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  1. Article ; Online: New approaches for direct conversion of patient fibroblasts into neural cells.

    Gopalakrishnan, Suhasni / Hor, Pooja / Ichida, Justin K

    Brain research

    2017  Volume 1656, Page(s) 2–13

    Abstract: Recent landmark studies have demonstrated the production of disease-relevant human cell types by two different methods; differentiation of stem cells using external morphogens or lineage conversion using genetic factors. Directed differentiation changes ... ...

    Abstract Recent landmark studies have demonstrated the production of disease-relevant human cell types by two different methods; differentiation of stem cells using external morphogens or lineage conversion using genetic factors. Directed differentiation changes embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into a desired cell type by providing developmental cues in an in vitro environment. Direct reprogramming is achieved by the introduction of exogenous lineage specific transcription factors to convert any somatic cell type into another, thereby bypassing an intermediate pluripotent stage. A variety of somatic cell types such as blood, keratinocytes and fibroblasts can be used to derive iPSC cells. However, the process is time consuming,laborious, expensive and gives rise to cells with reported epigenetic heterogeneity even amongst different iPSC lines from same patient which could propagate phenotypic variability. A major concern with the use of pluripotent cells as starting material for cell replacement therapy is their incomplete differentiation and their propensity to form tumors following transplantation. In comparison, transcription factor mediated reprogramming offers a direct route to target cell types. This could allow for rapid comparison of large cohorts of patient and control samples at a given time for disease modeling. Additionally, transcription factors that drive maturation may yield more functionally mature cells than directed differentiation. Several studies have demonstrated the feasibility of generating of cell types such as cardiomyocytes, hepatocytes, and neurons from fibroblasts. Here, we will discuss recent advances and key challenges regarding direct reprogramming of somatic cell types into diverse neural cells. This article is part of a Special Issue entitled SI: Exploiting human neurons.
    MeSH term(s) Animals ; Cellular Reprogramming Techniques ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Humans ; Neurons/cytology ; Neurons/metabolism
    Language English
    Publishing date 2017-02-01
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 1200-2
    ISSN 1872-6240 ; 0006-8993
    ISSN (online) 1872-6240
    ISSN 0006-8993
    DOI 10.1016/j.brainres.2015.10.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Control of Ig gene assembly: lessons from premature activation.

    Gopalakrishnan, Suhasni / Collins, Patrick L / Oltz, Eugene M

    The EMBO journal

    2013  Volume 32, Issue 10, Page(s) 1350–1351

    MeSH term(s) Animals ; Histones/metabolism ; Interferon Regulatory Factors/metabolism ; Precursor Cells, B-Lymphoid/physiology ; V(D)J Recombination/physiology
    Chemical Substances Histones ; Interferon Regulatory Factors ; interferon regulatory factor-4
    Language English
    Publishing date 2013-04-23
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.1038/emboj.2013.94
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Generation of inner ear hair cells by direct lineage conversion of primary somatic cells.

    Menendez, Louise / Trecek, Talon / Gopalakrishnan, Suhasni / Tao, Litao / Markowitz, Alexander L / Yu, Haoze V / Wang, Xizi / Llamas, Juan / Huang, Chichou / Lee, James / Kalluri, Radha / Ichida, Justin / Segil, Neil

    eLife

    2020  Volume 9

    Abstract: The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular ... ...

    Abstract The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular dysfunction. Their paucity and inaccessibility has limited the search for otoprotective and regenerative strategies. Growing hair cells in vitro would provide a route to overcome this experimental bottleneck. We report a combination of four transcription factors (
    MeSH term(s) Animals ; Cell Lineage ; Fibroblasts/physiology ; Hair Cells, Auditory, Inner/physiology ; Labyrinth Supporting Cells/physiology ; Mice/physiology ; Mice, Transgenic ; Tail ; Transcription Factors/metabolism
    Chemical Substances Transcription Factors
    Keywords covid19
    Language English
    Publishing date 2020-06-30
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.55249
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Detection of chromosomal alteration after infusion of gene-edited allogeneic CAR T cells.

    Sasu, Barbra J / Opiteck, Gregory J / Gopalakrishnan, Suhasni / Kaimal, Vivek / Furmanak, Tom / Huang, David / Goswami, Angshumala / He, Ying / Chen, Jiamin / Nguyen, Anh / Balakumaran, Arun / Shah, Nirav N / Hamadani, Mehdi / Bone, Kathleen M / Prashad, Sacha / Bowen, Michael A / Pertel, Thomas / Embree, Heather D / Gidwani, Shalini G /
    Chang, David / Moore, Alison / Leonard, Mark / Amado, Rafael G

    Molecular therapy : the journal of the American Society of Gene Therapy

    2022  Volume 31, Issue 3, Page(s) 676–685

    Abstract: A chromosome 14 inversion was found in a patient who developed bone marrow aplasia following treatment with allogeneic chimeric antigen receptor (CAR) Tcells containing gene edits made with transcription activator-like effector nucleases (TALEN). TALEN ... ...

