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  1. Content type: Research

    MMP-9-dependent proteolysis of histone H3 N-terminal tail (H3NT) is an important mechanism for activation of gene expression during osteoclast differentiation. Like other enzymes targeting their substrates wit...

    Authors: Yonghwan Shin, Nikhil B. Ghate, Byoungsan Moon, Kyungpyo Park, Wange Lu and Woojin An

    Citation: Epigenetics & Chromatin 2019 12:25

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  2. Content type: Research

    Histone acetylation plays an important role in DNA replication and repair because replicating chromatin is subject to dynamic changes in its structures. However, its precise mechanism remains elusive. In this ...

    Authors: Chiaki Noguchi, Tanu Singh, Melissa A. Ziegler, Jasmine D. Peake, Lyne Khair, Ana Aza, Toru M. Nakamura and Eishi Noguchi

    Citation: Epigenetics & Chromatin 2019 12:24

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  3. Content type: Research

    Transcription from the integrated HIV-1 promoter is directly governed by its chromatin environment, and the nucleosome-1 downstream from the transcription start site directly impedes transcription from the HIV...

    Authors: Chuan Li, Guillaume Mousseau and Susana T. Valente

    Citation: Epigenetics & Chromatin 2019 12:23

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  4. Content type: Research

    Stem cell differentiation involves major chromatin reorganisation, heterochromatin formation and genomic relocalisation of structural proteins, including heterochromatin protein 1 gamma (HP1γ). As the principa...

    Authors: Meike Wiese, Andrew J. Bannister, Srinjan Basu, Wayne Boucher, Kai Wohlfahrt, Maria A. Christophorou, Michael L. Nielsen, David Klenerman, Ernest D. Laue and Tony Kouzarides

    Citation: Epigenetics & Chromatin 2019 12:21

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  5. Content type: Research

    Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone...

    Authors: Jiji T. Kurup, Ion J. Campeanu and Benjamin L. Kidder

    Citation: Epigenetics & Chromatin 2019 12:20

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  6. Content type: Review

    The ATP-dependent chromatin remodelling complex BAF (= mammalian SWI/SNF complex) is crucial for the regulation of gene expression and differentiation. In the course of evolution from yeast to mammals, the BAF...

    Authors: Amelie Alfert, Natalia Moreno and Kornelius Kerl

    Citation: Epigenetics & Chromatin 2019 12:19

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  7. Content type: Research

    The genome of some vole rodents exhibit large blocks of heterochromatin coupled to their sex chromosomes. The DNA composition and transcriptional activity of these heterochromatin blocks have been studied, but...

    Authors: Kathrin S. Heinz, Alexander Rapp, Corella S. Casas-Delucchi, Anne Lehmkuhl, Ismael Romero-Fernández, Antonio Sánchez, Oliver H. Krämer, J. Alberto Marchal and M. Cristina Cardoso

    Citation: Epigenetics & Chromatin 2019 12:18

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  8. Content type: Research

    Epigenetic modifications have a central role in transcriptional regulation. While several studies using next-generation sequencing have revealed genome-wide associations between epigenetic modifications and tr...

    Authors: Hiroto S. Fukushima, Hiroyuki Takeda and Ryohei Nakamura

    Citation: Epigenetics & Chromatin 2019 12:17

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  9. Content type: Research

    The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine chromatin accessibility. While many studies have reported a positive correlation between gene expression and promoter a...

    Authors: Rebekah R. Starks, Anilisa Biswas, Ashish Jain and Geetu Tuteja

    Citation: Epigenetics & Chromatin 2019 12:16

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  10. Content type: Research

    Recently, we showed that PARP1 is involved in cotranscriptional splicing, possibly by bridging chromatin to RNA and recruiting splicing factors. It also can influence alternative splicing decisions through the...

    Authors: Elena A. Matveeva, Qamar M. H. Al-Tinawi, Eric C. Rouchka and Yvonne N. Fondufe-Mittendorf

    Citation: Epigenetics & Chromatin 2019 12:15

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  11. Content type: Research

    Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted gen...

    Authors: René A. M. Dirks, Guido van Mierlo, Hindrik H. D. Kerstens, Andreia S. Bernardo, Julianna Kobolák, István Bock, Julien Maruotti, Roger A. Pedersen, András Dinnyés, Martijn A. Huynen, Alice Jouneau and Hendrik Marks

    Citation: Epigenetics & Chromatin 2019 12:14

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  12. Content type: Research

    DNA methylation plays important roles in the regulation of nervous system development and in cellular responses to environmental stimuli such as light-derived signals. Despite great efforts in understanding th...

    Authors: Jianlin He, Xiguang Xu, Aboozar Monavarfeshani, Sharmi Banerjee, Michael A. Fox and Hehuang Xie

    Citation: Epigenetics & Chromatin 2019 12:13

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  13. Content type: Research

    ATP-dependent chromatin remodelling complexes are responsible for establishing and maintaining the positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and non-cod...

