeva, Marija Pezer, Dalin Li, Maja Hanić, Dermot McGovern, Edouard Louis, Souad Rahmouni, Gordan Lauc, Michel Georges, Yurii S Aulchenko
Pubblicato in: Frontiers in Mircrobiology, Numero 1664302X, 2022, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2022.811922

Complement activation induces excessive T cell cytotoxicity in severe COVID-19

Autori: Philipp Georg, Rosario Astaburuaga-García, Lorenzo Bonaguro, Sophia Brumhard, Laura Michalick, Lena, J. Lippert, Tomislav Kostevc, Christiane Gäbel, Maria Schneider, Mathias Streitz, Vadim Demichev, Ioanna Gemünd, Matthias Barone, Pinkus Tober-Lau, Elisa T. Helbig, David Hillus, Lev Petrov, Julia Stein, Hannah-Philine Dey, Daniela Paclik, Christina Iwert, Michael Mülleder, Simran, Kaur Aulakh,
Pubblicato in: Cell, Numero 00928674, 2021, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2021.12.040

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Autori: Urmo Võsa; Annique Claringbould; Annique Claringbould; Harm-Jan Westra; Marc Jan Bonder; Patrick Deelen; Biao Zeng; Holger Kirsten; Ashis Saha; Roman Kreuzhuber; Roman Kreuzhuber; Roman Kreuzhuber; Seyhan Yazar; Harm Brugge; Roy Oelen; Dylan H. de Vries; Monique G. P. van der Wijst; Silva Kasela; Natalia Pervjakova; Isabel Alves; Marie-Julie Favé; Mawusse Agbessi; Mark W. Christiansen; Rick Jans
Pubblicato in: Nature Genetics, Numero 24, 2021, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-021-00913-z

Differential Gene Expression in Circulating CD14+ Monocytes Indicates the Prognosis of Critically Ill Patients with Sepsis

Autori: Anke Liepelt; Philipp Hohlstein; Hendrik Gussen; Jia Xue; Anna C. Aschenbrenner; Anna C. Aschenbrenner; Thomas Ulas; Lukas Buendgens; Klaudia Theresa Warzecha; Matthias Bartneck; Tom Luedde; Christian Trautwein; Joachim L. Schultze; Alexander Koch; Frank Tacke; Frank Tacke
Pubblicato in: Journal of Clinical Medicine, Numero 7, 2020, Pagina/e 127, ISSN 2077-0383
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.18154/rwth-2020-04417

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Autori: Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna D. Gemünd, Nikoletta Rovina, Shobhit Agrawal, Kilian Dahm, Mart
Pubblicato in: Genome Medicine, Numero 13/1, 2021, ISSN 1756-994X
Editore: BioMed Central
DOI: 10.1186/s13073-020-00823-5

A novel unconventional T cell population enriched in Crohn's disease

Autori: Rosati, Elisa, Gabriela Rios Martini, Mikhail V. Pogorelyy, Anastasia A. Minervina, Frauke Degenhardt, Mareike Wendorff, Soner Sari, Gabriele Mayr, Antonella Fazio, Christel Marie Dowds, Charlotte Hauser, Florian Tran, Witigo von Schönfels, Julius Pochhammer, Maria A. Salnikova, Charlot Jaeckel, Johannes Boy Gigla, Sanaz Sedghpour Sabet, Matthias Hübenthal, Esther Schiminsky, Stefan Schreiber, P
Pubblicato in: Gut, 2022, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2021-325373

Towards a European health research and innovation cloud (HRIC)

