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Author: Nicole Stoesser

Rankings

  • All-time downloads: 150,142 (rank: 985 )
  • Categories:
    • bioinformatics: 14,410 (rank: 596 )
    • epidemiology: 36,584 (rank: 699 )
    • evolutionary biology: 392 (rank: 20,707 (tie) )
    • genomics: 1,954 (rank: 14,786 (tie) )
    • infectious diseases: 80,632 (rank: 871 )
    • microbiology: 8,843 (rank: 2,320 )

Downloads per author, site-wide

Preprints

Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

epidemiology more details view paper
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    • Site-wide: 287
    • In epidemiology: 62
  • Year to date:
    • Site-wide: 220
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    • Site-wide: 1,476

Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom

infectious diseases more details view paper
  • Downloaded 20,469 times
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    • Site-wide: 524
    • In infectious diseases: 193
  • Year to date:
    • Site-wide: 2,862
  • Since beginning of last month:
    • Site-wide: 3,140

The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom

infectious diseases more details view paper
  • Downloaded 15,471 times
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    • Site-wide: 725
    • In infectious diseases: 257
  • Year to date:
    • Site-wide: 8,804
  • Since beginning of last month:
    • Site-wide: 9,469

Virus detection and identification in minutes using single-particle imaging and deep learning

infectious diseases more details view paper
  • Downloaded 11,712 times
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    • Site-wide: 1,048
    • In infectious diseases: 340
  • Year to date:
    • Site-wide: 4,753
  • Since beginning of last month:
    • Site-wide: 8,478

Increased infections, but not viral burden, with a new SARS-CoV-2 variant

infectious diseases more details view paper
  • Downloaded 8,955 times
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    • Site-wide: 1,469
    • In infectious diseases: 442
  • Year to date:
    • Site-wide: 9,674
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    • Site-wide: 13,393

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

bioinformatics more details view paper
  • Downloaded 8,752 times
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    • Site-wide: 1,512
    • In bioinformatics: 75
  • Year to date:
    • Site-wide: 50,071
  • Since beginning of last month:
    • Site-wide: 118,952

Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

infectious diseases more details view paper
  • Downloaded 7,053 times
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    • Site-wide: 1,989
    • In infectious diseases: 565
  • Year to date:
    • Site-wide: 4,013
  • Since beginning of last month:
    • Site-wide: 11,769

Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

infectious diseases more details view paper
  • Downloaded 4,463 times
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    • Site-wide: 3,698
    • In infectious diseases: 862
  • Year to date:
    • Site-wide: 1,701
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SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus

infectious diseases more details view paper
  • Downloaded 2,809 times
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    • Site-wide: 7,166
    • In infectious diseases: 1,251
  • Year to date:
    • Site-wide: 46,068
  • Since beginning of last month:
    • Site-wide: 101,542

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,423 times
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    • Site-wide: 8,903
    • In bioinformatics: 892
  • Year to date:
    • Site-wide: 58,762
  • Since beginning of last month:
    • Site-wide: 66,450

OMICRON-ASSOCIATED CHANGES IN SARS-COV-2 SYMPTOMS IN THE UNITED KINGDOM

epidemiology more details view paper
  • Downloaded 2,198 times
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    • Site-wide: 10,263
    • In epidemiology: 1,196
  • Year to date:
    • Site-wide: 567
  • Since beginning of last month:
    • Site-wide: 2,192

SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population

infectious diseases more details view paper
  • Downloaded 2,111 times
  • Download rankings, all-time:
    • Site-wide: 10,945
    • In infectious diseases: 1,768
  • Year to date:
    • Site-wide: 2,637
  • Since beginning of last month:
    • Site-wide: 14,795

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

infectious diseases more details view paper
  • Downloaded 1,811 times
  • Download rankings, all-time:
    • Site-wide: 13,717
    • In infectious diseases: 1,983
  • Year to date:
    • Site-wide: 7,501
  • Since beginning of last month:
    • Site-wide: 4,860

The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers

infectious diseases more details view paper
  • Downloaded 1,798 times
  • Download rankings, all-time:
    • Site-wide: 13,877
    • In infectious diseases: 1,805
  • Year to date:
    • Site-wide: 68,791
  • Since beginning of last month:
    • Site-wide: 42,709

Anti-spike antibody response to natural SARS-CoV-2 infection in the general population

infectious diseases more details view paper
  • Downloaded 1,790 times
  • Download rankings, all-time:
    • Site-wide: 13,973
    • In infectious diseases: 1,855
  • Year to date:
    • Site-wide: 12,833
  • Since beginning of last month:
    • Site-wide: 45,044

Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

infectious diseases more details view paper
  • Downloaded 1,501 times
  • Download rankings, all-time:
    • Site-wide: 18,248
    • In infectious diseases: 2,054
  • Year to date:
    • Site-wide: 124,597
  • Since beginning of last month:
    • Site-wide: 180,325

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

bioinformatics more details view paper
  • Downloaded 1,399 times
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    • Site-wide: 20,341
    • In bioinformatics: 2,205
  • Year to date:
    • Site-wide: 63,062
  • Since beginning of last month:
    • Site-wide: 42,556

