Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)
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{"title"=>"Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)", "type"=>"journal", "authors"=>[{"first_name"=>"Felix M.", "last_name"=>"Key", "scopus_author_id"=>"56342110600"}, {"first_name"=>"Benjamin", "last_name"=>"Peter", "scopus_author_id"=>"37034791900"}, {"first_name"=>"Megan Y.", "last_name"=>"Dennis", "scopus_author_id"=>"15130981100"}, {"first_name"=>"Emilia", "last_name"=>"Huerta-Sánchez", "scopus_author_id"=>"6504236582"}, {"first_name"=>"Wei", "last_name"=>"Tang", "scopus_author_id"=>"57059678700"}, {"first_name"=>"Ludmila", "last_name"=>"Prokunina-Olsson", "scopus_author_id"=>"16426739500"}, {"first_name"=>"Rasmus", "last_name"=>"Nielsen", "scopus_author_id"=>"56008936500"}, {"first_name"=>"Aida M.", "last_name"=>"Andrés", "scopus_author_id"=>"35557401400"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84908335988", "pmid"=>"25329461", "sgr"=>"84908335988", "doi"=>"10.1371/journal.pgen.1004681", "isbn"=>"1553-7390", "issn"=>"15537404", "pui"=>"600311064"}, "id"=>"71f68a41-4445-3aa1-bcf3-43b27a428781", "abstract"=>"Interferon lambda 4 gene (IFNL4) encodes IFN-λ4, a new member of the IFN-λ family with antiviral activity. In humans IFNL4 open reading frame is truncated by a polymorphic frame-shift insertion that eliminates IFN-λ4 and turns IFNL4 into a polymorphic pseudogene. Functional IFN-λ4 has antiviral activity but the elimination of IFN-λ4 through pseudogenization is strongly associated with improved clearance of hepatitis C virus (HCV) infection. We show that functional IFN-λ4 is conserved and evolutionarily constrained in mammals and thus functionally relevant. However, the pseudogene has reached moderately high frequency in Africa, America, and Europe, and near fixation in East Asia. In fact, the pseudogenizing variant is among the 0.8% most differentiated SNPs between Africa and East Asia genome-wide. Its raise in frequency is associated with additional evidence of positive selection, which is strongest in East Asia, where this variant falls in the 0.5% tail of SNPs with strongest signatures of recent positive selection genome-wide. Using a new Approximate Bayesian Computation (ABC) approach we infer that the pseudogenizing allele appeared just before the out-of-Africa migration and was immediately targeted by moderate positive selection; selection subsequently strengthened in European and Asian populations resulting in the high frequency observed today. This provides evidence for a changing adaptive process that, by favoring IFN-λ4 inactivation, has shaped present-day phenotypic diversity and susceptibility to disease.", "link"=>"http://www.mendeley.com/research/selection-variant-associated-improved-viral-clearance-drives-local-adaptive-pseudogenization-interfe", "reader_count"=>41, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>28, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Brazil"=>2, "United Kingdom"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1720653"], "description"=>"<p>F<sub>ST</sub> values and for F<sub>ST</sub>, XP-EHH, iHS and Fay and Wu's H (FW) the empirical P-values are shown for rs368234815 in every population.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207040, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.t001", "stats"=>{"downloads"=>3, "page_views"=>43, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_ST_values_and_for_F_ST_XP_EHH_iHS_and_Fay_and_Wu_s_H_FW_the_empirical_P_values_are_shown_for_rs368234815_in_every_population_/1207040", "title"=>"F<sub>ST</sub> values and for F<sub>ST</sub>, XP-EHH, iHS and Fay and Wu's H (FW) the empirical P-values are shown for rs368234815 in every population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720647"], "description"=>"<p>American populations of European and African origin (CEU, ASW) are placed near the geographic area of origin. For full population names see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#s4\" target=\"_blank\">Methods</a>.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207034, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.g002", "stats"=>{"downloads"=>1, "page_views"=>215, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequency_of_rs368234815_916_G_allele_blue_and_TT_allele_green_for_each_population_from_the_1000_Genomes_dataset_/1207034", "title"=>"Allele frequency of rs368234815 - ΔG allele (blue) and TT allele (green) for each population from the 1000 Genomes dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720656"], "description"=>"<p>ABC results and inferred parameter estimates for the SDN model.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207043, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.t003", "stats"=>{"downloads"=>1, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ABC_results_and_inferred_parameter_estimates_for_the_SDN_model_/1207043", "title"=>"ABC results and inferred parameter estimates for the SDN model.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720650"], "description"=>"<p>Map of the <i>IFNL</i> locus with locations of relevant SNPs (from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#pgen-1004681-t002\" target=\"_blank\"><b>Table 2</b></a>) and the inferred recombination hotspot based on recombination rates from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#pgen.1004681-Frazer1\" target=\"_blank\">[60]</a>.