Autori: F. M. Aarestrup, A. Albeyatti, W. J. Armitage, L. Augello, R. Balling, N. Benhabiles, G. Bertolini, J. G. Bjaalie,M. Black, N. Blomberg, P. Bogaert, M. Bubak, B. Claerhout, L. Clarke, B. De Meulder, G. D’Errico, A. Di Meglio, N. Forgo, C. Gans-Combe, A. E. Gray, I. Gut, A. Gyllenberg, G. Hemmrich-Stanisak, L. Hjorth, Y. Ioannidis, S. Jarmalaite, A. Kel, F. Kherif, J. O. Korbel, C. Larue, M. Lasz
Pubblicato in: Genome Medicine, Numero 1756994X, 2020, ISSN 1756-994X
Editore: BioMed Central
DOI: 10.1186/s13073-020-0713-z

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases

Autori: Konrad Aden, Ateequr Rehman, Silvio Waschina, Wei-Hung Pan, Alesia Walker, Marianna Lucio, Alejandro Mena Nunez, Richa Bharti, Johannes Zimmerman, Johannes Bethge, Berenice Schulte, Dominik Schulte, Andre Franke, Susanna Nikolaus, Johann Oltmann Schroeder, Doris Vandeputte, Jeroen Raes, Silke Szymczak, Georg H Waetzig, Rainald Zeuner, Philippe Schmitt-Kopplin, Christoph Kaleta, Stefan Schreiber, P
Pubblicato in: Gastroenterology, 2019, ISSN 0016-5085
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2019.07.025

Monocytes and Macrophages in COVID-19

Autori: Rainer Knoll, Joachim L. Schultze, Jonas Schulte-Schrepping
Pubblicato in: Frontiers in Immunology, Numero 16624548, 2021, ISSN 1662-4548
Editore: Frontiers Research Foundation
DOI: 10.3389/fimmu.2021.720109

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine

Autori: Vibeke Andersen, Uffe Holmskov, Signe Sørensen, Mohamad Jawhara, Karina Andersen, Anette Bygum, Lone Hvid, Jakob Grauslund, Jimmi Wied, Henning Glerup, Ulrich Fredberg, Jan Villadsen, Søren Kjær, Jan Fallingborg, Seyed Moghadd, Torben Knudsen, Jacob Brodersen, Jesper Frøjk, Jens Dahlerup, Ole Nielsen, Robin Christensen, Anders Bojesen, Grith Sorensen, Steffen Thiel, Nils Færgeman, Ivan Brands
Pubblicato in: Nutrients, Numero 9/5, 2017, Pagina/e 499, ISSN 2072-6643
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu9050499

Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation

Autori: Xia Shen, Lucija Klarić, Sodbo Sharapov, Massimo Mangino, Zheng Ning, Di Wu, Irena Trbojević-Akmačić, Maja Pučić-Baković, Igor Rudan, Ozren Polašek, Caroline Hayward, Timothy D. Spector, James F. Wilson, Gordan Lauc, Yurii S. Aulchenko
Pubblicato in: Nature Communications, Numero 8/1, 2017, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-017-00453-3

Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases

Autori: Susanna Nikolaus, Berenice Schulte, Natalie Al-Massad, Florian Thieme, Dominik M. Schulte, Johannes Bethge, Ateequr Rehman, Florian Tran, Konrad Aden, Robert Häsler, Natalie Moll, Gregor Schütze, Markus J. Schwarz, Georg H. Waetzig, Philip Rosenstiel, Michael Krawczak, Silke Szymczak, Stefan Schreiber
Pubblicato in: Gastroenterology, Numero 153/6, 2017, Pagina/e 1504-1516.e2, ISSN 0016-5085
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2017.08.028

Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases:protocol for a prospective cohort study of prognostic factors and personalised medicine

Autori: Christensen, Robin; Heitmann, Berit L; Andersen, Karina Winther; Nielsen, Ole Haagen; Sørensen, Signe Bek; Jawhara, Mohamad; Bygum, Anette; Hvid, Lone; Grauslund, Jakob; Wied, Jimmi; Glerup, Henning; Fredberg, Ulrich; Villadsen, Jan Alexander; Kjær, Søren Geill; Fallingborg, Jan; Moghadd, Seyed A G R; Knudsen, Torben; Brodersen, Jacob; Frøjk, Jesper; Dahlerup, Jens Frederik; Bojesen, Anders Bo
Pubblicato in: BMJ Open, Numero 1, 2018, ISSN 2044-6055
Editore: BMJ Publishing Group
DOI: 10.1136/bmjopen-2017-018166