    Abstract A chromosome 14 inversion was found in a patient who developed bone marrow aplasia following treatment with allogeneic chimeric antigen receptor (CAR) Tcells containing gene edits made with transcription activator-like effector nucleases (TALEN). TALEN editing sites were not involved at either breakpoint. Recombination signal sequences (RSSs) were found suggesting recombination-activating gene (RAG)-mediated activity. The inversion represented a dominant clone detected in the context of decreasing absolute CAR Tcell and overall lymphocyte counts. The inversion was not associated with clinical consequences and wasnot detected in the drug product administered to this patient or in any drug product used in this or other trials using the same manufacturing processes. Neither was the inversion detected in this patient at earlier time points or in any other patient enrolled in this or other trials treated with this or other product lots. This case illustrates that spontaneous, possibly RAG-mediated, recombination events unrelated to gene editing can occur in adoptive cell therapy studies, emphasizes the need for ruling out off-target gene editing sites, and illustrates that other processes, such as spontaneous V(D)J recombination, can lead to chromosomal alterations in infused cells independent of gene editing.
    MeSH term(s) Humans ; Gene Editing ; Transcription Activator-Like Effector Nucleases/genetics ; T-Lymphocytes ; Receptors, Chimeric Antigen/genetics ; Immunotherapy, Adoptive/adverse effects ; Hematopoietic Stem Cell Transplantation
    Chemical Substances Transcription Activator-Like Effector Nucleases (EC 3.1.-) ; Receptors, Chimeric Antigen
    Language English
    Publishing date 2022-12-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2010592-7
    ISSN 1525-0024 ; 1525-0016
    ISSN (online) 1525-0024
    ISSN 1525-0016
    DOI 10.1016/j.ymthe.2022.12.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Generation of inner ear hair cells by direct lineage conversion of primary somatic cells

    Louise Menendez / Talon Trecek / Suhasni Gopalakrishnan / Litao Tao / Alexander L Markowitz / Haoze V Yu / Xizi Wang / Juan Llamas / Chichou Huang / James Lee / Radha Kalluri / Justin Ichida / Neil Segil

    eLife, Vol

    2020  Volume 9

    Abstract: The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular ... ...

    Abstract The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular dysfunction. Their paucity and inaccessibility has limited the search for otoprotective and regenerative strategies. Growing hair cells in vitro would provide a route to overcome this experimental bottleneck. We report a combination of four transcription factors (Six1, Atoh1, Pou4f3, and Gfi1) that can convert mouse embryonic fibroblasts, adult tail-tip fibroblasts and postnatal supporting cells into induced hair cell-like cells (iHCs). iHCs exhibit hair cell-like morphology, transcriptomic and epigenetic profiles, electrophysiological properties, mechanosensory channel expression, and vulnerability to ototoxin in a high-content phenotypic screening system. Thus, direct reprogramming provides a platform to identify causes and treatments for hair cell loss, and may help identify future gene therapy approaches for restoring hearing.
    Keywords inner ear ; reprogramming ; sensory hair cell ; screening ; ototoxin ; regeneration ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: DNA methylation in development and human disease.

    Gopalakrishnan, Suhasni / Van Emburgh, Beth O / Robertson, Keith D

    Mutation research

    2008  Volume 647, Issue 1-2, Page(s) 30–38

    Abstract: DNA methylation is a heritable and stable epigenetic mark associated with transcriptional repression. Changes in the patterns and levels of global and regional DNA methylation regulate development and contribute directly to disease states such as cancer. ...

    Abstract DNA methylation is a heritable and stable epigenetic mark associated with transcriptional repression. Changes in the patterns and levels of global and regional DNA methylation regulate development and contribute directly to disease states such as cancer. Recent findings provide intriguing insights into the epigenetic crosstalk between DNA methylation, histone modifications, and small interfering RNAs in the control of cell development and carcinogenesis. In this review, we summarize the recent studies in DNA methylation primarily focusing on the interplay between different epigenetic modifications and their potential role in gene silencing in development and disease. Although the molecular mechanisms involved in the epigenetic crosstalk are not fully understood, unraveling their precise regulation is important not only for understanding the underpinnings of cellular development and cancer, but also for the design of clinically relevant and efficient therapeutics using stem cells and anticancer drugs that target tumor initiating cells.
    MeSH term(s) Animals ; Cell Differentiation ; DNA Methylation ; Epigenesis, Genetic ; Gene Silencing ; Growth and Development/genetics ; Humans ; Models, Genetic ; Neoplasms/genetics ; Pluripotent Stem Cells/physiology ; Polycomb-Group Proteins ; Repressor Proteins/metabolism
    Chemical Substances Polycomb-Group Proteins ; Repressor Proteins
    Language English
    Publishing date 2008-08-20
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 206607-5
    ISSN 1873-135X ; 0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
    ISSN (online) 1873-135X
    ISSN 0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
    DOI 10.1016/j.mrfmmm.2008.08.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Iroquois Proteins Promote Skeletal Joint Formation by Maintaining Chondrocytes in an Immature State.

