Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities (MedBioinformatics)

Livrables

Promotional material outlining the project's rationale and objectives.

Final report on outreach and dissemination activities

A detailed list of all dissemination activities carried out during the project, with assessment of their impact and degree of compliance with the Communication Plan.

MedBioinformatics website

Website to be updated until the end of the project.

Publications

Patología dual en Depresión: recomendaciones en el tratamiento

Auteurs: Judit Tirado Muñoz, Adriana Farré, Joan Mestre-Pintó, Nestor Szerman, Marta Torrens
Publié dans: Adicciones, Numéro 30/1, 2018, Page(s) 66, ISSN 0214-4840
Éditeur: Socidrogalcohol
DOI: 10.20882/adicciones.868

Ensembl 2017

Auteurs: Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Dani
Publié dans: Nucleic Acids Research, Numéro 45/D1, 2017, Page(s) D635-D642, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkw1104

Binge ethanol drinking during adolescence modifies cocaine responses in mice

Auteurs: Anna Esteve-Arenys, Irene Gracia-Rubio, Lídia Cantacorps, Oscar J Pozo, Josep Marcos, Marta Rodríguez-Árias, José Miñarro, Olga Valverde
Publié dans: Journal of Psychopharmacology, Numéro 31/1, 2016, Page(s) 86-95, ISSN 0269-8811
Éditeur: SAGE Publications
DOI: 10.1177/0269881116681457

Exposure of adolescent mice to 3,4-methylenedioxypyrovalerone increases the psychostimulant, rewarding and reinforcing effects of cocaine in adulthood

Auteurs: R López-Arnau, M A Luján, L Duart-Castells, D Pubill, J Camarasa, O Valverde, E Escubedo
Publié dans: British Journal of Pharmacology, Numéro 174/10, 2017, Page(s) 1161-1173, ISSN 0007-1188
Éditeur: Wiley-Blackwell
DOI: 10.1111/bph.13771

Maternal Separation Impairs Cocaine-Induced Behavioural Sensitization in Adolescent Mice

Auteurs: Irene Gracia-Rubio, Elena Martinez-Laorden, Maria Moscoso-Castro, M. Victoria Milanés, M. Luisa Laorden, Olga Valverde
Publié dans: PLOS ONE, Numéro 11/12, 2016, Page(s) e0167483, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0167483

SynergyFinder: a web application for analyzing drug combination dose–response matrix data

Auteurs: Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
Publié dans: Bioinformatics, Numéro 33/15, 2017, Page(s) 2413-2415, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx162

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

Auteurs: K Karube, A Enjuanes, I Dlouhy, P Jares, D Martin-Garcia, F Nadeu, G R Ordóñez, J Rovira, G Clot, C Royo, A Navarro, B Gonzalez-Farre, A Vaghefi, G Castellano, C Rubio-Perez, D Tamborero, J Briones, A Salar, J M Sancho, S Mercadal, E Gonzalez-Barca, L Escoda, H Miyoshi, K Ohshima, K Miyawaki, K Kato, K Akashi, A Mozos, L Colomo, M Alcoceba, A Valera, A Carrió, D Costa, N Lopez-Bigas, R Schmitz,
Publié dans: Leukemia, Numéro 32/3, 2017, Page(s) 675-684, ISSN 0887-6924
Éditeur: Nature Publishing Group
DOI: 10.1038/leu.2017.251

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

Auteurs: E I Andersson, S Pützer, B Yadav, O Dufva, S Khan, L He, L Sellner, A Schrader, G Crispatzu, M Oleś, H Zhang, S Adnan-Awad, S Lagström, D Bellanger, J P Mpindi, S Eldfors, T Pemovska, P Pietarinen, A Lauhio, K Tomska, C Cuesta-Mateos, E Faber, S Koschmieder, T H Brümmendorf, S Kytölä, E-R Savolainen, T Siitonen, P Ellonen, O Kallioniemi, K Wennerberg, W Ding, M-H Stern, W Huber, S Anders, J
Publié dans: Leukemia, Numéro 32/3, 2017, Page(s) 774-787, ISSN 0887-6924
Éditeur: Nature Publishing Group
DOI: 10.1038/leu.2017.252

Cognitive impairments associated with alterations in synaptic proteins induced by the genetic loss of adenosine A 2A receptors in mice

Auteurs: Maria Moscoso-Castro, Marc López-Cano, Irene Gracia-Rubio, Francisco Ciruela, Olga Valverde
Publié dans: Neuropharmacology, Numéro 126, 2017, Page(s) 48-57, ISSN 0028-3908
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.neuropharm.2017.08.027