Overview of methodologies for T-cell receptor repertoire analysis

Autori: Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke
Pubblicato in: BMC Biotechnology, Numero 17/1, 2017, ISSN 1472-6750
Editore: BioMed Central
DOI: 10.1186/s12896-017-0379-9

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

Autori: Yukihide Momozawa, Julia Dmitrieva, Emilie Théâtre, Valérie Deffontaine, Souad Rahmouni, Benoît Charloteaux, François Crins, Elisa Docampo, Mahmoud Elansary, Ann-Stephan Gori, Christelle Lecut, Rob Mariman, Myriam Mni, Cécile Oury, Ilya Altukhov, Dmitry Alexeev, Yuri Aulchenko, Leila Amininejad, Gerd Bouma, Frank Hoentjen, Mark Löwenberg, Bas Oldenburg, Marieke J. Pierik, Andrea E. vander M
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-04365-8

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

Autori: Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike Sophie David, Claus Scholz, Foo Shihui, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit,
Pubblicato in: Cell, Numero 172/3, 2018, Pagina/e 500-516.e16, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2017.11.042

Systems Medicine in Chronic Inflammatory Diseases

Autori: Joachim L. Schultze, Philip Rosenstiel
Pubblicato in: Immunity, Numero 48/4, 2018, Pagina/e 608-613, ISSN 1074-7613
Editore: Cell Press
DOI: 10.1016/j.immuni.2018.03.022

The resilience of the intestinal microbiota influences health and disease

Autori: Felix Sommer, Jacqueline Moltzau Anderson, Richa Bharti, Jeroen Raes, Philip Rosenstiel
Pubblicato in: Nature Reviews Microbiology, Numero 15/10, 2017, Pagina/e 630-638, ISSN 1740-1526
Editore: Nature Publishing Group
DOI: 10.1038/nrmicro.2017.58

Glycosylation of Immunoglobulin G Associates With Clinical Features of Inflammatory Bowel Diseases

Autori: Mirna Šimurina, Noortje de Haan, Frano Vučković, Nicholas A. Kennedy, Jerko Štambuk, David Falck, Irena Trbojević-Akmačić, Florent Clerc, Genadij Razdorov, Anna Khon, Anna Latiano, Renata D'Incà, Silvio Danese, Stephan Targan, Carol Landers, Marla Dubinsky, Dermot P.B. McGovern, Vito Annese, Manfred Wuhrer, Gordan Lauc, Harry Campbell, Vlatka Zoldoš, Iain K. Permberton, Daniel Kolarich, D
Pubblicato in: Gastroenterology, Numero 154/5, 2018, Pagina/e 1320-1333.e10, ISSN 0016-5085
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2018.01.002

Profiling and genetic control of the murine immunoglobulin G glycome

Autori: Jasminka Krištić, Olga O. Zaytseva, Ramesh Ram, Quang Nguyen, Mislav Novokmet, Frano Vučković, Marija Vilaj, Irena Trbojević-Akmačić, Marija Pezer, Kathleen M. Davern, Grant Morahan, Gordan Lauc
Pubblicato in: Nature Chemical Biology, Numero 14/5, 2018, Pagina/e 516-524, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-018-0034-3

Low galactosylation of IgG associates with higher risk for future diagnosis of rheumatoid arthritis during 10 years of follow-up

Autori: Ivan Gudelj, Perttu P. Salo, Irena Trbojević-Akmačić, Malena Albers, Dragan Primorac, Markus Perola, Gordan Lauc
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Numero 1864/6, 2018, Pagina/e 2034-2039, ISSN 0925-4439
Editore: Elsevier BV
DOI: 10.1016/j.bbadis.2018.03.018

