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List of works by Richard A. Young

3D Chromosome Regulatory Landscape of Human Pluripotent Cells.

scientific article

A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer

scientific article published on 05 April 2017

A Phase Separation Model for Transcriptional Control.

scientific article published on March 2017

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

scientific article

A chemoattractant cytokine associated with granulomas in tuberculosis and silicosis

scientific article

A chromatin landmark and transcription initiation at most promoters in human cells

scientific article (publication date: 13 July 2007)

A common set of gene regulatory networks links metabolism and growth inhibition

scientific article

A genome-scale in vivo loss-of-function screen identifies Phf6 as a lineage-specific regulator of leukemia cell growth

scientific article

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

scientific article

A mammalian SRB protein associated with an RNA polymerase II holoenzyme

scientific article

A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast.

scientific article

A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID.

scientific article

A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis.

scientific article published on 16 September 2013

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

scientific article published on 28 January 2016

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

scientific article published on 6 March 2017

ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry

scientific article published on 09 December 2019

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia

scientific article published on December 2008

Abstract 3583: Thymocyte selection-associated HMG box protein (TOX) induces genomic instability in T-cell acute lymphoblastic leukemia

Activated signal transduction kinases frequently occupy target genes

scientific article published on 01 July 2006

Activating phosphorylation of the Kin28p subunit of yeast TFIIH by Cak1p

scientific article

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

scientific article

Activation of the LMO2 oncogene through a somatically acquired neomorphic promoter in T-cell acute lymphoblastic leukemia.

scientific article published on 7 March 2017

Activation of the p53 Transcriptional Program Sensitizes Cancer Cells to Cdk7 Inhibitors.

scientific article

Activation without a vital ingredient

scientific article published in Nature

Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells

scientific article published on 27 December 2011

An Activator Target in the RNA Polymerase II Holoenzyme ⬇️

scientific article published on May 1, 1998

An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae.

scientific article

Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET

scientific article

Association of Cdk-activating kinase subunits with transcription factor TFIIH

scientific article (publication date: 16 March 1995)

Attenuated host resistance against Mycobacterium bovis BCG infection in mice lacking osteopontin

scientific article

Author Correction: Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

scientific article published in Nature

BET bromodomain inhibition as a therapeutic strategy to target c-Myc

scientific article (publication date: 16 September 2011)

BET bromodomain proteins regulate enhancer function during adipogenesis.

scientific article published on 14 February 2018

Bayesian estimation of transcript levels using a general model of array measurement noise

scientific article

Binding of pRB to the PHD protein RBP2 promotes cellular differentiation

scientific article

Biomolecular Condensates in the Nucleus

scientific article published on 16 July 2020

Biomolecular condensates and cancer

scientific article published on 31 December 2020

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

article

CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer.

scientific article

CDK7-dependent transcriptional addiction in triple-negative breast cancer.

scientific article

CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation

scientific article published on 03 September 2020

Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells

scientific article published on 31 March 2020

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.

scientific article

Chromatin immunoprecipitation and microarray-based analysis of protein location

scientific article

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

scientific article

Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells

scientific article

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.

scientific article

Coactivator condensation at super-enhancers links phase separation and gene control

scientific article published in Science

Combining location and expression data for principled discovery of genetic regulatory network models

scientific article

Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits

scientific article published on 23 November 2020

Computational discovery of gene modules and regulatory networks

scientific article published on 12 October 2003

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

scientific article (publication date: 8 August 2008)

Connecting transcriptional control to chromosome structure and human disease.

scientific article published on January 2010

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes

scientific article

Control of developmental regulators by Polycomb in human embryonic stem cells

scientific article (publication date: 21 April 2006)

Control of pancreas and liver gene expression by HNF transcription factors

scientific article

Control of the Embryonic Stem Cell State ⬇️

scientific article (publication date: 18 March 2011)

Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers

scientific article

Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.

scholarly article

Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia.

