Publications Authored by Pelin Yilmaz

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:

Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A M Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2018 Jul;36(7):660

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July 2018

The importance of designating type material for uncultured taxa.

Authors:

Maria Chuvochina Christian Rinke Donovan H Parks Michael S Rappé Gene W Tyson Pelin Yilmaz William B Whitman Philip Hugenholtz

Syst Appl Microbiol 2018 Jul 18. Epub 2018 Jul 18.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia. Electronic address:

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July 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:

Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A Murat Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2018 Feb;36(2):196

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February 2018

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences.

Authors:

Pablo Yarza Pelin Yilmaz Katrin Panzer Frank Oliver Glöckner Marlis Reich

Mar Genomics 2017 Dec 1;36:33-39. Epub 2017 Jun 1.

University of Bremen, Molecular Ecology, BreMarE, Leobener Str. 5, 28359 Bremen, Germany. Electronic address:

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December 2017

25 years of serving the community with ribosomal RNA gene reference databases and tools.

Authors:

Frank Oliver Glöckner Pelin Yilmaz Christian Quast Jan Gerken Alan Beccati Andreea Ciuprina Gerrit Bruns Pablo Yarza Jörg Peplies Ralf Westram Wolfgang Ludwig

J Biotechnol 2017 Nov 23;261:169-176. Epub 2017 Jun 23.

Department for Microbiology, Technical University Munich, D-85354 Freising, Germany.

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November 2017

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer .

Authors:

Jessika Füssel Sebastian Lücker Pelin Yilmaz Boris Nowka Maartje A H J van Kessel Patric Bourceau Philipp F Hach Sten Littmann Jasmine Berg Eva Spieck Holger Daims Marcel M M Kuypers Phyllis Lam

Sci Adv 2017 Nov 1;3(11):e1700807. Epub 2017 Nov 1.

Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany.

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November 2017

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Authors:

Alan Beccati Jan Gerken Christian Quast Pelin Yilmaz Frank Oliver Glöckner

BMC Bioinformatics 2017 Sep 30;18(1):433. Epub 2017 Sep 30.

Department of Life Sciences & Chemistry, Jacobs University gGmbH, Bremen, Germany.

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September 2017

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:

Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A M Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2017 Aug;35(8):725-731

Department of Energy Joint Genome Institute, Walnut Creek, California, USA.

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August 2017

UniEuk: Time to Speak a Common Language in Protistology!

J Eukaryot Microbiol 2017 05 21;64(3):407-411. Epub 2017 Apr 21.

Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France.

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May 2017

Plant specimen contextual data consensus.

Authors:

Petra Ten Hoopen Ramona L Walls Ethalinda Ks Cannon Guy Cochrane James Cole Anjanette Johnston Ilene Karsch-Mizrachi Pelin Yilmaz

Gigascience 2016 12;5(1):1-4

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsius str. 1, Bremen 28359, Germany.

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December 2016

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

Authors:

Alex R Hardisty Finn Bacall Niall Beard Maria-Paula Balcázar-Vargas Bachir Balech Zoltán Barcza Sarah J Bourlat Renato De Giovanni Yde de Jong Francesca De Leo Laura Dobor Giacinto Donvito Donal Fellows Antonio Fernandez Guerra Nuno Ferreira Yuliya Fetyukova Bruno Fosso Jonathan Giddy Carole Goble Anton Güntsch Robert Haines Vera Hernández Ernst Hannes Hettling Dóra Hidy Ferenc Horváth Dóra Ittzés Péter Ittzés Andrew Jones Renzo Kottmann Robert Kulawik Sonja Leidenberger Päivi Lyytikäinen-Saarenmaa Cherian Mathew Norman Morrison Aleksandra Nenadic Abraham Nieva de la Hidalga Matthias Obst Gerard Oostermeijer Elisabeth Paymal Graziano Pesole Salvatore Pinto Axel Poigné Francisco Quevedo Fernandez Monica Santamaria Hannu Saarenmaa Gergely Sipos Karl-Heinz Sylla Marko Tähtinen Saverio Vicario Rutger Aldo Vos Alan R Williams Pelin Yilmaz

BMC Ecol 2016 10 20;16(1):49. Epub 2016 Oct 20.

Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.

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October 2016

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources.

Authors:

Nicolas Tsesmetzis Pelin Yilmaz Peter C Marks Nikos C Kyrpides Ian M Head Bart P Lomans

Stand Genomic Sci 2016 12;11:78. Epub 2016 Oct 12.

Shell Global Solutions International B.V., Rijswijk, Netherlands.

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October 2016

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle.

Authors:

Clara Martínez-Pérez Wiebke Mohr Carolin R Löscher Julien Dekaezemacker Sten Littmann Pelin Yilmaz Nadine Lehnen Bernhard M Fuchs Gaute Lavik Ruth A Schmitz Julie LaRoche Marcel M M Kuypers

Nat Microbiol 2016 Sep 12;1(11):16163. Epub 2016 Sep 12.

Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.

