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  1. Content type: Research

    Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms shaping community assemblage. However, quantifying immigration impact remains challenging especially at individua...

    Authors: Ran Mei, Jinha Kim, Fernanda P. Wilson, Benjamin T. W. Bocher and Wen-Tso Liu

    Citation: Microbiome 2019 7:65

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  2. Content type: Research

    The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to t...

    Authors: Typhaine Le Doujet, Concetta De Santi, Terje Klemetsen, Erik Hjerde, Nils-Peder Willassen and Peik Haugen

    Citation: Microbiome 2019 7:64

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  3. Content type: Research

    Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrop...

    Authors: Hazem Sharaf, Richard R. Rodrigues, Jinyoung Moon, Bo Zhang, Kerri Mills and Mark A. Williams

    Citation: Microbiome 2019 7:63

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  4. Content type: Letter to the Editor

    Metagenomic next-generation sequencing (mNGS) experiments involving small amounts of nucleic acid input are highly susceptible to erroneous conclusions resulting from unintentional sequencing of occult contami...

    Authors: M. S. Zinter, M. Y. Mayday, K. K. Ryckman, L. L. Jelliffe-Pawlowski and J. L. DeRisi

    Citation: Microbiome 2019 7:62

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  5. Content type: Short report

    Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly...

    Authors: Krithika Arumugam, Caner Bağcı, Irina Bessarab, Sina Beier, Benjamin Buchfink, Anna Górska, Guanglei Qiu, Daniel H. Huson and Rohan B. H. Williams

    Citation: Microbiome 2019 7:61

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  6. Content type: Research

    Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cu...

    Authors: Matthias T. Buhmann, Dominik Abt, Oliver Nolte, Thomas R. Neu, Sebastian Strempel, Werner C. Albrich, Patrick Betschart, Valentin Zumstein, Antonia Neels, Katharina Maniura-Weber and Qun Ren

    Citation: Microbiome 2019 7:60

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  7. Content type: Research

    The Mariana Trench is the deepest known site in the Earth’s oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic commun...

    Authors: Jiwen Liu, Yanfen Zheng, Heyu Lin, Xuchen Wang, Meng Li, Yang Liu, Meng Yu, Meixun Zhao, Nikolai Pedentchouk, David J. Lea-Smith, Jonathan D. Todd, Clayton R. Magill, Wei-Jia Zhang, Shun Zhou, Delei Song, Haohui Zhong…

    Citation: Microbiome 2019 7:47

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  8. Content type: Research

    Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known ab...

    Authors: Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard and Mogens Nicolaisen

    Citation: Microbiome 2019 7:59

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  10. Content type: Research

    Revealing the relationship between plants and fungi is very important in understanding biodiversity maintenance, community stability, and ecosystem functioning. However, differences in the community and networ...

    Authors: Hui Yao, Xiang Sun, Chao He, Pulak Maitra, Xing-Chun Li and Liang-Dong Guo

    Citation: Microbiome 2019 7:57

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  11. Content type: Research

    The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. ...

    Authors: Aleksandra Checinska Sielaff, Camilla Urbaniak, Ganesh Babu Malli Mohan, Victor G. Stepanov, Quyen Tran, Jason M. Wood, Jeremiah Minich, Daniel McDonald, Teresa Mayer, Rob Knight, Fathi Karouia, George E. Fox and Kasthuri Venkateswaran

    Citation: Microbiome 2019 7:50

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  12. Content type: Research

    Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing...

    Authors: Frédéric Raymond, Maurice Boissinot, Amin Ahmed Ouameur, Maxime Déraspe, Pier-Luc Plante, Sewagnouin Rogia Kpanou, Ève Bérubé, Ann Huletsky, Paul H. Roy, Marc Ouellette, Michel G. Bergeron and Jacques Corbeil

    Citation: Microbiome 2019 7:56

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  13. Content type: Research

    Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentou...