Maternal alcohol binge drinking induces persistent neuroinflammation associated with myelin damage and behavioural dysfunctions in offspring mice

Auteurs: Lídia Cantacorps, Silvia Alfonso-Loeches, Maria Moscoso-Castro, Javier Cuitavi, Irene Gracia-Rubio, Raúl López-Arnau, Elena Escubedo, Consuelo Guerri, Olga Valverde
Publié dans: Neuropharmacology, Numéro 123, 2017, Page(s) 368-384, ISSN 0028-3908
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.neuropharm.2017.05.034

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Auteurs: David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P. Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Genome Medicine, Numéro 10/1, 2018, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-018-0531-8

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Auteurs: Jing Tang, Zia-ur-Rehman Tanoli, Balaguru Ravikumar, Zaid Alam, Anni Rebane, Markus Vähä-Koskela, Gopal Peddinti, Arjan J. van Adrichem, Janica Wakkinen, Alok Jaiswal, Ella Karjalainen, Prson Gautam, Liye He, Elina Parri, Suleiman Khan, Abhishekh Gupta, Mehreen Ali, Laxman Yetukuri, Anna-Lena Gustavsson, Brinton Seashore-Ludlow, Anne Hersey, Andrew R. Leach, John P. Overington, Gretchen Repasky,
Publié dans: Cell Chemical Biology, Numéro 25/2, 2018, Page(s) 224-229.e2, ISSN 2451-9456
Éditeur: Elsevier
DOI: 10.1016/j.chembiol.2017.11.009

comoRbidity: an R package for the systematic analysis of disease comorbidities

Auteurs: Alba Gutiérrez-Sacristán, Àlex Bravo, Alexia Giannoula, Miguel A Mayer, Ferran Sanz, Laura I Furlong
Publié dans: Bioinformatics, 2018, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty315

Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients

Auteurs: Liye He, Jing Tang, Emma I. Andersson, Sanna Timonen, Steffen Koschmieder, Krister Wennerberg, Satu Mustjoki, Tero Aittokallio
Publié dans: Cancer Research, Numéro 78/9, 2018, Page(s) 2407-2418, ISSN 0008-5472
Éditeur: American Association for Cancer Research
DOI: 10.1158/0008-5472.CAN-17-3644

Identifying temporal patterns in patient disease trajectories using dynamic time warping: A population-based study

Auteurs: Alexia Giannoula, Alba Gutierrez-Sacristán, Álex Bravo, Ferran Sanz, Laura I. Furlong
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-22578-1

Ensembl 2018

Auteurs: Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R Laird, Ilias Lavidas, Zhicheng Liu, Jane E Loveland, Thomas Maurel, Willia
Publié dans: Nucleic Acids Research, Numéro 46/D1, 2017, Page(s) D754-D761, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx1098

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

Auteurs: J. Pinero, N. Queralt-Rosinach, A. Bravo, J. Deu-Pons, A. Bauer-Mehren, M. Baron, F. Sanz, L. I. Furlong
Publié dans: Database, Numéro 2015/0, 2015, Page(s) bav028-bav028, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/bav028

A systems approach identifies time-dependent associations of multimorbidities with pancreatic cancer risk

Auteurs: P. Gomez-Rubio, V. Rosato, M. Márquez, C. Bosetti, E. Molina-Montes, M. Rava, J. Piñero, C. W. Michalski, A. Farré, X. Molero, M. Löhr, L. Ilzarbe, J. Perea, W. Greenhalf, M. O’Rorke, A. Tardón, T. Gress, V. M. Barberá, T. Crnogorac-Jurcevic, L. Muñoz-Bellvís, E. Domínguez-Muñoz, A. Gutiérrez-Sacristán, J. Balsells, E. Costello, C. Guillén-Ponce, J. Huang, M. Iglesias, J. Kleeff, B.
Publié dans: Annals of Oncology, Numéro 28/7, 2017, Page(s) 1618-1624, ISSN 0923-7534
Éditeur: Oxford University Press
DOI: 10.1093/annonc/mdx167

Genetic and functional characterization of disease associations explains comorbidity

Auteurs: Carlota Rubio-Perez, Emre Guney, Daniel Aguilar, Janet Piñero, Javier Garcia-Garcia, Barbara Iadarola, Ferran Sanz, Narcís Fernandez-Fuentes, Laura I. Furlong, Baldo Oliva
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-04939-4