    Authors: Katherine A. Giles, Cathryn M. Gould, Qian Du, Ksenia Skvortsova, Jenny Z. Song, Madhavi P. Maddugoda, Joanna Achinger-Kawecka, Clare Stirzaker, Susan J. Clark and Phillippa C. Taberlay

    Citation: Epigenetics & Chromatin 2019 12:12

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  14. Content type: Research

    Epithelial to mesenchymal transition (EMT) plays a crucial role in cancer propagation. It can be orchestrated by the activation of multiple signaling pathways, which have been found to be highly coordinated wi...

    Authors: Congcong Lu, Simone Sidoli, Katarzyna Kulej, Karen Ross, Cathy H. Wu and Benjamin A. Garcia

    Citation: Epigenetics & Chromatin 2019 12:11

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  15. Content type: Research

    Wilson disease (WD) is an autosomal recessive disease caused by mutations in ATP7B encoding a copper transporter. Consequent copper accumulation results in a variable WD clinical phenotype involving hepatic, neur...

    Authors: Charles E. Mordaunt, Dorothy A. Kieffer, Noreene M. Shibata, Anna Członkowska, Tomasz Litwin, Karl-Heinz Weiss, Yihui Zhu, Christopher L. Bowlus, Souvik Sarkar, Stewart Cooper, Yu-Jui Yvonne Wan, Mohamed R. Ali, Janine M. LaSalle and Valentina Medici

    Citation: Epigenetics & Chromatin 2019 12:10

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  16. Content type: Research

    Although clinical data support an association between paternal alcohol use and deficits in child neurocognitive development, the relationship between paternal drinking and alcohol-induced growth phenotypes rem...

    Authors: Richard C. Chang, Haiqing Wang, Yudhishtar Bedi and Michael C. Golding

    Citation: Epigenetics & Chromatin 2019 12:9

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  17. Content type: Research

    The cell-cycle inhibitor p57kip2 plays a critical role in mammalian development by coordinating cell proliferation and differentiation in many cell types. p57kip2 expression is finely regulated by several epigene...

    Authors: Oriella Andresini, Marianna Nicoletta Rossi, Francesca Matteini, Stefano Petrai, Tiziana Santini and Rossella Maione

    Citation: Epigenetics & Chromatin 2019 12:8

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  18. Content type: Review

    Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dy...

    Authors: Bridget E. Collins, Celeste B. Greer, Benjamin C. Coleman and J. David Sweatt

    Citation: Epigenetics & Chromatin 2019 12:7

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  19. Content type: Research

    Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and, in ...

    Authors: José L. Ruiz, Rakiswendé S. Yerbanga, Thierry Lefèvre, Jean B. Ouedraogo, Victor G. Corces and Elena Gómez-Díaz

    Citation: Epigenetics & Chromatin 2019 12:5

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  20. Content type: Research

    Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytos...

    Authors: Sara Wernig-Zorc, Mukesh Pratap Yadav, Pradeep Kumar Kopparapu, Mats Bemark, Hallgerdur Lind Kristjansdottir, Per-Ola Andersson, Chandrasekhar Kanduri and Meena Kanduri

    Citation: Epigenetics & Chromatin 2019 12:4

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  21. Content type: Research

    The 5 hydroxymethylation (5hmC) mark and TET DNA dioxygenases play a pivotal role in embryonic stem cell differentiation and animal development. However, very little is known about TET enzymes in lineage deter...

    Authors: Dimitrios Cakouros, Sarah Hemming, Kahlia Gronthos, Renjing Liu, Andrew Zannettino, Songtao Shi and Stan Gronthos

    Citation: Epigenetics & Chromatin 2019 12:3

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  22. Content type: Research

    Boundaries in the Drosophila bithorax complex delimit autonomous regulatory domains that activate the parasegment (PS)-specific expression of homeotic genes. The Fab-7 boundary separates the iab-6 and iab-7 regul...

    Authors: Anna Fedotova, Chaevia Clendinen, Artem Bonchuk, Vladic Mogila, Tsutomu Aoki, Pavel Georgiev and Paul Schedl

    Citation: Epigenetics & Chromatin 2019 12:2

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  23. Content type: Research

    The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, char...

    Authors: Sumaiya A. Islam, Sarah J. Goodman, Julia L. MacIsaac, Jelena Obradović, Ronald G. Barr, W. Thomas Boyce and Michael S. Kobor

    Citation: Epigenetics & Chromatin 2019 12:1

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  24. Content type: Research

    5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TE...