    Authors: Estelle Couradeau, Ana Giraldo-Silva, Francesca De Martini and Ferran Garcia-Pichel

    Citation: Microbiome 2019 7:55

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  15. Content type: Research

    Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiom...

    Authors: Aaron J. Prussin II, Pedro J. Torres, John Shimashita, Steven R. Head, Kyle J. Bibby, Scott T. Kelley and Linsey C. Marr

    Citation: Microbiome 2019 7:53

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  16. Content type: Software

    Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables...

    Authors: Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson and Erik Kristiansson

    Citation: Microbiome 2019 7:52

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  18. Content type: Research

    A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we...

    Authors: Charlotte van der Veer, Rosanne Y. Hertzberger, Sylvia M. Bruisten, Hanne L. P. Tytgat, Jorne Swanenburg, Alie de Kat Angelino-Bart, Frank Schuren, Douwe Molenaar, Gregor Reid, Henry de Vries and Remco Kort

    Citation: Microbiome 2019 7:49

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  20. Content type: Software

    Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical s...

    Authors: Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Connell, Jung-Jin Lee, Bryton Fett, Frederic D. Bushman and Kyle Bittinger

    Citation: Microbiome 2019 7:46

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  21. Content type: Research

    Evidence from preclinical and clinical studies suggests that interactions among the brain, gut, and microbiota may affect the pathophysiology of irritable bowel syndrome (IBS). As disruptions in central and pe...

    Authors: Jennifer S. Labus, Vadim Osadchiy, Elaine Y. Hsiao, Julien Tap, Muriel Derrien, Arpana Gupta, Kirsten Tillisch, Boris Le Nevé, Cecilia Grinsvall, Maria Ljungberg, Lena Öhman, Hans Törnblom, Magnus Simren and Emeran A. Mayer

    Citation: Microbiome 2019 7:45

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  23. Content type: Research

    Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pa...

    Authors: Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Annelies Geirnaert, Rachelle Prantil-Baun, Diogo M. Camacho, David B. Chou, Sasan Jalili-Firoozinezhad, Tomás de Wouters, Magdalena Kasendra, Michael Super, Mark J. Cartwright, Camilla A. Richmond, David T. Breault, Christophe Lacroix and Donald E. Ingber

    Citation: Microbiome 2019 7:43

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  24. Content type: Methodology

    Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagen...

    Authors: Tingting Zheng, Jun Li, Yueqiong Ni, Kang Kang, Maria-Anna Misiakou, Lejla Imamovic, Billy K. C. Chow, Anne A. Rode, Peter Bytzer, Morten Sommer and Gianni Panagiotou

    Citation: Microbiome 2019 7:42

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  25. Content type: Research

    Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely ...

    Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf and Danielle G. Lemay

    Citation: Microbiome 2019 7:41

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  26. Content type: Methodology

    The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis...

    Authors: Will PM Rowe, Anna Paola Carrieri, Cristina Alcon-Giner, Shabhonam Caim, Alex Shaw, Kathleen Sim, J. Simon Kroll, Lindsay J. Hall, Edward O. Pyzer-Knapp and Martyn D. Winn

    Citation: Microbiome 2019 7:40

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  27. Content type: Research

    There are complex interactions between aging, frailty, diet, and the gut microbiota; modulation of the gut microbiota by diet could lead to healthier aging. The purpose of this study was to test the effect of ...

    Authors: Tam T. T. Tran, Fabien J. Cousin, Denise B. Lynch, Ravi Menon, Jennifer Brulc, Jillian R.-M. Brown, Eileen O’Herlihy, Ludovica F. Butto, Katie Power, Ian B. Jeffery, Eibhlís M. O’Connor and Paul W. O’Toole

    Citation: Microbiome 2019 7:39

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  28. Content type: Correction

    Following publication of the original article [1], the authors identified wrong citations in the maintext.

