Nucleic Acids Research

Papers
(The TQCC of Nucleic Acids Research is 16. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-04-01 to 2025-04-01.)
ArticleCitations
Correction to ‘Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs’7714
Correction to ‘Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM’5768
Correction to ‘EMPIAR: The Electron Microscopy Public Image Archive’4786
Correction to ‘ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress’3833
Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds3477
Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair3470
Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system3114
NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome2986
R2DT: a comprehensive platform for visualizing RNA secondary structure1966
A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators1886
Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase1847
Argonaute CSR-1A promotes H3K9me3 maintenance to protect somatic development in offspring1728
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses1692
A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers1598
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states1561
Centromeric localization of αKNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions1441
SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complex1427
Conformational reorganization and phase separation drive hyper-editing of ADR-2–ADBP-1 complex1417
Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits1342
Eukaryotic initiation factors eIF4F and eIF4B promote translation termination upon closed-loop formation1280
Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics1253
Correction ‘LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNA’1203
Mitochondrial exonuclease EXOG supports DNA integrity by the removal of single-stranded DNA flaps1178
The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates1094
Correction to ‘High mobility group AT-hook 1 (HMGA1) is an important positive regulator of hepatitis B virus (HBV) that is reciprocally upregulated by HBV X protein’992
Correction to ‘In vivo analysis of Pim-1 deficiency’967
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis916
Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites881
Widespread translational control regulates retinal development in mouse812
Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI758
BFVD—a large repository of predicted viral protein structures738
Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase703
Deep learning-assisted genome-wide characterization of massively parallel reporter assays696
7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy674
Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes664
mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation633
Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis inPseudomonas aeruginosa620
CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells613
Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter612
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity594
Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics581
USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress578
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenicEscherichia coli556
Editor's Note on ‘PCAF regulates the stability of the transcriptional regulator and cyclin-dependent kinase inhibitor p27Kip1’488
Correction to ‘EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants’488
Correction to ‘linker histone H1 modulates defense priming and immunity in plants’474
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning465
PHF8 facilitates transcription recovery following DNA double-strand break repair461
Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events456
STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading443
Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster428
Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates411
Retraction of ‘DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27’411
Expression of concern on ‘Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR409
Expression of Concern on ‘Mutually exclusive splicing regulates the Nav 1.6 sodium channel function through a combinatorial mechanism that involves three distinct splicing regulatory elements and thei392
Expression of concern to ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’383
Novel archaeal ribosome dimerization factor facilitating unique 30S–30S dimerization379
Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display378
The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures372
Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish370
Retraction of ‘Nuclear CaMKII enhances histone H3 phosphorylation and remodels chromatin during cardiac hypertrophy’368
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters346
Telomemore enables single-cell analysis of cell cycle and chromatin condensation325
A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis322
Large serine integrases utilise scavenged phage proteins as directionality cofactors322
Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance314
An evolved, orthogonal ssDNA generator for targeted hypermutation of multiple genomic loci309
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’296
Correction to ‘MiR-145 directly targets p70S6K1 in cancer cells to inhibit tumor growth and angiogenesis’294
Correction to ‘Stabilization of XIAP mRNA through the RNA binding protein HuR regulated by cellular polyamines’289
Correction to ‘The European Genome-phenome Archive in 2021’275
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes270
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research266
Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly260
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database259
BioSamples database: FAIRer samples metadata to accelerate research data management258
A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation255
MediaDive: the expert-curated cultivation media database250
CaeNDR, the Caenorhabditis Natural Diversity Resource249
Paralogous translation factors target distinct mRNAs to differentially regulate tolerance to oxidative stress in yeast242
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort241
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide241
ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules239
Phage defence loci of Streptococcus thermophilus—tip of the anti-phage iceberg?233
p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis227
Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome225
Correction to ‘Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach’220
Correction to ‘CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells’215
Editor's note on ‘Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene’215
Correction to ‘Four additional natural 7-deazaguanine derivatives in phages and how to make them’210
Correction to ‘hnRNPA1 couples nuclear export and translation of specific mRNAs downstream of FGF-2/S6K2 signalling’210
Editor's Note on ‘Influence of correct secondary and tertiary RNA folding on the binding of cellular factors to the HCV IRES’208
Correction to ‘Clerocidin interacts with the cleavage complex of Streptococcus pneumoniae topoisomerase IV to induce selective irreversible DNA damage’207
Correction to ‘Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R’207
Correction to ‘Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch’206
Correction to ‘EMDB—the Electron Microscopy Data Bank’205
Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers200
Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers199
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing197
Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Ψ55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro193
RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment185
KRCC1, a modulator of the DNA damage response182
SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks175
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets175
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes175
Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC167
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection166
Correction to ‘Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases’164
Correction to ‘ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation’163
Correction to ‘Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I’163
Correction to ‘Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome’162
Correction to ‘DisProt in 2024: improving function annotation of intrinsically disordered proteins’161
Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution160
Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells158
A new level of RNA-based plant protection: dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber mosaic virus156
Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice154
Optimizing gRNA selection for high-penetrance F0 CRISPR screening for interrogating disease gene function153
APE1 condensation in nucleoli of non-cancer cells depends on rRNA transcription and forming G-quadruplex RNA structures153
mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability151
Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity150
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline148
Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation148
BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures144
Comprehensive profiling of L1 retrotransposons in mouse144
HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia142
Correction to ‘Mechanistic insights into the alternative ribosome recycling by HflXr’142
Correction to ‘Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data’141
Correction to ‘Genome manipulation by guide-directed Argonaute cleavage’138
Correction to ‘Click display: a rapid and efficient in vitro protein display method for directed evolution’136
Identification of a novel endogenous long non-coding RNA that inhibits selenoprotein P translation136
In vivotargets ofSalmonellaFinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid135
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions132
RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation132
Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM131
Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria130
Circular L-RNA aptamer promotes target recognition and controls gene activity129
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms128
tRNA queuosine modification is involved in biofilm formation and virulence in bacteria128
Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency126
Implication of nucleotides near the 3′ end of 16S rRNA in guarding the translational reading frame126
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation124
Three-way contact analysis characterizes the higher order organization of the Tcra locus121
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation120
Single-cell gene regulation network inference by large-scale data integration120
Four additional natural 7-deazaguanine derivatives in phages and how to make them120
RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET119
Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors119
Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans117
scMAGIC: accurately annotating single cells using two rounds of reference-based classification116
ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair114
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)114
Stochastic scanning events on the GCN4 mRNA 5’ untranslated region generate cell-to-cell heterogeneity in the yeast nutritional stress response114
Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes114
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models113
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins112
Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining112
CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids112
FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes111
DNA molecular combing-based replication fork directionality profiling109
Landscape of semi-extractable RNAs across five human cell lines108
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase108
Predicting functional consequences of SNPs on mRNA translation via machine learning107
Two type I topoisomerases maintain DNA topology in human mitochondria107
Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells107
Archaeal Hel308 suppresses recombination through a catalytic switch that controls DNA annealing107
Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3105
AlphaFind: discover structure similarity across the proteome in AlphaFold DB104
N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2104
Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution104
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo104
Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex103
Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq103
Monocyte chemoattractant protein-induced protein 1 directly degrades viral miRNAs with a specific motif and inhibits KSHV infection103
Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis103
Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation102
Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington’s disease101
CYCLeR—a novel tool for the full isoform assembly and quantification of circRNAs101
Yeast transcription factor Msn2 binds to G4 DNA99
Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors99
Replication protein A dynamically re-organizes on primer/template junctions to permit DNA polymerase δ holoenzyme assembly and initiation of DNA synthesis99
Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction98
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program97
Structural characterization of the ANTAR antiterminator domain bound to RNA97
Thyclotides, tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-2197
Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich95
The FLIP-FIGNL1 complex regulates the dissociation of RAD51/DMC1 in homologous recombination and replication fork restart95
Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX1794
Occurrence and stability of anion–π interactions between phosphate and nucleobases in functional RNA molecules93
Orphan nuclear receptors-induced ALT-associated PML bodies are targets for ALT inhibition93
Inhibition of DNA replication initiation by silver nanoclusters91
The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues91
Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain90
Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex90
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases89
Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells89
A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria89
GDPF: a data resource for the distribution of prokaryotic protein families across the global biosphere88
TTSBBC: triplex target site biomarkers and barcodes in cancer88
Single-molecule characterization of SV40 replisome and novel factors: human FPC and Mcm1087
CCPE: cell cycle pseudotime estimation for single cell RNA-seq data87
Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity87
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress86
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data86
TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms86
GCMS-ID: a webserver for identifying compounds from gas chromatography mass spectrometry experiments85
Toehold clipping: A mechanism for remote control of DNA strand displacement84
Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population84
Genome-scale top-down strategy to generate viable genome-reduced phages84
Coordinated DNA polymerization by Polγ and the region of LonP1 regulated proteolysis83
Distinct mobility patterns of BRCA2 molecules at DNA damage sites82
An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity82
Genomic patterns of transcription–replication interactions in mouse primary B cells82
mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes81
Visualization of oxidized guanine nucleotides accumulation in living cells with split MutT81
To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus81
Sustained pigmentation causes DNA damage and invokes translesion polymerase Polκ for repair in melanocytes81
ADARp150 counteracts whole genome duplication80
SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression80
PharmGWAS: a GWAS-based knowledgebase for drug repurposing80
Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP79
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome79
COLOCdb: a comprehensive resource for multi-model colocalization of complex traits78
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data78
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data78
RNA-directed peptide synthesis across a nicked loop78
An archaeal transcription factor EnfR with a novel ‘eighth note’ fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA178
Weak-cooperative binding of a long single-stranded DNA chain on a surface78
A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis78
Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer77
Assessing base-resolution DNA mechanics on the genome scale77
Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels77
UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF277
Development of a novel tobramycin dependent riboswitch76
The Burkholderia cenocepacia iron starvation σ factor, OrbS, possesses an on-board iron sensor76
‘SAXS-osmometer’ method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state76
MAMI: a comprehensive database of mother–infant microbiome and probiotic resources76
Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems76
Small RNA-mediated genetic switches coordinate ALG-3/4 small RNA pathway function76
Mutations in the non-codingRNU4ATACgene affect the homeostasis and function of the Integrator complex75
Structural basis for the allosteric regulation and dynamic assembly of DNMT3B75
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes74
Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface74
High mobility group AT-hook 1 (HMGA1) is an important positive regulator of hepatitis B virus (HBV) that is reciprocally upregulated by HBV X protein74
Comparison of genome architecture at two stages of male germline cell differentiation inDrosophila73
Usage of the H3 variants during the S-phase of the cell cycle in Physarum polycephalum73
Nanopores map the acid-base properties of a single site in a single DNA molecule72
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping72
Sequence diversity of apidaecin-like peptides arresting the terminating ribosome71
Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger71
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes70
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