    Authors: Qin Ma, Zhengzheng Xu, Huan Lu, Ziying Xu, Yuanyuan Zhou, Bifeng Yuan and Weimin Ci

    Citation: Epigenetics & Chromatin 2018 11:75

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  25. Content type: Methodology

    Our understanding of eukaryotic gene regulation is limited by the complexity of protein–DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. ...

    Authors: Derek H. Janssens, Steven J. Wu, Jay F. Sarthy, Michael P. Meers, Carrie H. Myers, James M. Olson, Kami Ahmad and Steven Henikoff

    Citation: Epigenetics & Chromatin 2018 11:74

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  26. Content type: Review

    Age reprogramming represents a novel method for generating patient-specific tissues for transplantation. It bypasses the de-differentiation/redifferentiation cycle that is characteristic of the induced pluripo...

    Authors: Prim B. Singh and Andrew G. Newman

    Citation: Epigenetics & Chromatin 2018 11:73

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  27. Content type: Research

    Lysine-specific histone demethylase 5C (KDM5C) belongs to the jumonji family of demethylases and is specific for the di- and tri-demethylation of lysine 4 residues on histone 3 (H3K4 me2/3). KDM5C is expressed...

    Authors: Youni Kim, Youngeun Jeong, Kujin Kwon, Tayaba Ismail, Hyun-Kyung Lee, Chowon Kim, Jeen-Woo Park, Oh-Shin Kwon, Beom-Sik Kang, Dong-Seok Lee, Tae Joo Park, Taejoon Kwon and Hyun-Shik Lee

    Citation: Epigenetics & Chromatin 2018 11:72

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  28. Content type: Research

    Polycomb repressive complex 2 (PRC2) is responsible for establishing and maintaining histone H3K27 methylation during cell differentiation and proliferation. H3K27 can be mono-, di-, or trimethylated, resultin...

    Authors: Weipeng Mu, Joshua Starmer, Della Yee and Terry Magnuson

    Citation: Epigenetics & Chromatin 2018 11:71

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  29. Content type: Research

    Epithelial mesenchymal transition (EMT) is tightly regulated by a network of transcription factors (EMT-TFs). Among them is the nuclear factor ZEB2, a member of the zinc-finger E-box binding homeobox family. Z...

    Authors: Nicolas Skrypek, Kenneth Bruneel, Cindy Vandewalle, Eva De Smedt, Bieke Soen, Nele Loret, Joachim Taminau, Steven Goossens, Niels Vandamme and Geert Berx

    Citation: Epigenetics & Chromatin 2018 11:70

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  30. Content type: Research

    The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or con...

    Authors: Narendra Singh Yadav, Janardan Khadka, Katherine Domb, Assaf Zemach and Gideon Grafi

    Citation: Epigenetics & Chromatin 2018 11:69

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  31. Content type: Correction

    After publication of this article [1], it was noticed Duane Smoot and Hassan Ashktorab who made and provided the cell line HFE145 were not included in the author list.

    Authors: Saikat Bhattacharya, Divya Reddy, Vinod Jani, Nikhil Gadewal, Sanket Shah, Raja Reddy, Kakoli Bose, Uddhavesh Sonavane, Rajendra Joshi, Duane Smoot, Hassan Ashktorab and Sanjay Gupta

    Citation: Epigenetics & Chromatin 2018 11:67

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    The original article was published in Epigenetics & Chromatin 2017 10:48

  32. Content type: Research

    Bidirectional promoters (BPs) are prevalent in eukaryotic genomes. However, it is poorly understood how the cell integrates different epigenomic information, such as transcription factor (TF) binding and chrom...

    Authors: Fatemeh Behjati Ardakani, Kathrin Kattler, Karl Nordström, Nina Gasparoni, Gilles Gasparoni, Sarah Fuchs, Anupam Sinha, Matthias Barann, Peter Ebert, Jonas Fischer, Barbara Hutter, Gideon Zipprich, Charles D. Imbusch, Bärbel Felder, Jürgen Eils, Benedikt Brors…

    Citation: Epigenetics & Chromatin 2018 11:66

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  33. Content type: Research

    In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin, as evidenced by microscopy observations and DamID mapping of lamina-associated domains (LAD...

    Authors: Alexey V. Pindyurin, Artem A. Ilyin, Anton V. Ivankin, Mikhail V. Tselebrovsky, Valentina V. Nenasheva, Elena A. Mikhaleva, Ludo Pagie, Bas van Steensel and Yuri Y. Shevelyov

    Citation: Epigenetics & Chromatin 2018 11:65

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  34. Content type: Research

    Meiotic recombination hotspots control the frequency and distribution of Spo11 (Rec12)-initiated recombination in the genome. Recombination occurs within and is regulated in part by chromatin structure, but re...