    Authors: So-Jeong Kim, Jong-Geol Kim, Sang-Hoon Lee, Soo-Je Park, Joo-Han Gwak, Man-Young Jung, Won-Hyung Chung, Eun-Jin Yang, Jisoo Park, Jinyoung Jung, Yoonsoo Hahn, Jang-Cheon Cho, Eugene L. Madsen, Francisco Rodriguez-Valera, Jung-Ho Hyun and Sung-Keun Rhee

    Citation: Microbiome 2019 7:38

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    The original article was published in Microbiome 2019 7:29

  29. Content type: Research

    Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local infl...

    Authors: Meera K. Shenoy, Douglas W. Fadrosh, Din L. Lin, William Worodria, Patrick Byanyima, Emmanuel Musisi, Sylvia Kaswabuli, Josephine Zawedde, Ingvar Sanyu, Emily Chang, Serena Fong, Kathryn McCauley, J. Lucian Davis, Laurence Huang and Susan V. Lynch

    Citation: Microbiome 2019 7:37

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  30. Content type: Research

    Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of norm...

    Authors: John Anthony Yason, Yi Ran Liang, Chin Wen Png, Yongliang Zhang and Kevin Shyong Wei Tan

    Citation: Microbiome 2019 7:30

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  31. Content type: Methodology

    Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets o...

    Authors: Weizhi Song, Bernd Wemheuer, Shan Zhang, Kerrin Steensen and Torsten Thomas

    Citation: Microbiome 2019 7:36

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  32. Content type: Research

    Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being anal...

    Authors: Pablo Fresia, Verónica Antelo, Cecilia Salazar, Matías Giménez, Bruno D’Alessandro, Ebrahim Afshinnekoo, Christopher Mason, Gastón H. Gonnet and Gregorio Iraola

    Citation: Microbiome 2019 7:35

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  33. Content type: Research

    Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whe...

    Authors: Nina Iszatt, Stefan Janssen, Virissa Lenters, Cecilie Dahl, Hein Stigum, Rob Knight, Siddhartha Mandal, Shyamal Peddada, Antonio González, Tore Midtvedt and Merete Eggesbø

    Citation: Microbiome 2019 7:34

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  34. Content type: Research

    Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied ...

    Authors: Zhi-Bo Zhao, Ji-Zheng He, Stefan Geisen, Li-Li Han, Jun-Tao Wang, Ju-Pei Shen, Wen-Xue Wei, Yun-Ting Fang, Pei-Pei Li and Li-Mei Zhang

    Citation: Microbiome 2019 7:33

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  37. Content type: Research

    Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, ...

    Authors: So-Jeong Kim, Jong-Geol Kim, Sang-Hoon Lee, Soo-Je Park, Joo-Han Gwak, Man-Young Jung, Won-Hyung Chung, Eun-Jin Yang, Jisoo Park, Jinyoung Jung, Yoonsoo Hahn, Jang-Cheon Cho, Eugene L. Madsen, Francisco Rodriguez-Valera, Jung-Ho Hyun and Sung-Keun Rhee

    Citation: Microbiome 2019 7:29

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    The Correction to this article has been published in Microbiome 2019 7:38

  38. Content type: Research

    Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classi...

    Authors: Ilias Lagkouvardos, Till R. Lesker, Thomas C. A. Hitch, Eric J. C. Gálvez, Nathiana Smit, Klaus Neuhaus, Jun Wang, John F. Baines, Birte Abt, Bärbel Stecher, Jörg Overmann, Till Strowig and Thomas Clavel

    Citation: Microbiome 2019 7:28

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  39. Content type: Research

    Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibioti...

    Authors: Johan S. Sáenz, Tamires Valim Marques, Rafael Simões Coelho Barone, José Eurico Possebon Cyrino, Susanne Kublik, Joseph Nesme, Michael Schloter, Susanne Rath and Gisle Vestergaard

    Citation: Microbiome 2019 7:24

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  40. Content type: Research

    Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms. This is of particular relevance to species in zoo-based conservat...