    Askary, Amjad / Mork, Lindsey / Paul, Sandeep / He, Xinjun / Izuhara, Audrey K / Gopalakrishnan, Suhasni / Ichida, Justin K / McMahon, Andrew P / Dabizljevic, Sonja / Dale, Rodney / Mariani, Francesca V / Crump, J Gage

    Developmental cell

    2015  Volume 35, Issue 3, Page(s) 358–365

    Abstract: An early event in skeletal joint development is the specification of articular chondrocytes at the joint surface. Articular chondrocytes are distinct in producing lower levels of cartilage matrix and not being replaced by bone, yet how they acquire these ...

    Abstract An early event in skeletal joint development is the specification of articular chondrocytes at the joint surface. Articular chondrocytes are distinct in producing lower levels of cartilage matrix and not being replaced by bone, yet how they acquire these properties remains poorly understood. Here, we show that two members of the Iroquois transcriptional repressor family, Irx7 and Irx5a, function to block chondrocyte maturation at the developing hyoid joint of zebrafish. These Irx factors suppress the production of cartilage matrix at the joint in part by preventing the activation of a col2a1a enhancer by Sox9a. Further, both zebrafish Irx7 and mouse IRX1 are able to repress cartilage matrix production in a murine chondrogenic cell line. Iroquois proteins may therefore have a conserved role in keeping chondrocytes in an immature state, with the lower levels of cartilage matrix produced by these immature cells contributing to joint flexibility.
    MeSH term(s) Animals ; Bone and Bones/metabolism ; Cartilage, Articular/metabolism ; Cartilage, Articular/pathology ; Cell Differentiation/physiology ; Chondrocytes/metabolism ; Transcription Factors/metabolism ; Zebrafish/metabolism
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2015-11-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2015.10.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci.

    Predeus, Alexander V / Gopalakrishnan, Suhasni / Huang, Yue / Tang, Jun / Feeney, Ann J / Oltz, Eugene M / Artyomov, Maxim N

    Journal of immunology (Baltimore, Md. : 1950)

    2013  Volume 192, Issue 3, Page(s) 1064–1070

    Abstract: The assembly and expression of mouse Ag receptor genes are controlled by a collection of cis-acting regulatory elements, including transcriptional promoters and enhancers. Although many powerful enhancers have been identified for Ig (Ig) and TCR (Tcr) ... ...

    Abstract The assembly and expression of mouse Ag receptor genes are controlled by a collection of cis-acting regulatory elements, including transcriptional promoters and enhancers. Although many powerful enhancers have been identified for Ig (Ig) and TCR (Tcr) loci, it remained unclear whether additional regulatory elements remain undiscovered. In this study, we use chromatin profiling of pro-B cells to define 38 epigenetic states in mouse Ag receptor loci, each of which reflects a distinct regulatory potential. One of these chromatin states corresponds to known transcriptional enhancers and identifies a new set of candidate elements in all three Ig loci. Four of the candidates were subjected to functional assays, and all four exhibit enhancer activity in B but not in T lineage cells. The new regulatory elements identified by focused chromatin profiling most likely have important functions in the creation, refinement, and expression of Ig repertoires.
    MeSH term(s) Acetylation ; Animals ; B-Lymphocytes/metabolism ; Cell Lineage ; Chromatin/genetics ; Chromatin Immunoprecipitation ; Computational Biology ; DNA-Binding Proteins/deficiency ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Gene Expression Regulation ; Genes, Immunoglobulin ; Histones/metabolism ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin Light Chains/genetics ; Lymphopoiesis ; Methylation ; Mice ; Mice, Inbred C57BL ; Pre-B Cell Receptors/genetics ; Protein Processing, Post-Translational ; Receptors, Antigen, B-Cell/genetics ; Transcription Factors/metabolism
    Chemical Substances Chromatin ; DNA-Binding Proteins ; Histones ; Immunoglobulin Heavy Chains ; Immunoglobulin Light Chains ; Pre-B Cell Receptors ; Rag2 protein, mouse ; Receptors, Antigen, B-Cell ; Transcription Factors
    Language English
    Publishing date 2013-12-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.1302800
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions.