scientific article

Core transcriptional regulatory circuitry in human embryonic stem cells

scientific article

Core transcriptional regulatory circuitry in human hepatocytes

scientific article published on 2 May 2006

Corrigendum: Small genomic insertions form enhancers that misregulate oncogenes

scientific article published on June 2017

Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors

scientific article published on 29 August 2016

CpG island structure and trithorax/polycomb chromatin domains in human cells

scientific article published on 20 July 2012

Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma

scientific article published on 6 March 2018

Cumulative Toll-Like Receptor Activation in Human Macrophages Treated with Whole Bacteria ⬇️

scientific article published on May 15, 2003

D-cyclins repress apoptosis in hematopoietic cells by controlling death receptor Fas and its ligand FasL.

scientific article published on 31 July 2014

DHODH modulates transcriptional elongation in the neural crest and melanoma

scientific article

Deciphering gene expression regulatory networks.

scientific article

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

scientific article

Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations.

scientific article published on 13 May 2010

Direct lineage conversion of adult mouse liver cells and B lymphocytes to neural stem cells

scientific article

Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.

scientific article

Dissecting the regulatory circuitry of a eukaryotic genome

scientific article (publication date: 25 November 1998)

Divergent transcription from active promoters

scientific article (publication date: 19 December 2008)

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

scientific article

Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs

scientific article published on 15 August 2019

E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints

scientific article

EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma

scientific article published on 18 January 2018

Editing DNA Methylation in the Mammalian Genome

scientific article published on September 2016

Embryonic stem cell-based mapping of developmental transcriptional programs

scientific article published on 13 November 2011

Enhancer Features that Drive Formation of Transcriptional Condensates

scientific article published on 01 August 2019

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

scientific article

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer.

scientific article published on 26 January 2016

Epitope tagging of the human endoplasmic reticulum HSP70 protein, BiP, to facilitate analysis of BiP--substrate interactions.

scientific article

Erratum: Mediator and cohesin connect gene expression and chromatin architecture

scientific article published in Nature

Evidence for an instructive mechanism of de novo methylation in cancer cells.

scientific article

Evidence that gene activation and silencing during stem cell differentiation requires a transcriptionally paused intermediate state

scientific article

Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo

scientific article

Fifty years after Jacob and Monod: what are the unanswered questions in molecular biology?

scientific article published in May 2011

Foxp3 occupancy and regulation of key target genes during T-cell stimulation

scientific article

Functional antagonism between RNA polymerase II holoenzyme and global negative regulator NC2 in vivo

scientific article

Functional association of Gdown1 with RNA polymerase II poised on human genes

scientific article

Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes

scientific article

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.

scientific article

Genome expression on the World Wide Web

scientific article published on 01 May 1999

Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues

scientific article

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation

scientific article

Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins.

scientific article

Genome-wide localization of small molecules

scientific article

Genome-wide location and function of DNA binding proteins

scientific article (publication date: 22 December 2000)

Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex.

scientific article published on April 2002

Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage

scientific article

Global and Hox-specific roles for the MLL1 methyltransferase

scientific article

Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters

scientific article published on 26 January 2006

Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

scientific article published on September 2010

Global position and recruitment of HATs and HDACs in the yeast genome.

scientific article published on October 2004

Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons

scientific article

Grounded: transcriptional pausing in naive mESCs

scientific article published on 01 May 2012

H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment

scientific article

Heat shock fusion proteins as vehicles for antigen delivery into the major histocompatibility complex class I presentation pathway ⬇️

scientific article published on November 25, 1997

High MITF Expression is Associated with Super-enhancers and Suppressed by CDK7 Inhibition in Melanoma.

scientific article

High-resolution computational models of genome binding events.

scientific article published on August 2006

Histone H3K27ac separates active from poised enhancers and predicts developmental state

scientific article

Host factor for coliphage Qβ RNA replication: Presence in procaryotes and association with the 30S ribosomal subunit inEscherichia coli ⬇️

scientific article published on May 20, 1977

Human Hsp60: bacterial expression, purification, development of monoclonal antibodies and a sandwich ELISA for quantitation.