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207037, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.g004", "stats"=>{"downloads"=>3, "page_views"=>69, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_the_IFNL_locus_with_locations_of_relevant_SNPs_from_Table_2_and_the_inferred_recombination_hotspot_based_on_recombination_rates_from_60_/1207037", "title"=>"Map of the <i>IFNL</i> locus with locations of relevant SNPs (from <b>Table 2</b>) and the inferred recombination hotspot based on recombination rates from [60].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720667", "https://ndownloader.figshare.com/files/1720668", "https://ndownloader.figshare.com/files/1720669", "https://ndownloader.figshare.com/files/1720670", "https://ndownloader.figshare.com/files/1720672", "https://ndownloader.figshare.com/files/1720673", "https://ndownloader.figshare.com/files/1720674", "https://ndownloader.figshare.com/files/1720675", "https://ndownloader.figshare.com/files/1720676", "https://ndownloader.figshare.com/files/1720677", "https://ndownloader.figshare.com/files/1720678", "https://ndownloader.figshare.com/files/1720679", "https://ndownloader.figshare.com/files/1720680", "https://ndownloader.figshare.com/files/1720681", "https://ndownloader.figshare.com/files/1720682", "https://ndownloader.figshare.com/files/1720683", "https://ndownloader.figshare.com/files/1720684", "https://ndownloader.figshare.com/files/1720685", "https://ndownloader.figshare.com/files/1720686", "https://ndownloader.figshare.com/files/1720687"], "description"=>"<div><p>Interferon lambda 4 gene (<i>IFNL4</i>) encodes IFN-λ4, a new member of the IFN-λ family with antiviral activity. In humans <i>IFNL4</i> open reading frame is truncated by a polymorphic frame-shift insertion that eliminates IFN-λ4 and turns <i>IFNL4</i> into a polymorphic pseudogene. Functional IFN-λ4 has antiviral activity but the elimination of IFN-λ4 through pseudogenization is strongly associated with improved clearance of hepatitis C virus (HCV) infection. We show that functional IFN-λ4 is conserved and evolutionarily constrained in mammals and thus functionally relevant. However, the pseudogene has reached moderately high frequency in Africa, America, and Europe, and near fixation in East Asia. In fact, the pseudogenizing variant is among the 0.8% most differentiated SNPs between Africa and East Asia genome-wide. Its raise in frequency is associated with additional evidence of positive selection, which is strongest in East Asia, where this variant falls in the 0.5% tail of SNPs with strongest signatures of recent positive selection genome-wide. Using a new Approximate Bayesian Computation (ABC) approach we infer that the pseudogenizing allele appeared just before the out-of-Africa migration and was immediately targeted by moderate positive selection; selection subsequently strengthened in European and Asian populations resulting in the high frequency observed today. This provides evidence for a changing adaptive process that, by favoring IFN-λ4 inactivation, has shaped present-day phenotypic diversity and susceptibility to disease.</p></div>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207054, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004681.s001", "https://dx.doi.org/10.1371/journal.pgen.1004681.s002", "https://dx.doi.org/10.1371/journal.pgen.1004681.s003", "https://dx.doi.org/10.1371/journal.pgen.1004681.s004", "https://dx.doi.org/10.1371/journal.pgen.1004681.s005", "https://dx.doi.org/10.1371/journal.pgen.1004681.s006", "https://dx.doi.org/10.1371/journal.pgen.1004681.s007", "https://dx.doi.org/10.1371/journal.pgen.1004681.s008", "https://dx.doi.org/10.1371/journal.pgen.1004681.s009", "https://dx.doi.org/10.1371/journal.pgen.1004681.s010", "https://dx.doi.org/10.1371/journal.pgen.1004681.s011", "https://dx.doi.org/10.1371/journal.pgen.1004681.s012", "https://dx.doi.org/10.1371/journal.pgen.1004681.s013", "https://dx.doi.org/10.1371/journal.pgen.1004681.s014", "https://dx.doi.org/10.1371/journal.pgen.1004681.s015", "https://dx.doi.org/10.1371/journal.pgen.1004681.s016", "https://dx.doi.org/10.1371/journal.pgen.1004681.s017", "https://dx.doi.org/10.1371/journal.pgen.1004681.s018", "https://dx.doi.org/10.1371/journal.pgen.1004681.s019", "https://dx.doi.org/10.1371/journal.pgen.1004681.s020"], "stats"=>{"downloads"=>122, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Selection_on_a_Variant_Associated_with_Improved_Viral_Clearance_Drives_Local_Adaptive_Pseudogenization_of_Interferon_Lambda_4_IFNL4_/1207054", "title"=>"Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (<i>IFNL4</i>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720649"], "description"=>"<p>All XP-EHH values are connected by a fitting curve (yellow line). The 1% tail of the genomic empirical distribution is indicated by the horizontal, dashed line. (<b>d</b>) Haplotype structure in the same region as above, for an African (YRI), European (CEU), and East Asian (CHS) population. Columns represent SNPs with a derived allele frequency >5% in at least one population (n = 99 SNPs), with the ancestral allele in white, and the derived allele in black. Lines represent the haplotypes they fall in, as inferred with SHAPEIT by the 1000 Genomes consortium <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#pgen.1004681-McVean1\" target=\"_blank\">[24]</a>. Haplotypes were sorted based on rs368234815 (red arrow) and SNPs in perfect LD with it in CHS (black arrows); see also <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#pgen-1004681-t002\" target=\"_blank\">Table 2</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004681#pgen-1004681-g004\" target=\"_blank\">Figure 4</a>. The bar on the left-hand side of each plot indicates the haplotypes that carry the TT allele (red) or the ΔG allele (blue).