    Gopalakrishnan, Suhasni / Sullivan, Beth A / Trazzi, Stefania / Della Valle, Giuliano / Robertson, Keith D

    Human molecular genetics

    2009  Volume 18, Issue 17, Page(s) 3178–3193

    Abstract: DNA methylation is an epigenetically imposed mark of transcriptional repression that is essential for maintenance of chromatin structure and genomic stability. Genome-wide methylation patterns are mediated by the combined action of three DNA ... ...

    Abstract DNA methylation is an epigenetically imposed mark of transcriptional repression that is essential for maintenance of chromatin structure and genomic stability. Genome-wide methylation patterns are mediated by the combined action of three DNA methyltransferases: DNMT1, DNMT3A and DNMT3B. Compelling links exist between DNMT3B and chromosome stability as emphasized by the mitotic defects that are a hallmark of ICF syndrome, a disease arising from germline mutations in DNMT3B. Centromeric and pericentromeric regions are essential for chromosome condensation and the fidelity of segregation. Centromere regions contain distinct epigenetic marks, including dense DNA hypermethylation, yet the mechanisms by which DNA methylation is targeted to these regions remains largely unknown. In the present study, we used a yeast two-hybrid screen and identified a novel interaction between DNMT3B and constitutive centromere protein CENP-C. CENP-C is itself essential for mitosis. We confirm this interaction in mammalian cells and map the domains responsible. Using siRNA knock downs, bisulfite genomic sequencing and ChIP, we demonstrate for the first time that CENP-C recruits DNA methylation and DNMT3B to both centromeric and pericentromeric satellite repeats and that CENP-C and DNMT3B regulate the histone code in these regions, including marks characteristic of centromeric chromatin. Finally, we demonstrate that loss of CENP-C or DNMT3B leads to elevated chromosome misalignment and segregation defects during mitosis and increased transcription of centromeric repeats. Taken together, our data reveal a novel mechanism by which DNA methylation is targeted to discrete regions of the genome and contributes to chromosomal stability.
    MeSH term(s) Cell Line ; Centromere/genetics ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA (Cytosine-5-)-Methyltransferases/metabolism ; DNA Methylation ; HCT116 Cells ; HeLa Cells ; Histone Code ; Humans ; Protein Binding ; Two-Hybrid System Techniques ; DNA Methyltransferase 3B
    Chemical Substances Chromosomal Proteins, Non-Histone ; centromere protein C ; DNA (Cytosine-5-)-Methyltransferases (EC 2.1.1.37)
    Language English
    Publishing date 2009-05-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddp256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Unifying model for molecular determinants of the preselection Vβ repertoire.

    Gopalakrishnan, Suhasni / Majumder, Kinjal / Predeus, Alexander / Huang, Yue / Koues, Olivia I / Verma-Gaur, Jiyoti / Loguercio, Salvatore / Su, Andrew I / Feeney, Ann J / Artyomov, Maxim N / Oltz, Eugene M

    Proceedings of the National Academy of Sciences of the United States of America

    2013  Volume 110, Issue 34, Page(s) E3206–15

    Abstract: The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are ... ...

    Abstract The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We quantified Vβ use in the preselection Tcrb repertoire and report relative contributions of 13 distinct features that may shape their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and predicted quality of recombination signal sequences (RSSs). We show that, in contrast to functional Vβ gene segments, all pseudo-Vβ segments are sequestered in transcriptionally silent chromatin, which effectively suppresses wasteful recombination. Importantly, computational analyses provide a unifying model, revealing a minimum set of five parameters that are predictive of Vβ use, dominated by chromatin modifications associated with transcription, but largely independent of precise spatial proximity to DβJβ clusters. This learned model-building strategy may be useful in predicting the relative contributions of epigenetic, spatial, and RSS features in shaping preselection V repertoires at other antigen receptor loci. Ultimately, such models may also predict how designed or naturally occurring alterations of these loci perturb the preselection use of variable gene segments.
    MeSH term(s) Animals ; Chromatin/immunology ; Chromatin Immunoprecipitation ; Computational Biology/methods ; DNA Primers/genetics ; Gene Expression Regulation/immunology ; Genes, T-Cell Receptor beta/genetics ; Genes, T-Cell Receptor beta/immunology ; High-Throughput Nucleotide Sequencing ; Immunoglobulin Variable Region/genetics ; Luciferases ; Mice ; Mice, Inbred C57BL ; Models, Immunological ; Regression Analysis ; V(D)J Recombination/genetics ; V(D)J Recombination/immunology
    Chemical Substances Chromatin ; DNA Primers ; Immunoglobulin Variable Region ; Luciferases (EC 1.13.12.-)
    Language English
    Publishing date 2013-08-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1304048110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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