    Authors: Aaron J. Storey, Hsin-Ping Wang, Reine U. Protacio, Mari K. Davidson, Alan J. Tackett and Wayne P. Wahls

    Citation: Epigenetics & Chromatin 2018 11:64

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  35. Content type: Research

    Placental inflammation, often presenting as acute chorioamnionitis (aCA), is commonly associated with preterm birth. Preterm birth can have both immediate and long-term adverse effects on the health of the bab...

    Authors: Chaini Konwar, E. Magda Price, Li Qing Wang, Samantha L. Wilson, Jefferson Terry and Wendy P. Robinson

    Citation: Epigenetics & Chromatin 2018 11:63

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  36. Content type: Research

    Preservation of genome integrity by complete, error-free DNA duplication prior to cell division and by correct DNA damage repair is paramount for the development and maintenance of an organism. This holds true...

    Authors: Francesco Natale, Annina Scholl, Alexander Rapp, Wei Yu, Cathia Rausch and M. Cristina Cardoso

    Citation: Epigenetics & Chromatin 2018 11:61

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  37. Content type: Research

    Reactive oxygen species (ROS)-induced oxidative stress is well known to play a major role in male infertility. Sperm are sensitive to ROS damaging effects because as male germ cells form mature sperm they prog...

    Authors: Sarah Wyck, Carolina Herrera, Cristina E. Requena, Lilli Bittner, Petra Hajkova, Heinrich Bollwein and Raffaella Santoro

    Citation: Epigenetics & Chromatin 2018 11:60

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  38. Content type: Research

    The mechanism by which protein complexes interact to regulate the deposition of post-translational modifications of histones remains poorly understood. This is particularly important at regulatory regions, suc...

    Authors: Louie N. van de Lagemaat, Maria Flenley, Magnus D. Lynch, David Garrick, Simon R. Tomlinson, Kamil R. Kranc and Douglas Vernimmen

    Citation: Epigenetics & Chromatin 2018 11:59

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  39. Content type: Research

    The parthenogenetic marbled crayfish (Procambarus virginalis) is a novel species that has rapidly invaded and colonized various different habitats. Adaptation to different environments appears to be independent o...

    Authors: Fanny Gatzmann, Cassandra Falckenhayn, Julian Gutekunst, Katharina Hanna, Günter Raddatz, Vitor Coutinho Carneiro and Frank Lyko

    Citation: Epigenetics & Chromatin 2018 11:57

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  40. Content type: Research

    G9a and the related enzyme GLP were originally identified as histone lysine methyltransferases and then shown to also methylate several other non-histone proteins.

    Authors: Takeshi Tsusaka, Masaki Kikuchi, Tadahiro Shimazu, Takehiro Suzuki, Yoshihiro Sohtome, Mai Akakabe, Mikiko Sodeoka, Naoshi Dohmae, Takashi Umehara and Yoichi Shinkai

    Citation: Epigenetics & Chromatin 2018 11:56

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  41. Content type: Research

    Genomic imprinting leads to maternal expression of IGF2R in both mouse and opossum. In mouse, the antisense long noncoding (lnc) RNA Airn, which is paternally expressed from the differentially methylated region (...

    Authors: Shunsuke Suzuki, Geoffrey Shaw and Marilyn B. Renfree

    Citation: Epigenetics & Chromatin 2018 11:55

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  42. Content type: Research

    DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the first genome-wide analysis of monozygotic (MZ) twin ...

    Authors: Jenny van Dongen, Erik A. Ehli, Rick Jansen, Catharina E. M. van Beijsterveldt, Gonneke Willemsen, Jouke J. Hottenga, Noah A. Kallsen, Shanna A. Peyton, Charles E. Breeze, Cornelis Kluft, Bastiaan T. Heijmans, Meike Bartels, Gareth E. Davies and Dorret I. Boomsma

    Citation: Epigenetics & Chromatin 2018 11:54

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  43. Content type: Research

    Contact domains of chromatin serve as a fundamental unit to regulate action of enhancers for target genes. Looping between a pair of CCCTC-binding factor (CTCF)-binding sites in convergent orientations underli...

    Authors: Taro Tsujimura, Osamu Takase, Masahiro Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano and Keiichi Hishikawa

    Citation: Epigenetics & Chromatin 2018 11:51

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  44. Content type: Research

    There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specific manner by a group of nuclear-encoded mtDNA-specific replication factors. Thi...

    Authors: Xin Sun and Justin C. St John

    Citation: Epigenetics & Chromatin 2018 11:53

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  45. Content type: Research

    Compensatory liver hyperplasia—or regeneration—induced by two-thirds partial hepatectomy (PH) permits the study of synchronized activation of mammalian gene expression, particularly in relation to cell prolife...

    Authors: Leonor Rib, Dominic Villeneuve, Shilpi Minocha, Viviane Praz, Nouria Hernandez, Nicolas Guex and Winship Herr

    Citation: Epigenetics & Chromatin 2018 11:52

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