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

microbiology more details view paper
  • Downloaded 1,358 times
  • Download rankings, all-time:
    • Site-wide: 21,308
    • In microbiology: 1,149
  • Year to date:
    • Site-wide: 177,817
  • Since beginning of last month:
    • Site-wide: 172,894

Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

infectious diseases more details view paper
  • Downloaded 1,354 times
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    • Site-wide: 21,407
    • In infectious diseases: 3,494
  • Year to date:
    • Site-wide: 1,084
  • Since beginning of last month:
    • Site-wide: 3,543

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli

microbiology more details view paper
  • Downloaded 1,296 times
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    • Site-wide: 22,915
    • In microbiology: 1,240
  • Year to date:
    • Site-wide: 155,288
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    • Site-wide: 160,206

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

genomics more details view paper
  • Downloaded 956 times
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    • Site-wide: 36,341
    • In genomics: 2,816
  • Year to date:
    • Site-wide: 128,053
  • Since beginning of last month:
    • Site-wide: 114,365

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

microbiology more details view paper
  • Downloaded 890 times
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    • Site-wide: 40,410
    • In microbiology: 2,216
  • Year to date:
    • Site-wide: 174,095
  • Since beginning of last month:
    • Site-wide: 130,356

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

microbiology more details view paper
  • Downloaded 873 times
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    • Site-wide: 41,547
    • In microbiology: 2,410
  • Year to date:
    • Site-wide: 93,292
  • Since beginning of last month:
    • Site-wide: 98,461

Flanker: a tool for comparative genomics of gene flanking regions

bioinformatics more details view paper
  • Downloaded 865 times
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    • Site-wide: 42,160
    • In bioinformatics: 4,461
  • Year to date:
    • Site-wide: 47,984
  • Since beginning of last month:
    • Site-wide: 32,703

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

bioinformatics more details view paper
  • Downloaded 864 times
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    • Site-wide: 42,188
    • In bioinformatics: 4,168
  • Year to date:
    • Site-wide: 129,998
  • Since beginning of last month:
    • Site-wide: 173,098

Increasing test specificity without impairing sensitivity - lessons learned from SARS-CoV-2 serology

infectious diseases more details view paper
  • Downloaded 718 times
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    • Site-wide: 55,193
    • In infectious diseases: 3,726
  • Year to date:
    • Site-wide: 32,165
  • Since beginning of last month:
    • Site-wide: 47,208

Transmission dynamics and between-species interactions of multidrug-resistant Enterobacteriaceae

epidemiology more details view paper
  • Downloaded 678 times
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    • Site-wide: 59,931
    • In epidemiology: 2,715
  • Year to date:
    • Site-wide: 147,873
  • Since beginning of last month:
    • Site-wide: 94,251

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

microbiology more details view paper
  • Downloaded 650 times
  • Download rankings, all-time:
    • Site-wide: 63,368
    • In microbiology: 3,646
  • Year to date:
    • Site-wide: 119,239
  • Since beginning of last month:
    • Site-wide: 140,489

Novel blaKPC-carrying species identified in the hospital environment

microbiology more details view paper
  • Downloaded 616 times
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    • Site-wide: 67,931
    • In microbiology: 3,918
  • Year to date:
    • Site-wide: 170,426
  • Since beginning of last month:
    • Site-wide: 119,556

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

microbiology more details view paper
  • Downloaded 604 times
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    • Site-wide: 69,805
    • In microbiology: 4,066
  • Year to date:
    • Site-wide: 131,577
  • Since beginning of last month:
    • Site-wide: 120,406

Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

genomics more details view paper
  • Downloaded 580 times
  • Download rankings, all-time:
    • Site-wide: 73,399
    • In genomics: 4,752
  • Year to date:
    • Site-wide: 141,228
  • Since beginning of last month:
    • Site-wide: 159,219

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

microbiology more details view paper
  • Downloaded 565 times
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    • Site-wide: 75,791
    • In microbiology: 4,565
  • Year to date:
    • Site-wide: 124,992
  • Since beginning of last month:
    • Site-wide: 162,581

Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

microbiology more details view paper
  • Downloaded 543 times
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    • Site-wide: 79,572
    • In microbiology: 4,734
  • Year to date:
    • Site-wide: 167,486
  • Since beginning of last month:
    • Site-wide: 150,581

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

genomics more details view paper
  • Downloaded 509 times
  • Download rankings, all-time:
    • Site-wide: 85,791
    • In genomics: None
  • Year to date:
    • Site-wide: 4,842
  • Since beginning of last month:
    • Site-wide: 1,164

Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

epidemiology more details view paper
  • Downloaded 488 times
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    • Site-wide: 90,022
    • In epidemiology: 3,680
  • Year to date:
    • Site-wide: 170,459
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    • Site-wide: 177,325

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

genomics more details view paper
  • Downloaded 483 times
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    • Site-wide: 91,026
    • In genomics: 5,544
  • Year to date:
    • Site-wide: 115,768
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    • Site-wide: 76,014

Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018

infectious diseases more details view paper
  • Downloaded 454 times
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    • Site-wide: 97,470
    • In infectious diseases: 4,887
  • Year to date:
    • Site-wide: 90,774
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    • Site-wide: 65,002

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

evolutionary biology more details view paper
  • Downloaded 421 times
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    • Site-wide: 105,253
    • In evolutionary biology: 4,969
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    • Site-wide: 79,722
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    • Site-wide: 111,812

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

microbiology more details view paper
  • Downloaded 398 times
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    • Site-wide: 110,852
    • In microbiology: 7,221
  • Year to date:
    • Site-wide: 119,718
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    • Site-wide: 128,460

Genomic network analysis of an environmental and livestock IncF plasmid population

bioinformatics more details view paper
  • Downloaded 395 times
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    • Site-wide: 111,656
    • In bioinformatics: 9,018
  • Year to date:
    • Site-wide: 127,763
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    • Site-wide: 92,302

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

microbiology more details view paper
  • Downloaded 375 times
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    • Site-wide: 116,891
    • In microbiology: 7,455
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    • Site-wide: 178,512
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    • Site-wide: 184,977

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

microbiology more details view paper
  • Downloaded 370 times
  • Download rankings, all-time:
    • Site-wide: 118,247
    • In microbiology: 7,528
  • Year to date:
    • Site-wide: 182,258
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    • Site-wide: 184,725

The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination

infectious diseases more details view paper
  • Downloaded 353 times
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    • Site-wide: 123,110
    • In infectious diseases: 5,926
  • Year to date:
    • Site-wide: 18,290
  • Since beginning of last month:
    • Site-wide: 41,294

Molecular epidemiology of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK

infectious diseases more details view paper
  • Downloaded 340 times
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    • Site-wide: 126,492
    • In infectious diseases: 6,578
  • Year to date:
    • Site-wide: 27,809
  • Since beginning of last month:
    • Site-wide: 40,752

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

microbiology more details view paper
  • Downloaded 309 times
  • Download rankings, all-time:
    • Site-wide: 135,674
    • In microbiology: 9,066
  • Year to date:
    • Site-wide: 170,243
  • Since beginning of last month:
    • Site-wide: 130,277

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

infectious diseases more details view paper
  • Downloaded 303 times
  • Download rankings, all-time:
    • Site-wide: 137,625
    • In infectious diseases: None
  • Year to date:
    • Site-wide: 10,690
  • Since beginning of last month:
    • Site-wide: 20,587

Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing

epidemiology more details view paper
  • Downloaded 297 times
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    • Site-wide: 139,266
    • In epidemiology: 5,502
  • Year to date:
    • Site-wide: 155,646
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    • Site-wide: 177,327

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

microbiology more details view paper
  • Downloaded 291 times
  • Download rankings, all-time:
    • Site-wide: 141,121
    • In microbiology: 10,865
  • Year to date:
    • Site-wide: 44,870
  • Since beginning of last month:
    • Site-wide: 37,619

Plasmid overlap and evolution between Enterobacterales isolates from bloodstream infections and non-human compartments

genomics more details view paper
  • Downloaded 263 times
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    • Site-wide: 149,259
    • In genomics: None
  • Year to date:
    • Site-wide: 13,227
  • Since beginning of last month:
    • Site-wide: 1,748

Antimicrobial resistance surveillance: can we estimate resistance in bloodstream infections from other types of specimen?

infectious diseases more details view paper
  • Downloaded 240 times
  • Download rankings, all-time:
    • Site-wide: 156,114
    • In infectious diseases: 6,484
  • Year to date:
    • Site-wide: 111,558
  • Since beginning of last month:
    • Site-wide: 100,249

Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records

infectious diseases more details view paper
  • Downloaded 239 times
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    • Site-wide: 156,225
    • In infectious diseases: 6,932
  • Year to date:
    • Site-wide: 15,209
  • Since beginning of last month:
    • Site-wide: 43,225

Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

infectious diseases more details view paper
  • Downloaded 231 times
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    • Site-wide: 158,521
    • In infectious diseases: 6,507
  • Year to date:
    • Site-wide: 151,677
  • Since beginning of last month:
    • Site-wide: 170,374

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

epidemiology more details view paper
  • Downloaded 211 times
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    • Site-wide: 163,834
    • In epidemiology: 6,785
  • Year to date:
    • Site-wide: 53,725
  • Since beginning of last month:
    • Site-wide: 60,594

Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.

infectious diseases more details view paper
  • Downloaded 181 times
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    • Site-wide: 171,428
    • In infectious diseases: 6,954
  • Year to date:
    • Site-wide: 84,201
  • Since beginning of last month:
    • Site-wide: 74,181

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

genomics more details view paper
  • Downloaded 116 times
  • Download rankings, all-time:
    • Site-wide: 183,675
    • In genomics: None
  • Year to date:
    • Site-wide: 39,715
  • Since beginning of last month:
    • Site-wide: 6,633

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