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2020 – today
- 2024
[c53]Luc Mottin
, Nona Naderi, Anaïs Mottaz, Pierre-André Michel, Lennart F. Johansson, Morris A. Swertz, Andrew Stubbs, Emilie Pasche, Julien Gobeill, Patrick Ruch:
Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. MIE 2024: 1684-1688- 2023
- [j21]Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch:
Assessing the use of supplementary materials to improve genomic variant discovery. Database J. Biol. Databases Curation 2023 (2023) - [j20]Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch:
COVoc and COVTriage: novel resources to support literature triage. Bioinform. 39(1) (2023) - [j19]Luc Mottin, Jean-Philippe Goldman, Christoph Jäggli, Rita Achermann, Julien Gobeill, Julien Knafou, Julien Ehrsam, Alexandre Wicky, Camille L. Gerard, Tanja Schwenk, Mélinda Charrier, Petros Tsantoulis, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch:
Multilingual RECIST classification of radiology reports using supervised learning. Frontiers Digit. Health 5 (2023) - 2022
- [c52]Luc Mottin, Jean-Philippe Goldman, Christoph Jäggli, Rita Achermann, Julien Gobeill, Julien Knafou, Julien Ehrsam, Alexandre Wicky, Camille L. Gerard, Tanja Schwenk, Mélinda Charrier, Petros Tsantoulis, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch:
Classification of oncology treatment responses from radiology reports with supervised machine learning. AMIA 2022 - [c51]Jean-Philippe Goldman, Luc Mottin, Jamil Zaghir, Daniel Keszthelyi, Belinda Lokaj, Hugues Turbé, Julien Gobeill, Patrick Ruch, Julien Ehrsam, Christian Lovis:
Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. MIE 2022: 849-853 - 2021
- [c50]Déborah Caucheteur, Emilie Pasche, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Clinical Trials 2021. TREC 2021 - 2020
- [j18]Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N. Arighi, Patrick Ruch:
UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database J. Biol. Databases Curation 2020 (2020) - [j17]András Hatos, Borbála Hajdu-Soltész, Alexander Miguel Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykaç Fas, Claudio Bassot, Guillermo I. Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucía B. Chemes, Norman E. Davey, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan:
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48(Database-Issue): D269-D276 (2020) - [j16]Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch:
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. 48(Webserver-Issue): W12-W16 (2020) - [c49]Julien Gobeill, Patrick Ruch, Rodolphe Meyer:
Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? MIE 2020: 312-316 - [c48]Déborah Caucheteur, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Daniel J. Stekhoven, Valérie Barbié, Patrick Ruch:
Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. MIE 2020: 884-888 - [c47]Emilie Pasche, Déborah Caucheteur, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Precision Medicine 2020. TREC 2020
2010 – 2019
- 2019
- [c46]Julien Gobeill, Emilie Pasche, Patrick Ruch:
Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. CICLing (1) 2019: 233-246 - [c45]Nona Naderi, Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. CLEF (Working Notes) 2019 - [c44]Déborah Caucheteur, Emilie Pasche, Julien Gobeill, Anaïs Mottaz, Luc Mottin, Patrick Ruch:
Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. TREC 2019 - 2018
- [j15]Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch:
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation 2018: bay104 (2018) - [j14]Aurore Britan, Isabelle Cusin, Valérie Hinard, Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Daniel Dinis Teixeira, Pierre-André Michel, Patrick Ruch, Pascale Gaudet:
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database J. Biol. Databases Curation 2018: bay129 (2018) - [c43]Julien Gobeill, Patrick Ruch:
Instance-based Learning for ICD10 Categorization. CLEF (Working Notes) 2018 - 2017
- [j13]Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch:
Triage by ranking to support the curation of protein interactions. Database J. Biol. Databases Curation 2017: bax040 (2017) - [j12]Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch:
Improving average ranking precision in user searches for biomedical research datasets. Database J. Biol. Databases Curation 2017: bax083 (2017) - [c42]Emilie Pasche, Julien Gobeill, Luc Mottin, Anaïs Mottaz, Douglas Teodoro, Paul Van Rijen, Patrick Ruch:
Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC 2017 - [i2]Arnaud Gaudinat, Jonas Beausire, Megan Fuss, Elisa Banfi, Julien Gobeill, Patrick Ruch:
Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. CoRR abs/1708.08669 (2017) - [i1]Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch:
Improving average ranking precision in user searches for biomedical research datasets. CoRR abs/1709.03061 (2017) - 2016
- [j11]Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch:
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. Database J. Biol. Databases Curation 2016 (2016) - [c41]Luc Mottin, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Arnaud Gaudinat, Patrick Ruch:
BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. CLEF (Working Notes) 2016: 94-102 - 2015
- [j10]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch:
Deep Question Answering for protein annotation. Database J. Biol. Databases Curation 2015 (2015) - [c40]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Instance-Based Learning for Tweet Monitoring and Categorization. CLEF 2015: 235-240 - [c39]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. TREC 2015 - 2014
- [j9]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database J. Biol. Databases Curation 2014 (2014) - [j8]Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu:
Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation 2014 (2014) - [j7]Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch:
Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. 15(S-1): S15 (2014) - [c38]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. CLEF (Working Notes) 2014: 1491-1499 - [c37]Dina Vishnyakova, Julien Gobeill, Fatma Oezdemir-Zaech, Olivier Kreim, Thérèse Vachon, Thierry Cladé, Xavier Haenning, Dmitri Mikhailov, Patrick Ruch:
Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. MIE 2014: 995-999 - [c36]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Patrick Ruch:
Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. TREC 2014 - 2013
- [j6]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database J. Biol. Databases Curation 2013 (2013) - [j5]Anne-Lise Veuthey, Alan J. Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios:
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinform. 14: 104 (2013) - [c35]Dina Vishnyakova, Julien Gobeill, Patrick Ruch:
Using a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. CLEF (Working Notes) 2013 - [c34]Emilie Pasche, Julien Gobeill, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. MedInfo 2013: 1068 - [c33]Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodríguez, Norbert Fuhr, Adam Funk, Alba Garcia Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gomez, Robert Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth J. F. Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Iván Martínez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, João R. M. Palotti, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecher, Angus Roberts, Patrick Ruch, Alexander Sachs, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel Angel Tinte, Zdenka Uresová, Alejandro Vargas, Dina Vishnyakova:
Khresmoi - Multilingual Semantic Search of Medical Text and Images. MedInfo 2013: 1266 - 2012
- [c32]Julien Gobeill, Patrick Ruch:
BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. CLEF (Online Working Notes/Labs/Workshop) 2012 - [c31]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
A User-Friendly Tool for Medical-Related Patent Retrieval. EFMI-STC 2012: 121-125 - [c30]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
An advanced search engine for patent analytics in medicinal chemistry. MIE 2012: 204-209 - [c29]Dina Vishnyakova, Emilie Pasche, Julien Gobeill, Arnaud Gaudinat, Christian Lovis, Patrick Ruch:
Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. MIE 2012: 210-214 - 2011
- [c28]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Dina Vishnyakova, Arnaud Gaudinat, Patrick Ruch, Christian Lovis:
Using Multimodal Mining to Drive Clinical Guidelines Development. MIE 2011: 477-481 - [c27]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Chemical IR Track 2011. TREC 2011 - [c26]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Medical Records Track 2011. TREC 2011 - 2010
- [c25]Douglas Teodoro, Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. CLEF (Notebook Papers/LABs/Workshops) 2010 - [c24]Douglas Teodoro, Emilie Pasche, Dina Vishnyakova, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. NTCIR 2010: 309-317 - [c23]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM site Report for TREC Chemistry 2010: Impact of Citations Feeback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. TREC 2010