Dual Depression

Auteurs: Adriana Farré, Judit Tirado-Muñoz, Marta Torrens
Publié dans: Addictive Disorders & Their Treatment, Numéro 16/4, 2017, Page(s) 180-186, ISSN 1531-5754
Éditeur: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/ADT.0000000000000118

Maternal separation increases alcohol-drinking behaviour and reduces endocannabinoid levels in the mouse striatum and prefrontal cortex

Auteurs: Marta Portero-Tresserra, Irene Gracia-Rubio, Lídia Cantacorps, Oscar J. Pozo, Alejandro Gómez-Gómez, Antoni Pastor, Raúl López-Arnau, Rafael de la Torre, Olga Valverde
Publié dans: European Neuropsychopharmacology, Numéro 28/4, 2018, Page(s) 499-512, ISSN 0924-977X
Éditeur: Elsevier BV
DOI: 10.1016/j.euroneuro.2018.02.003

Altered brain functional connectivity and behaviour in a mouse model of maternal alcohol binge-drinking

Auteurs: Lídia Cantacorps, Héctor González-Pardo, Jorge L. Arias, Olga Valverde, Nélida M. Conejo
Publié dans: Progress in Neuro-Psychopharmacology and Biological Psychiatry, Numéro 84, 2018, Page(s) 237-249, ISSN 0278-5846
Éditeur: Elsevier BV
DOI: 10.1016/j.pnpbp.2018.03.006

Psychiatric comorbidity and intimate partner violence among women who inject drugs in Europe: a cross-sectional study

Auteurs: Judit Tirado-Muñoz, Gail Gilchrist, Gabriele Fischer, Avril Taylor, Jacek Moskalewicz, Cinzia Giammarchi, Birgit Köchl, Alison Munro, Katarzyna Dąbrowska, April Shaw, Lucia Di Furia, Isabella Leeb, Caroline Hopf, Marta Torrens
Publié dans: Archives of Women's Mental Health, Numéro 21/3, 2018, Page(s) 259-269, ISSN 1434-1816
Éditeur: Springer Verlag
DOI: 10.1007/s00737-017-0800-3

Replicability and Prediction: Lessons and Challenges from GWAS

Auteurs: Urko M. Marigorta, Juan Antonio Rodríguez, Greg Gibson, Arcadi Navarro
Publié dans: Trends in Genetics, Numéro 34/7, 2018, Page(s) 504-517, ISSN 0168-9525
Éditeur: Elsevier BV
DOI: 10.1016/j.tig.2018.03.005

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014

Auteurs: Anders Boeck Jensen, Teresa Adeltoft Ajslev, Søren Brunak, Thorkild I A Sørensen
Publié dans: BMJ Open, Numéro 5/12, 2015, Page(s) e008702, ISSN 2044-6055
Éditeur: BMJ Publishing Group
DOI: 10.1136/bmjopen-2015-008702

Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model

Auteurs: Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang
Publié dans: Computational and Structural Biotechnology Journal, Numéro 13, 2015, Page(s) 504-513, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2015.09.001

How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease

Auteurs: S. G. Ellesoe, A. B. Jensen, L. H. A ngquist, V. E. Hjortdal, L. A. Larsen, S. Brunak
Publié dans: World Journal for Pediatric and Congenital Heart Surgery, Numéro 7/2, 2016, Page(s) 169-177, ISSN 2150-1351
Éditeur: Sage Periodicals Press
DOI: 10.1177/2150135115615786

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

Auteurs: David Ellinghaus, Luke Jostins, Sarah L Spain, Adrian Cortes, Jörn Bethune, Buhm Han, Yu Rang Park, Soumya Raychaudhuri, Jennie G Pouget, Matthias Hübenthal, Trine Folseraas, Yunpeng Wang, Tonu Esko, Andres Metspalu, Harm-Jan Westra, Lude Franke, Tune H Pers, Rinse K Weersma, Valerie Collij, Mauro D'Amato, Jonas Halfvarson, Anders Boeck Jensen, Wolfgang Lieb, Franziska Degenhardt, Andreas J Fors
Publié dans: Nature Genetics, Numéro 48/5, 2016, Page(s) 510-518, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/ng.3528

Methods for High-Throughput Drug Combination Screening and Synergy Scoring

Auteurs: Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, Jing Tang
Publié dans: bioRxiv, 2016, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1101/051698