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September 2016

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Authors:

Alexey M Kozlov Jiajie Zhang Pelin Yilmaz Frank Oliver Glöckner Alexandros Stamatakis

Nucleic Acids Res 2016 06 10;44(11):5022-33. Epub 2016 May 10.

The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany.

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June 2016

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Authors:

Katrin Panzer Pelin Yilmaz Michael Weiß Lothar Reich Michael Richter Jutta Wiese Rolf Schmaljohann Antje Labes Johannes F Imhoff Frank Oliver Glöckner Marlis Reich

PLoS One 2015 30;10(7):e0134377. Epub 2015 Jul 30.

University of Bremen, Molecular Ecology, FB2, Leobener Str. 2, 28359, Bremen, Germany.

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May 2016

Expanding the World of Marine Bacterial and Archaeal Clades.

Authors:

Pelin Yilmaz Pablo Yarza Josephine Z Rapp Frank O Glöckner

Front Microbiol 2015 8;6:1524. Epub 2016 Jan 8.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Life Sciences and Chemistry, Jacobs UniversityBremen, Germany.

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January 2016

The magnitude of gonadotoxicity of chemotherapy drugs on ovarian follicles and granulosa cells varies depending upon the category of the drugs and the type of granulosa cells.

Authors:

Aytac Yuksel Gamze Bildik Filiz Senbabaoglu Nazli Akin Macit Arvas Fehmi Unal Yagmur Kilic Isil Karanfil Baldan Eryılmaz Pelin Yilmaz Can Ozkanbaş Cagatay Taskiran Senai Aksoy Yılmaz Guzel Basak Balaban Umit Ince Akira Iwase Bulent Urman Ozgur Oktem

Hum Reprod 2015 Dec 13;30(12):2926-35. Epub 2015 Oct 13.

Department of Obstetrics and Gynecology, Koc University School of Medicine, Istanbul, Turkey American Hospital Women's Health Center, Comprehensive Cancer Care and Fertility Preservation Programs, Assisted Reproduction Unit, Istanbul, Turkey

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December 2015

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs.

Authors:

Judith M Klatt Sebastian Haas Pelin Yilmaz Dirk de Beer Lubos Polerecky

Environ Microbiol 2015 Sep 4;17(9):3301-13. Epub 2015 Mar 4.

Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany.

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September 2015

Minimum Information about a Biosynthetic Gene cluster.

Authors:

Marnix H Medema Renzo Kottmann Pelin Yilmaz Matthew Cummings John B Biggins Kai Blin Irene de Bruijn Yit Heng Chooi Jan Claesen R Cameron Coates Pablo Cruz-Morales Srikanth Duddela Stephanie Düsterhus Daniel J Edwards David P Fewer Neha Garg Christoph Geiger Juan Pablo Gomez-Escribano Anja Greule Michalis Hadjithomas Anthony S Haines Eric J N Helfrich Matthew L Hillwig Keishi Ishida Adam C Jones Carla S Jones Katrin Jungmann Carsten Kegler Hyun Uk Kim Peter Kötter Daniel Krug Joleen Masschelein Alexey V Melnik Simone M Mantovani Emily A Monroe Marcus Moore Nathan Moss Hans-Wilhelm Nützmann Guohui Pan Amrita Pati Daniel Petras F Jerry Reen Federico Rosconi Zhe Rui Zhenhua Tian Nicholas J Tobias Yuta Tsunematsu Philipp Wiemann Elizabeth Wyckoff Xiaohui Yan Grace Yim Fengan Yu Yunchang Xie Bertrand Aigle Alexander K Apel Carl J Balibar Emily P Balskus Francisco Barona-Gómez Andreas Bechthold Helge B Bode Rainer Borriss Sean F Brady Axel A Brakhage Patrick Caffrey Yi-Qiang Cheng Jon Clardy Russell J Cox René De Mot Stefano Donadio Mohamed S Donia Wilfred A van der Donk Pieter C Dorrestein Sean Doyle Arnold J M Driessen Monika Ehling-Schulz Karl-Dieter Entian Michael A Fischbach Lena Gerwick William H Gerwick Harald Gross Bertolt Gust Christian Hertweck Monica Höfte Susan E Jensen Jianhua Ju Leonard Katz Leonard Kaysser Jonathan L Klassen Nancy P Keller Jan Kormanec Oscar P Kuipers Tomohisa Kuzuyama Nikos C Kyrpides Hyung-Jin Kwon Sylvie Lautru Rob Lavigne Chia Y Lee Bai Linquan Xinyu Liu Wen Liu Andriy Luzhetskyy Taifo Mahmud Yvonne Mast Carmen Méndez Mikko Metsä-Ketelä Jason Micklefield Douglas A Mitchell Bradley S Moore Leonilde M Moreira Rolf Müller Brett A Neilan Markus Nett Jens Nielsen Fergal O'Gara Hideaki Oikawa Anne Osbourn Marcia S Osburne Bohdan Ostash Shelley M Payne Jean-Luc Pernodet Miroslav Petricek Jörn Piel Olivier Ploux Jos M Raaijmakers José A Salas Esther K Schmitt Barry Scott Ryan F Seipke Ben Shen David H Sherman Kaarina Sivonen Michael J Smanski Margherita Sosio Evi Stegmann Roderich D Süssmuth Kapil Tahlan Christopher M Thomas Yi Tang Andrew W Truman Muriel Viaud Jonathan D Walton Christopher T Walsh Tilmann Weber Gilles P van Wezel Barrie Wilkinson Joanne M Willey Wolfgang Wohlleben Gerard D Wright Nadine Ziemert Changsheng Zhang Sergey B Zotchev Rainer Breitling Eriko Takano Frank Oliver Glöckner