scientific article published on February 1994

Human macrophage activation programs induced by bacterial pathogens

scientific article

Identification of a cancer stem cell-specific function for the histone deacetylases, HDAC1 and HDAC7, in breast and ovarian cancer.

scientific article published on 03 October 2016

Identification of the gal4 suppressor Sug1 as a subunit of the yeast 26S proteasome

scientific article published in Nature

Insights into host responses against pathogens from transcriptional profiling.

scientific article

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

scientific article

Integrated genomic analyses of de novo pathways underlying atypical meningiomas

scientific article published on 14 February 2017

Integrated genomic analyses of de novo pathways underlying atypical meningiomas.

scientific article

Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression

scientific article

Interplay of Positive and Negative Regulators in Transcription Initiation by RNA Polymerase II Holoenzyme ⬇️

scientific article published on August 1, 1998

JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia.

scientific article published on 25 June 2018

LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors

scientific article published on 29 June 2020

Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts.

scientific article

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

scientific article

Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration

scientific article published on October 2011

MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification

scientific article published on 28 December 2017

MYC and transcription elongation.

scientific article published on January 2014

Mapping key features of transcriptional regulatory circuitry in embryonic stem cells.

scientific article

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes ⬇️

scientific article (publication date: 11 April 2013)

Master transcription factors determine cell-type-specific responses to TGF-β signaling

scientific journal article

MeCP2 links heterochromatin condensates and neurodevelopmental disease

scientific article published on 22 July 2020

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

scientific article published on 25 September 2019

Mediator and cohesin connect gene expression and chromatin architecture

scientific article

Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells

scientific article published on October 2009

Models of human core transcriptional regulatory circuitries

scientific article

Multiple structural maintenance of chromosome complexes at transcriptional regulatory elements.

scientific article published on 24 October 2013

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

scholarly article

Nanog-like regulates endoderm formation through the Mxtx2-Nodal pathway.

scientific article published in March 2012

New Insights into Genome Structure: Genes of a Feather Stick Together.

scientific article published on September 2017

Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma

scientific article published on 01 December 2018

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

scientific article

Osteopontin expression correlates with clinical outcome in patients with mycobacterial infection.

scientific article published on July 2000

PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes

scientific article published on 12 June 2017

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

scientific article

Partitioning of cancer therapeutics in nuclear condensates

scientific article published on 01 June 2020

Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation.

scientific article

Pocket protein complexes are recruited to distinct targets in quiescent and proliferating cells

scientific article published on September 2005

Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity

scientific article published on July 2013

Polycomb complexes repress developmental regulators in murine embryonic stem cells

scientific article (publication date: 18 May 2006)

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

scientific article published on 07 August 2019

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

scientific article

Promoter-specific activation defects by a novel yeast TBP mutant compromised for TFIIB interaction

scientific article published on 01 November 2001

RNA polymerase II carboxy-terminal domain contributes to the response to multiple acidic activators in vitro ⬇️

scientific article published on 01 December 1991

RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling

scientific article published on 01 January 1996

RNA polymerase II holoenzymes and subcomplexes.

scientific article

RNA polymerase II subunit composition, stoichiometry, and phosphorylation

scientific article

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

scientific article

RNA-Mediated Feedback Control of Transcriptional Condensates

scientific article published on 09 December 2020

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

scientific article

Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas

scientific article published on 22 August 2016

Regulatory targets in the RNA polymerase II holoenzyme

scientific article published on 01 October 1998

Remodeling of yeast genome expression in response to environmental changes

scientific article

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene.

scientific article

Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer

scientific article published on 6 January 2016

Revisiting global gene expression analysis

scientific article

Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation

scientific article

Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells

scientific article

SMC complexes link gene expression and genome architecture

scientific article

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.

scientific article published on 18 August 2013

Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry

article

Selective inhibition of tumor oncogenes by disruption of super-enhancers

scientific article (publication date: 11 April 2013)

Serial regulation of transcriptional regulators in the yeast cell cycle

scientific article (publication date: 21 September 2001)

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

scientific article

Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.