N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells

Autori: Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Pubblicato in: Molecular & Cellular Proteomics, Numero 17/4, 2018, Pagina/e 631-642, ISSN 1535-9476
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.RA117.000129

The association between subclass-specific IgG Fc N-glycosylation profiles and hypertension in the Uygur, Kazak, Kirgiz, and Tajik populations

Autori: JN Liu, M Dolikun, J Štambuk, I Trbojević-Akmačić, J Zhang, H Wang, DQ Zheng, XY Zhang, HL Peng, ZY Zhao, D Liu, Y Sun, Q Sun, QH Li, JX Zhang, M Sun, WJ Cao, A Momčilović, G. Razdorov, LJ Wu, A Russell, YX Wang, MS Song, G Lauc, W Wang
Pubblicato in: Journal of Human Hypertension, 2018, ISSN 0950-9240
Editore: Nature Publishing Group
DOI: 10.1038/s41371-018-0071-0

Quantitative microbiome profiling links gut community variation to microbial load

Autori: Doris Vandeputte, Gunter Kathagen, Kevin D’hoe, Sara Vieira-Silva, Mireia Valles-Colomer, João Sabino, Jun Wang, Raul Y. Tito, Lindsey De Commer, Youssef Darzi, Séverine Vermeire, Gwen Falony, Jeroen Raes
Pubblicato in: Nature, Numero 551, 2017, Pagina/e 507-511, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/nature24460

Vedolizumab is associated with changes in innate rather than adaptive immunity in patients with inflammatory bowel disease

Autori: Sebastian Zeissig, Elisa Rosati, C Marie Dowds, Konrad Aden, Johannes Bethge, Berenice Schulte, Wei Hung Pan, Neha Mishra, Maaz Zuhayra, Marlies Marx, Maren Paulsen, Anne Strigli, Claudio Conrad, Dörthe Schuldt, Anupam Sinha, Henriette Ebsen, Sabin-Christin Kornell, Susanna Nikolaus, Alexander Arlt, Dieter Kabelitz, Mark Ellrichmann, Ulf Lützen, Philip C Rosenstiel, Andre Franke, Stefan Schreibe
Pubblicato in: Gut, 2018, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2018-316023

Evaluation of interleukin-6 and its soluble receptor components sIL-6R and sgp130 as markers of inflammation in inflammatory bowel diseases

Autori: Susanna Nikolaus, Georg H. Waetzig, Sven Butzin, Monika Ziolkiewicz, Natalie Al-Massad, Florian Thieme, Ulf Lövgren, Birgitte B. Rasmussen, Torsten M. Reinheimer, Dirk Seegert, Philip Rosenstiel, Silke Szymczak, Stefan Schreiber
Pubblicato in: International Journal of Colorectal Disease, Numero 33/7, 2018, Pagina/e 927-936, ISSN 0179-1958
Editore: Springer Verlag
DOI: 10.1007/s00384-018-3069-8

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome

Autori: Kate Joanne Howell, Judith Kraiczy, Komal M. Nayak, Marco Gasparetto, Alexander Ross, Claire Lee, Tim N. Mak, Bon-Kyoung Koo, Nitin Kumar, Trevor Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Pubblicato in: Gastroenterology, Numero 154/3, 2018, Pagina/e 585-598, ISSN 0016-5085
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2017.10.007

Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation

Autori: Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana T Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Marija Pezer, Gordan Lauc, Johann
Pubblicato in: Human Molecular Genetics, Numero 27/6, 2018, Pagina/e 1106-1121, ISSN 0964-6906
Editore: Oxford University Press
DOI: 10.1093/hmg/ddy006

Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases

Autori: Elisa Rosati, Mikhail V Pogorelyy, C Marie Dowds, Frederik T Moller, Signe B Sorensen, Yuri B Lebedev, Norbert Frey, Stefan Schreiber, Martina E Spehlmann, Vibeke Andersen, Ilgar Z Mamedov, Andre Franke
Pubblicato in: Journal of Crohn's and Colitis, 2019, ISSN 1873-9946
Editore: Elsevier Science
DOI: 10.1093/ecco-jcc/jjz179

aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data

Autori: Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Pubblicato in: BMC Genomics, Numero 20/1, 2019, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-019-5686-1

Biomarkers of Whole-Grain and Cereal-Fiber Intake in Human Studies: A Systematic Review of the Available Evidence and Perspectives

Autori: Mohamad Jawhara, Signe Bek Sørensen, Berit Lilienthal Heitmann, Vibeke Andersen
Pubblicato in: Nutrients, Numero 11/12, 2019, Pagina/e 2994, ISSN 2072-6643
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system

Autori: Goran Josipović, Vanja Tadić, Marija Klasić, Vladimir Zanki, Ivona Bečeheli, Felicia Chung, Akram Ghantous, Toma Keser, Josip Madunić, Maria Bošković, Gordan Lauc, Zdenko Herceg, Aleksandar Vojta, Vlatka Zoldoš
Pubblicato in: Nucleic Acids Research, Numero 47/18, 2019, Pagina/e 9637-9657, ISSN 0305-1048
Editore: Oxford University Press
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Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics

Autori: Stefanie Warnat-Herresthal, Konstantinos Perrakis, Bernd Taschler, Matthias Becker, Kevin Baßler, Marc Beyer, Patrick Günther, Jonas Schulte-Schrepping, Lea Seep, Kathrin Klee, Thomas Ulas, Torsten Haferlach, Sach Mukherjee, Joachim L. Schultze
Pubblicato in: iScience, Numero 23/1, 2020, Pagina/e 100780, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2019.100780

Update on the pathogenesis of central nervous system lupus

Autori: Dionysis Nikolopoulos, Antonis Fanouriakis, Dimitrios T. Boumpas
Pubblicato in: Current Opinion in Rheumatology, Numero 31/6, 2019, Pagina/e 669-677, ISSN 1040-8711
Editore: Lippincott Williams & Wilkins Ltd.
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Increased central adiposity is associated with pro-inflammatory immunoglobulin G N-glycans

Autori: Alyce C. Russell, Agnieszka Kepka, Irena Trbojević-Akmačić, Ivo Ugrina, Manshu Song, Jennie Hui, Michael Hunter, Simon M. Laws, Gordan Lauc, Wei Wang
Pubblicato in: Immunobiology, Numero 224/1, 2019, Pagina/e 110-115, ISSN 0171-2985
Editore: Elsevier BV
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Analysis of the B cell receptor repertoire in six immune-mediated diseases

Autori: R. J. M. Bashford-Rogers, L. Bergamaschi, E. F. McKinney, D. C. Pombal, F. Mescia, J. C. Lee, D. C. Thomas, S. M. Flint, P. Kellam, D. R. W. Jayne, P. A. Lyons, K. G. C. Smith
Pubblicato in: Nature, Numero 574/7776, 2019, Pagina/e 122-126, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-019-1595-3

ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING

Autori: Konrad Aden, Florian Tran, Go Ito, Raheleh Sheibani-Tezerji, Simone Lipinski, Jan W. Kuiper, Markus Tschurtschenthaler, Svetlana Saveljeva, Joya Bhattacharyya, Robert Häsler, Kareen Bartsch, Anne Luzius, Marlene Jentzsch, Maren Falk-Paulsen, Stephanie T. Stengel, Lina Welz, Robin Schwarzer, Björn Rabe, Winfried Barchet, Stefan Krautwald, Gunther Hartmann, Manolis Pasparakis, Richard S. Blumberg,
Pubblicato in: The Journal of Experimental Medicine, Numero 215/11, 2018, Pagina/e 2868-2886, ISSN 0022-1007
Editore: Rockefeller University Press
DOI: 10.1084/jem.20171029

Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity

Autori: Nikolaos I Panousis, George K Bertsias, Halit Ongen, Irini Gergianaki, Maria G Tektonidou, Maria Trachana, Luciana Romano-Palumbo, Deborah Bielser, Cedric Howald, Cristina Pamfil, Antonis Fanouriakis, Despoina Kosmara, Argyro Repa, Prodromos Sidiropoulos, Emmanouil T Dermitzakis, Dimitrios T Boumpas
Pubblicato in: Annals of the Rheumatic Diseases, Numero 78/8, 2019, Pagina/e 1079-1089, ISSN 0003-4967
Editore: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2018-214379

Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients

Autori: Sander Tuit, Camilla Salvagno, Theodore S. Kapellos, Cheei-Sing Hau, Lea Seep, Marie Oestreich, Kathrin Klee, Karin E. de Visser, Thomas Ulas, Joachim L. Schultze
Pubblicato in: Cell Reports, Numero 29/5, 2019, Pagina/e 1221-1235.e5, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2019.09.067

NCX1 represents an ionic Na+ sensing mechanism in macrophages

Autori: Patrick Neubert, Arne Homann, David Wendelborn, Anna-Lorena Bär, Luka Krampert, Maximilian Trum, Agnes Schröder, Stefan Ebner, Andrea Weichselbaum, Valentin Schatz, Peter Linz, Roland Veelken, Jonas Schulte-Schrepping, Anna C. Aschenbrenner, Thomas Quast, Christian Kurts, Sabrina Geisberger, Karl Kunzelmann, Karin Hammer, Katrina J. Binger, Jens Titze, Dominik N. Müller, Waldemar Kolanus, Joach
Pubblicato in: PLOS Biology, Numero 18/6, 2020, Pagina/e e3000722, ISSN 1545-7885
Editore: PLOS
DOI: 10.1371/journal.pbio.3000722

Regulatory T-cell Transcriptomic Reprogramming Characterizes Adverse Events by Checkpoint Inhibitors in Solid Tumors

Autori: Maria Grigoriou, Aggelos Banos, Aikaterini Hatzioannou, Andreas Kloetgen, Panagiotis Kouzis, Despoina Aggouraki, Roubini Zakopoulou, Giorgos Bamias, Eva Kassi, Dimitrios Mavroudis, Aristotelis Bamias, Dimitrios T. Boumpas, Aristotelis Tsirigos, Helen Gogas, Themis Alissafi, Panayotis Verginis
Pubblicato in: Cancer Immunology Research, Numero 9/7, 2021, Pagina/e 726-734, ISSN 2326-6066
Editore: American Association for Cancer Research Inc.
DOI: 10.1158/2326-6066.cir-20-0969

Defining trained immunity and its role in health and disease

Autori: Mihai G. Netea, Jorge Domínguez-Andrés, Luis B. Barreiro, Triantafyllos Chavakis, Maziar Divangahi, Elaine Fuchs, Leo A. B. Joosten, Jos W. M. van der Meer, Musa M. Mhlanga, Willem J. M. Mulder, Niels P. Riksen, Andreas Schlitzer, Joachim L. Schultze, Christine Stabell Benn, Joseph C. Sun, Ramnik J. Xavier, Eicke Latz
Pubblicato in: Nature Reviews Immunology, Numero 20/6, 2020, Pagina/e 375-388, ISSN 1474-1733
Editore: Nature Publishing Group
DOI: 10.1038/s41577-020-0285-6

Human variation in population-wide gene expression data predicts gene perturbation phenotype

Autori: Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LAB, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC.
Pubblicato in: iScience, 2022, ISSN 2589-0042
Editore: Elsevier Inc.
DOI: 10.1016/j.isci.2022.105328

Baseline IgG-Fc N-glycosylation profile is associated with long-term outcome in a cohort of early inflammatory arthritis patients