    Authors: Rachael E. Antwis, Katie L. Edwards, Bryony Unwin, Susan L. Walker and Susanne Shultz

    Citation: Microbiome 2019 7:27

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  41. Content type: Research

    Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a p...

    Authors: Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian A. Firek, Robyn Baker, Michael J. Morowitz and Jillian F. Banfield

    Citation: Microbiome 2019 7:26

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  42. Content type: Research

    Increased autoreactive antibodies have been reported in HIV disease; however, the mechanism accounting for autoantibody induction in HIV remains unknown.

    Authors: Zhenwu Luo, Min Li, Yongxia Wu, Zhefeng Meng, Lisa Martin, Lumin Zhang, Elizabeth Ogunrinde, Zejun Zhou, Shenghui Qin, Zhuang Wan, Maria Anna Julia Westerink, Stephanie Warth, Hui Liu, Ping Jin, David Stroncek, Quan-Zhen Li…

    Citation: Microbiome 2019 7:25

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  43. Content type: Research

    Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However,...

    Authors: Robert A. Quinn, Sandeep Adem, Robert H. Mills, William Comstock, Lindsay DeRight Goldasich, Gregory Humphrey, Alexander A. Aksenov, Alexei V. Melnik, Ricardo da Silva, Gail Ackermann, Nuno Bandeira, David J. Gonzalez, Doug Conrad, Anthony J. O’Donoghue, Rob Knight and Pieter C. Dorrestein

    Citation: Microbiome 2019 7:23

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  44. Content type: Correction

    Following publication of the original article [1], the authors reported a typographic error in the type of master mix kit used, the text should read as: “The qPCR was performed using Fast SYBR Green Master Mix...

    Authors: Efrem S. Lim, Cynthia Rodriguez and Lori R. Holtz

    Citation: Microbiome 2019 7:22

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    The original article was published in Microbiome 2018 6:87

  45. Content type: Correspondence

    How and when a newborn is first colonized by microbes continues to be of great interest due to its broad implications on human health and disease. Payne et al. express their opinion about our recent study in w...

    Authors: Efrem S. Lim, Cynthia Rodriguez and Lori R. Holtz

    Citation: Microbiome 2019 7:21

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    The Letter to the Editor to this article has been published in Microbiome 2019 7:20

  46. Content type: Letter to the Editor

    A recent publication by Lim et al. 2018 (Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community) strongly concluded that the microbiome of amniotic fluid primarily origin...

    Authors: M. S. Payne, J. A. Keelan and L. F. Stinson

    Citation: Microbiome 2019 7:20

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    The Correspondence to this article has been published in Microbiome 2019 7:21

  47. Content type: Research

    Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe d...

    Authors: Yiran Liang, Jing Zhan, Donghui Liu, Mai Luo, Jiajun Han, Xueke Liu, Chang Liu, Zheng Cheng, Zhiqiang Zhou and Peng Wang

    Citation: Microbiome 2019 7:19

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  48. Content type: Research

    The gut microbiome plays a fundamental role in the human host’s overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual,...

    Authors: J. Alfredo Blakeley-Ruiz, Alison R. Erickson, Brandi L. Cantarel, Weili Xiong, Rachel Adams, Janet K. Jansson, Claire M. Fraser and Robert L. Hettich

    Citation: Microbiome 2019 7:18

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  49. Content type: Software

    Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replic...

    Authors: Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R. Lesker, Peter Belmann, Matthew Z. DeMaere, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges and Alice C. McHardy

    Citation: Microbiome 2019 7:17

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  50. Content type: Research

    Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. Howe...

    Authors: Ke Yu, Shan Yi, Bing Li, Feng Guo, Xingxing Peng, Zhiping Wang, Yang Wu, Lisa Alvarez-Cohen and Tong Zhang

    Citation: Microbiome 2019 7:16

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