Nat Chem Biol 2015 Sep;11(9):625-31

1] Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany. [2] Jacobs University Bremen gGmbH, Bremen, Germany.

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September 2015

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Authors:

Brigitte Boeckmann Marina Marcet-Houben Jonathan A Rees Kristoffer Forslund Jaime Huerta-Cepas Matthieu Muffato Pelin Yilmaz Ioannis Xenarios Peer Bork Suzanna E Lewis Toni Gabaldón

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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July 2015

In vitro biological activities and fatty acid profiles of Pistacia terebinthus fruits and Pistacia khinjuk seeds.

Authors:

Işil Hacıbekiroğlu Pelin Köseoğlu Yılmaz Nesrin Haşimi Ersin Kılınç Veysel Tolan Ufuk Kolak

Nat Prod Res 2015 12;29(5):444-6. Epub 2014 Aug 12.

a Department of Analytical Chemistry , Faculty of Pharmacy, Bezmialem Vakif University , 34093 Istanbul , Turkey.

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May 2015

Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring.

Authors:

Judith M Klatt Mohammad A A Al-Najjar Pelin Yilmaz Gaute Lavik Dirk de Beer Lubos Polerecky

Appl Environ Microbiol 2015 Mar 9;81(6):2025-31. Epub 2015 Jan 9.

Max Planck Institute for Marine Microbiology, Bremen, Germany Department of Earth Sciences-Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands.

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March 2015

Chemical constituents and biological activities of Cirsium leucopsis, C. sipyleum, and C. eriophorum.

Authors:

Mehmet Boğa Pelin Köseoğlu Yilmaz Deniz Bariş Cebe Mashhad Fatima Bina S Siddiqui Ufuk Kolak

Z Naturforsch C 2014 Sep-Oct;69(9-10):381-90

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March 2015

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Authors:

Pablo Yarza Pelin Yilmaz Elmar Pruesse Frank Oliver Glöckner Wolfgang Ludwig Karl-Heinz Schleifer William B Whitman Jean Euzéby Rudolf Amann Ramon Rosselló-Móra

Nat Rev Microbiol 2014 09;12(9):635-45

Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190 Esporles, Balearic Islands, Spain.

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September 2014

Simultaneous determination of seven phthalic acid esters in beverages using ultrasound and vortex-assisted dispersive liquid-liquid microextraction followed by high-performance liquid chromatography.

Authors:

Pelin Köseoğlu Yılmaz Abdulselam Ertaş Ufuk Kolak

J Sep Sci 2014 Aug 27;37(16):2111-7. Epub 2014 Jun 27.

Department of Analytical Chemistry, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.

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August 2014

Genomic standards consortium projects.

Stand Genomic Sci 2014 Jun 15;9(3):599-601. Epub 2014 Feb 15.

Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA .

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June 2014

A metagenomics portal for a democratized sequencing world.

Authors:

Andreas Wilke Elizabeth M Glass Daniela Bartels Jared Bischof Daniel Braithwaite Mark D'Souza Wolfgang Gerlach Travis Harrison Kevin Keegan Hunter Matthews Renzo Kottmann Tobias Paczian Wei Tang William L Trimble Pelin Yilmaz Jared Wilkening Narayan Desai Folker Meyer

Methods Enzymol 2013 ;531:487-523

Argonne National Laboratory, Lemont, Illinois, USA; University of Chicago, Chicago, Illinois, USA.

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April 2014

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

Authors:

Elizabeth M Glass Yekaterina Dribinsky Pelin Yilmaz Hal Levin Robert Van Pelt Doug Wendel Andreas Wilke Jonathan A Eisen Sue Huse Anna Shipanova Mitch Sogin Jason Stajich Rob Knight Folker Meyer Lynn M Schriml

ISME J 2014 Jan 24;8(1):1-3. Epub 2013 Oct 24.

Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.

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January 2014

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Authors:

Pelin Yilmaz Laura Wegener Parfrey Pablo Yarza Jan Gerken Elmar Pruesse Christian Quast Timmy Schweer Jörg Peplies Wolfgang Ludwig Frank Oliver Glöckner

Nucleic Acids Res 2014 Jan 28;42(Database issue):D643-8. Epub 2013 Nov 28.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany, Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada, Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada, Ribocon GmbH, D-28359 Bremen, Germany, School of Engineering and Science, Jacobs University Bremen gGmbH, D-28759 Bremen, Germany and Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany.

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January 2014