2000 – 2009
- 2009
- [j4]Susanne M. Humphrey, Aurélie Névéol, Allen C. Browne, Julien Gobeill, Patrick Ruch, Stéfan Jacques Darmoni:
Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. J. Assoc. Inf. Sci. Technol. 60(12): 2530-2539 (2009) - [c22]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
QA-driven Guidelines Generation for Bacteriotherapy. AMIA 2009 - [c21]Julien Gobeill, Emilie Pasche, Douglas Teodoro, Patrick Ruch:
Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. CLEF (1) 2009: 444-451 - [c20]Julien Gobeill, Douglas Theodoro, Emilie Pasche, Patrick Ruch:
Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. CLEF (Working Notes) 2009 - [c19]Julien Gobeill, Douglas Theodoro, Patrick Ruch:
Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. CLEF (Working Notes) 2009 - [c18]Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis:
Biomedical Data Management: A Proposal Framework. MIE 2009: 175-179 - [c17]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic Medical Knowledge Acquisition Using Question-Answering. MIE 2009: 569-573 - [c16]Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
Report on the TREC 2009 Experiments: Chemical IR Track. TREC 2009 - 2008
- [j3]Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch:
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinform. 9(S-3) (2008) - [j2]Patrick Ruch, Julien Gobeill, Christian Lovis, Antoine Geissbühler:
Automatic medical encoding with SNOMED categories. BMC Medical Informatics Decis. Mak. 8(S-1): S6 (2008) - [c15]Patrick Ruch, Julien Gobeill, Imad Tbahriti, Antoine Geissbühler:
From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. AMIA 2008 - [c14]Julien Gobeill, Patrick Ruch:
First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. CLEF (Working Notes) 2008 - [c13]Julien Gobeill, Patrick Ruch, Xin Zhou:
Text-only Cross-language Image Search at Medical ImageCLEF 2008. CLEF (Working Notes) 2008 - [c12]Xin Zhou, Julien Gobeill, Henning Müller:
The MedGIFT Group at ImageCLEF 2008. CLEF 2008: 712-718 - [c11]Julien Gobeill, Patrick Ruch, Xin Zhou:
Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. CLEF 2008: 736-743 - [c10]Xin Zhou, Julien Gobeill, Henning Müller:
MedGIFT at ImageCLEF 2008. CLEF (Working Notes) 2008 - 2007
- [j1]Patrick Ruch, Célia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey:
Using argumentation to extract key sentences from biomedical abstracts. Int. J. Medical Informatics 76(2-3): 195-200 (2007) - [c9]Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller:
University and Hospitals of Geneva Participating at ImageCLEF 2007. CLEF 2007: 649-656 - [c8]Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller:
University and Hospitals of Geneva at ImageCLEF 2007. CLEF (Working Notes) 2007 - [c7]Imad Tbahriti, Anne-Lise Veuthey, Patrick Ruch, Julien Gobeill:
Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. CORIA 2007: 319-334 - [c6]Patrick Ruch, Antoine Geissbühler, Julien Gobeill, Frédéric Lisacek, Imad Tbahriti, Anne-Lise Veuthey, Alan R. Aronson:
Using Discourse Analysis to Improve Text Categorization in MEDLINE. MedInfo 2007: 710-715 - [c5]Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Patrick Ruch:
Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. TREC 2007 - 2006
- [c4]Patrick Ruch, Imad Tbahriti, Julien Gobeill, Alan R. Aronson:
Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. ACL 2006 - [c3]Julien Gobeill, Henning Müller, Patrick Ruch:
Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. CLEF 2006: 706-710 - [c2]Julien Gobeill, Henning Müller, Patrick Ruch:
Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. CLEF (Working Notes) 2006 - [c1]Patrick Ruch, Frédéric Ehrler, Julien Gobeill, Imad Tbahriti, Antonio Jimeno-Yepes:
Report on the TREC 2006 Experiment: Genomics Track. TREC 2006
Coauthor Index
[c53] [j21] [j20] [j19] [c52] [c51] [c50] [j18] [j17] [j16] [c49] [c48] [c47] [c46] [c45] [c44] [j15] [j14] [c43] [j13] [j12] [c42] [i2] [i1] [j11] [c41] [j10] [c40] [c39] [j9] [j8] [j7] [c38] [c37] [c36] [j6] [j5] [c35] [c34] [c33] [c32] [c31] [c30] [c29] [c28] [c27] [c26] [c25] [c24] [c23] [j4] [c22] [c21] [c20] [c19] [c18] [c17] [c16] [j3] [j2] [c15] [c14] [c13] [c11] [j1] [c9] [c8] [c7] [c6] [c5] [c4] [c3] [c2] [c1]
Douglas Teodoro
aka: Douglas Theodoro
aka: Douglas Theodoro
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