</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207036, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.g003", "stats"=>{"downloads"=>4, "page_views"=>75, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Empirical_P_values_of_the_F_ST_and_XP_EHH_analysis_depicted_as_dots_or_diamonds_respectively_in_the_30_Kb_genomic_locus_around_IFNL4_chr19_39724153_39754153_for_A_CHS_B_CHB_and_C_JPT_using_YRI_as_background_/1207036", "title"=>"Empirical P-values of the F<sub>ST</sub> and XP-EHH analysis (depicted as dots or diamonds, respectively) in the 30 Kb genomic locus around <i>IFNL4</i> (chr19:39724153–39754153) for (A) CHS, (B) CHB, and (C) JPT using YRI as background.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720654"], "description"=>"<p>Derived allele frequency (DAF), LD to rs368234815, and signatures of selection (empirical P-values for F<sub>ST</sub> and XP-EHH) for other relevant SNPs across the <i>IFNL</i>-locus.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207041, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.t002", "stats"=>{"downloads"=>6, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Derived_allele_frequency_DAF_LD_to_rs368234815_and_signatures_of_selection_empirical_P_values_for_F_ST_and_XP_EHH_for_other_relevant_SNPs_across_the_IFNL_locus_/1207041", "title"=>"Derived allele frequency (DAF), LD to rs368234815, and signatures of selection (empirical P-values for F<sub>ST</sub> and XP-EHH) for other relevant SNPs across the <i>IFNL</i>-locus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720636"], "description"=>"<p>Phylogenetic tree showing the dN/dS ratio of each lineage analyzed.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207026, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.g001", "stats"=>{"downloads"=>3, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_showing_the_dN_dS_ratio_of_each_lineage_analyzed_/1207026", "title"=>"Phylogenetic tree showing the dN/dS ratio of each lineage analyzed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-16 04:01:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1720652"], "description"=>"<p>We simulated one ancestral population that splits at the out-of-Africa event (at 51,000 years ago) into the African (AFR) and the non-African (non-AFR) populations, which experience subsequent migration. The star indicates the appearance of the focal mutation. In the first case the neutral (black) mutation appeared and evolved under neutrality in both populations. In the SDN model the advantageous mutation (red) is immediately under positive selection with strength s<sub>A</sub>, and time when selection started t<sub>mut</sub> (the prior parameter space for t<sub>mut</sub> is indicated by a green line); selection strength is allowed to change in the non-African population to s<sub>NA</sub>. In the SSV model the neutral (black) mutation appeared and evolved under neutrality, becoming advantageous in the non-African population (red line) at time t<sub>mut</sub>. Prior parameter spaces can be found in methods. (<b>B</b>) Posterior probabilities of the model choice for the different selection models under perfect additivity. (<b>C</b>) Posterior probabilities of the model choice for the different dominance models (and neutrality, NTR). For all models except NTR the posterior probability represent the sum for the SDN and SSV selection models. (<b>D</b>) Posterior probabilities of the model choice for the different selection models under the supra-additive model. In (<b>B</b>), (<b>C</b>), and (<b>D</b>), NTR has negligible posterior probability and is therefore not visible.</p>", "links"=>[], "tags"=>["snp", "Approximate Bayesian Computation", "frequency", "hcv", "east asia", "Hepatitis C virus", "humans IFNL 4", "abc", "Interferon Lambda 4", "Viral Clearance Drives"], "article_id"=>1207039, "categories"=>["Uncategorised"], "users"=>["Felix M. Key", "Benjamin Peter", "Megan Y. Dennis", "Emilia Huerta-Sanchez", "Wei Tang", "Ludmila Prokunina-Olsson", "Rasmus Nielsen", "Aida M. Andrés"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004681.g005", "stats"=>{"downloads"=>5, "page_views"=>112, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Graphical_representation_of_the_different_models_of_selection_tested_in_the_ABC_analysis_NTR_neutral_SDN_selection_on_a_de_novo_mutation_and_SSV_selection_on_standing_variation_/1207039", "title"=>"(A) Graphical representation of the different models of selection tested in the ABC analysis (NTR - neutral, SDN - selection on a de novo mutation, and SSV - selection on standing variation).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-16 04:01:51"}

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Relative Metric

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