Autori: Thomas Sénard; Irini Flouri; Frano Vučković; Garyfalia Papadaki; Panagiota Goutakoli; Aggelos Banos; Maja Pučić-Baković; Marija Pezer; George Bertsias; Gordan Lauc; Prodromos Sidiropoulos
Pubblicato in: Arthritis Research & Therapy, Numero 14786362, 2022, ISSN 1478-6362
Editore: Springer
DOI: 10.1186/s13075-022-02897-5

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Autori: Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro, Elena De Domenico, Daniel Wendisch, Martin Grasshoff, Theodore S. Kapellos, Michael Beckstette, Tal Pecht, Adem Saglam, Oliver Dietrich, Henrik E. Mei, Axel R. Schulz, Claudia Conrad, Désirée Kunkel, Ehsan Vafadarnejad, Chen
Pubblicato in: Cell, Numero 182/6, 2020, Pagina/e 1419-1440.e23, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2020.08.001

Genetic and Environmental Influences of Dietary Indices in a UK Female Twin Cohort

Autori: Olatz Mompeo, Rachel Gibson, Paraskevi Christofidou, Tim D. Spector, Cristina Menni, Massimo Mangino
Pubblicato in: Twin Research and Human Genetics, Numero 23/6, 2020, Pagina/e 330-337, ISSN 1832-4274
Editore: Australian Academic Press Pty Ltd.
DOI: 10.1017/thg.2020.84

Decreased Immunoglobulin G Core Fucosylation, A Player in Antibody-dependent Cell-mediated Cytotoxicity, is Associated with Autoimmune Thyroid Diseases

Autori: Tiphaine C. Martin, Mirna Šimurina, Marta Ząbczyńska, Marina Martinic Kavur, Magdalena Rydlewska, Marija Pezer, Kamila Kozłowska, Andrea Burri, Marija Vilaj, Renata Turek-Jabrocka, Milena Krnjajić-Tadijanović, Małgorzata Trofimiuk-Müldner, Ivo Ugrina, Anna Lityńska, Alicja Hubalewska-Dydejczyk, Irena Trbojevic-Akmacic, Ee Mun Lim, John P. Walsh, Ewa Pocheć, Tim D. Spector, Scott G. Wilso
Pubblicato in: Molecular & Cellular Proteomics, Numero 19/5, 2020, Pagina/e 774-792, ISSN 1535-9476
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra119.001860

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

Autori: Joana P. Bernardes, Neha Mishra, Florian Tran, Thomas Bahmer, Lena Best, Johanna I. Blase, Dora Bordoni, Jeanette Franzenburg, Ulf Geisen, Jonathan Josephs-Spaulding, Philipp Köhler, Axel Künstner, Elisa Rosati, Anna C. Aschenbrenner, Petra Bacher, Nathan Baran, Teide Boysen, Burkhard Brandt, Niklas Bruse, Jonathan Dörr, Andreas Dräger, Gunnar Elke, David Ellinghaus, Julia Fischer, Michael For
Pubblicato in: Immunity, Numero 53/6, 2020, Pagina/e 1296-1314.e9, ISSN 1074-7613
Editore: Cell Press
DOI: 10.1016/j.immuni.2020.11.017

A guide to systems-level immunomics

Autori: Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer, Joachim L. Schultze
Pubblicato in: nature immunology, Numero 15292908, 2022, ISSN 1529-2908
Editore: Nature Publishing Group
DOI: 10.1038/s41590-022-01309-9

COVID-19 and the human innate immune system

Autori: Joachim L. Schultze, Anna C. Aschenbrenner
Pubblicato in: Cell, Numero 184/7, 2021, Pagina/e 1671-1692, ISSN 0092-8674
Editore: Cell Press
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Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Autori: 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 Rosenstiel
Pubblicato in: Genome Medicine, Numero 1756994X, 2022, ISSN 1756-994X
Editore: BioMed Central
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Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