Improving the Sequence Ontology terminology for genomic variant annotation

Auteurs: Fiona Cunningham, Barry Moore, Nicole Ruiz-Schultz, Graham RS Ritchie, Karen Eilbeck
Publié dans: Journal of Biomedical Semantics, Numéro 6/1, 2015, ISSN 2041-1480
Éditeur: BioMed Central
DOI: 10.1186/s13326-015-0030-4

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Auteurs: Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Ferran Sanz, Laura I. Furlong
Publié dans: Bioinformatics, Numéro 32/14, 2016, Page(s) 2236-2238, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btw214

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Auteurs: Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
Publié dans: Database, Numéro 2016, 2016, Page(s) baw051, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baw051

Ensembl 2016

Auteurs: Andrew Yates, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas Maurel, William McLaren, Daniel N. Murphy, Rishi Nag,
Publié dans: Nucleic Acids Research, Numéro 44/D1, 2016, Page(s) D710-D716, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkv1157

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns

Auteurs: D. Digles, B. Zdrazil, J.-M. Neefs, H. Van Vlijmen, C. Herhaus, A. Caracoti, J. Brea, B. Roibás, M. I. Loza, N. Queralt-Rosinach, L. I. Furlong, A. Gaulton, L. Bartek, S. Senger, C. Chichester, O. Engkvist, C. T. Evelo, N. I. Franklin, D. Marren, G. F. Ecker, E. Jacoby
Publié dans: Med. Chem. Commun., Numéro 7/6, 2016, Page(s) 1237-1244, ISSN 2040-2503
Éditeur: Royal Society of Chemistry
DOI: 10.1039/C6MD00065G

The Ensembl Variant Effect Predictor

Auteurs: Hunt, Sarah E; Cunningham, Fiona; Riat, Harpreet Singh; Gil, Laurent; Flicek, Paul; McLaren, William; Thormann, Anja; Ritchie, Graham R. S.
Publié dans: Genome Biology 17(1) 122 (2016), Numéro 1, 2016, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-016-0974-4

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

Auteurs: Janet Piñero, Ariel Berenstein, Abel Gonzalez-Perez, Ariel Chernomoretz, Laura I. Furlong
Publié dans: Scientific Reports, Numéro 6, 2016, Page(s) 24570, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep24570

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

Auteurs: Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong
Publié dans: Database, Numéro 2016, 2016, Page(s) baw094, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baw094

Making sense of big data in health research: Towards an EU action plan

Auteurs: Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek, Norbert Graf, Vera Grimm, Henk-Jan Guchelaar, Yi-Ke Guo, Ivo Glynne Gut, Allan Hanbury, Shahid Hanif, Ralf-Dieter Hilgers, Ángel Ho
Publié dans: Genome Medicine, Numéro 8/1, 2016, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-016-0323-y

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

Auteurs: Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cat
Publié dans: Database, Numéro 2016, 2016, Page(s) baw121, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baw121

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Auteurs: Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong
Publié dans: Nucleic Acids Research, 2016, Page(s) gkw943, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkw943

General guidelines for biomedical software development

Auteurs: Silva LB, Jimenez RC, Blomberg N and Luis Oliveira J.
Publié dans: F1000Research, Numéro 6:273, 2017, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.10750.1

Using Electronic Health Records to Assess Depression and Cancer Comorbidities

Auteurs: Miguel A. Mayer, Alba Gutierrez-Sacristan, Angela Leis, Santiago De La Peña, Ferran Sanz, Laura I. Furlong
Publié dans: Stud Health Technol Inform., 2017, Page(s) 236-240
Éditeur: IOS Press
DOI: 10.3233/978-1-61499-753-5-236

Text mining and expert curation to develop a database on psychiatric diseases and their genes

Auteurs: Alba Gutiérrez Sacristán, Álex Bravo, Marta Portero, Olga Valverde, Antonio Armario, M.C. Blanco-Gandía, Adriana Farré, Lierni Fernández-Ibarrondo, Francina Fonseca, Jesús Giraldo, Angela Leis, Anna Mané, M.A. Mayer, Sandra Montagud-Romero, Roser Nadal, Jordi Ortiz, Francisco Javier Pavon, Ezequiel Perez, Marta Rodríguez-Arias, Antonia Serrano, Marta Torrens, Vincent Warnault, Ferran Sanz
Publié dans: Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Numéro Vol-1650, 2016, Page(s) 48-55, ISSN 1613-0073
Éditeur: CEUR Workshop Proceedings

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