scientific article

Small genomic insertions form enhancers that misregulate oncogenes

scientific article published on 09 February 2017

Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms

scientific article

Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming

scientific article (publication date: 22 February 2008)

Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma.

scientific article published on April 2016

Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis.

scientific article published in March 2017

Super-enhancers in the control of cell identity and disease

scientific article (publication date: 7 November 2013)

Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression.

scientific article

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

scientific article

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

scientific article published on 22 August 2014

Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly

scientific article

Systematic identification of culture conditions for induction and maintenance of naive human pluripotency

scientific article

TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia

scientific article published on 3 October 2017

TRIB2 reinforces the oncogenic transcriptional program controlled by the TAL1 complex in T-cell acute lymphoblastic leukemia

scientific article

Tandem promoters direct E. coli ribosomal RNA synthesis ⬇️

scientific article published on May 1, 1979

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

scientific article

Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor

scientific article

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

scientific journal article

Temporal Regulation of RNA Polymerase II by Srb10 and Kin28 Cyclin-Dependent Kinases ⬇️

scientific article published on July 1, 1998

Ten years of genetics and genomics: what have we achieved and where are we heading?

scientific article

The Msx1 Homeoprotein Recruits Polycomb to the Nuclear Periphery during Development

scientific article published on September 2011

The RNA polymerase II holoenzyme and its implications for gene regulation

scientific article (publication date: March 1995)

The TAL1 complex targets the FBXW7 tumor suppressor by activating miR-223 in human T cell acute lymphoblastic leukemia

scientific article published on 15 July 2013

The core centromere and Sgo1 establish a 50-kb cohesin-protected domain around centromeres during meiosis I

scientific article

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection

scientific article

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress

scientific article

The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset

scientific article

The kinetics of specific immune responses in rhesus monkeys inoculated with live recombinant BCG expressing SIV Gag, Pol, Env, and Nef proteins.

scientific article published on March 2000

The long noncoding RNA Wisper controls cardiac fibrosis and remodeling

scientific article published on June 2017

The plasticity of dendritic cell responses to pathogens and their components

scientific article

The rate of protein synthesis in hematopoietic stem cells is limited partly by 4E-BPs.

scientific article published on 04 August 2016

The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E. coli ⬇️

scientific article published on February 1, 1980

The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes

scientific article

The yeast A kinases differentially regulate iron uptake and respiratory function.

scientific article published on May 2000

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

scientific article published on 15 November 2018

Transcription factor trapping by RNA in gene regulatory elements

scientific article

Transcription of eukaryotic protein-coding genes

scientific article (publication date: 2000)

Transcription. Repressive transcription

scientific article

Transcriptional Addiction in Cancer.

scientific article published on February 2017

Transcriptional activating regions target a cyclin-dependent kinase.

scientific article

Transcriptional amplification in tumor cells with elevated c-Myc.

scientific article

Transcriptional regulation and its misregulation in disease.

scientific article

Transcriptional regulation of the Schizosaccharomyces pombe malic enzyme gene, mae2.

scientific article published in April 1999

Transcriptional regulation: contending with complexity

scientific article

Transcriptional regulatory code of a eukaryotic genome

scientific article

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia

scientific article published on 18 April 2006

Transcriptional regulatory networks in Saccharomyces cerevisiae

scientific article

Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.

scientific article published on January 2010

Transposition of the Escherichia coli insertion element gamma generates a five-base-pair repeat ⬇️

scientific article published on October 1, 1979

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

scientific article published on February 2007

Wnt signaling promotes reprogramming of somatic cells to pluripotency

scientific article (publication date: 7 August 2008)

X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner

scientific article

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

scientific article published on 30 November 2017

Yeast NC2 associates with the RNA polymerase II preinitiation complex and selectively affects transcription in vivo

scientific article

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state

scientific journal article

Zebrafish promoter microarrays identify actively transcribed embryonic genes.

scientific article published on 4 August 2006

c-Myc regulates transcriptional pause release

scientific article

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

scientific article published on 07 September 2020

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