Autori: Doris Vandeputte, Lindsey De Commer, Raul Y Tito, Gunter Kathagen, João Sabino, Séverine Vermeire, Karoline Faust, Jeroen Raes
Pubblicato in: Nature communications, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27098-7

Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese

Autori: Xiaoni Meng, Manshu Song, Marija Vilaj, Jerko Štambuk, Mamatyusupu Dolikun, Jie Zhang, Di Liu, Hao Wang, Xiaoyu Zhang, Jinxia Zhang, Weijie Cao, Ana Momčilović, Irena Trbojević-Akmačić, Xingang Li, Deqiang Zheng, Lijuan Wu, Xiuhua Guo, Youxin Wang, Gordan Lauc, Wei Wang
Pubblicato in: Journal of Personalized Medicine, Numero 11/7, 2021, Pagina/e 614, ISSN 2075-4426
Editore: MDPI
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Impact of fibre and red/processed meat intake on treatment outcomes among patients with chronic inflammatory diseases initiating biological therapy: A prospective cohort study

Autori: Silja H. Overgaard1,2,3*, Signe B. Sørensen1,4, Heidi L. Munk5, Anders B. Nexøe4,6,7, Henning Glerup8, Rikke H. Henriksen8, Tanja Guldmann8, Natalia Pedersen9, Sanaz Saboori9, Lone Hvid10, Jens F. Dahlerup11, Christian L. Hvas11, Mohamad Jawhara1,4,12, Karina W. Andersen1,12, Andreas K. Pedersen13, Ole H. Nielsen14, Fredrik Bergenheim14, Jacob B. Brodersen3,15, Berit L. Heitmann16,17, Thorhallur
Pubblicato in: Frontiers in Nutrition, Numero 2296861X, 2019, ISSN 2296-861X
Editore: Frontiers Media S.A.
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Therapeutic Interleukin-6 Trans-signaling Inhibition by Olamkicept (sgp130Fc) in Patients With Active Inflammatory Bowel Disease

Autori: Stefan Schreiber, Konrad Aden, Joana P. Bernardes, Claudio Conrad, Florian Tran, Hanna Höper, Valery Volk, Neha Mishra, Johanna Ira Blase, Susanna Nikolaus, Johannes Bethge, Tanja Kühbacher, Christoph Röcken, Minhu Chen, Ian Cottingham, Niclas Petri, Birgitte B. Rasmussen, Juliane Lokau, Lennart Lenk, Christoph Garbers, Friedrich Feuerhake, Stefan Rose-John, Georg H. Waetzig, Philip Rosenstiel
Pubblicato in: Gastroenterology, Numero 160/7, 2021, Pagina/e 2354-2366.e11, ISSN 0016-5085
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Crohn’s-associated invariant T cells (CAITs) recognise small sulfonate molecules on CD1d

Autori: Minervina, Anastasia A., Mikhail V. Pogorelyy, Steffen Paysen, Ulrich Luening, Frauke Degenhardt, Andre Franke, Paul G. Thomas, and Elisa Rosati
Pubblicato in: Gut, 2022, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2022-328684

An intrinsic role of IL-33 in Treg cell–mediated tumor immunoevasion

Autori: Aikaterini Hatzioannou, Aggelos Banos, Theodore Sakelaropoulos, Constantinos Fedonidis, Maria-Sophia Vidali, Maren Köhne, Kristian Händler, Louis Boon, Ana Henriques, Vasiliki Koliaraki, Panagiotis Georgiadis, Jerome Zoidakis, Aikaterini Termentzi, Marc Beyer, Triantafyllos Chavakis, Dimitrios Boumpas, Aristotelis Tsirigos, Panayotis Verginis
Pubblicato in: Nature Immunology, Numero 21/1, 2020, Pagina/e 75-85, ISSN 1529-2908
Editore: Nature Publishing Group
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